HEADER TRANSFERASE 01-JUL-09 3I3X TITLE STRUCTURAL BASIS FOR THE SUGAR NUCLEOTIDE AND ACYL CHAIN TITLE 2 SELECTIVITY OF LEPTOSPIRA INTERROGANS LPXA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACYL-[ACYL-CARRIER-PROTEIN]--UDP-N- COMPND 3 ACETYLGLUCOSAMINE O-ACYLTRANSFERASE; COMPND 4 CHAIN: A, B, C; COMPND 5 EC: 2.3.1.129; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEPTOSPIRA INTERROGANS; SOURCE 3 ORGANISM_TAXID: 173; SOURCE 4 GENE: LA3949, LA_3949, LPXA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LPXA, LEPTOSPIRA INTERROGANS LPXA, L. INTERROGANS LPXA, L. KEYWDS 2 INTERROGANS LPXA PRODUCT COMPLEX, ACYLTRANSFERASE, LIPID A KEYWDS 3 BIOSYNTHESIS, LIPID SYNTHESIS, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.H.WILLIAMS REVDAT 2 08-SEP-09 3I3X 1 AUTHOR REVDAT 1 01-SEP-09 3I3X 0 JRNL AUTH L.I.ROBINS,A.H.WILLIAMS,C.R.RAETZ JRNL TITL STRUCTURAL BASIS FOR THE SUGAR NUCLEOTIDE AND JRNL TITL 2 ACYL-CHAIN SELECTIVITY OF LEPTOSPIRA INTERROGANS JRNL TITL 3 LPXA. JRNL REF BIOCHEMISTRY V. 48 6191 2009 JRNL REFN ISSN 0006-2960 JRNL PMID 19456129 JRNL DOI 10.1021/BI900629E REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 41810 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2241 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3129 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.64 REMARK 3 BIN R VALUE (WORKING SET) : 0.2450 REMARK 3 BIN FREE R VALUE SET COUNT : 171 REMARK 3 BIN FREE R VALUE : 0.3260 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5959 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 159 REMARK 3 SOLVENT ATOMS : 315 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.19000 REMARK 3 B22 (A**2) : 1.19000 REMARK 3 B33 (A**2) : -1.78000 REMARK 3 B12 (A**2) : 0.59000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.296 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.221 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.922 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6252 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8476 ; 1.350 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 778 ; 7.605 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 275 ;34.535 ;24.545 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1004 ;14.288 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;15.356 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 962 ; 0.107 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4674 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3018 ; 0.200 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4170 ; 0.304 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 395 ; 0.138 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 175 ; 0.208 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 50 ; 0.271 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3837 ; 0.570 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6196 ; 1.046 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2415 ; 1.681 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2280 ; 2.867 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 3I3X COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JUL-09. REMARK 100 THE RCSB ID CODE IS RCSB053932. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JAN-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41810 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 46.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35% W/V PEG 3350, 0.4 M DIAMMONIUM REMARK 280 CITRATE, PH 7.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 53.47650 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -92.62402 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 106.95300 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 53.47650 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -92.62402 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 106.95300 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 311 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 305 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 334 LIES ON A SPECIAL POSITION. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 MET A 1 CG SD CE REMARK 470 MET B 1 CG SD CE REMARK 470 MET C 1 CG SD CE REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 609 O HOH B 622 2545 1.94 REMARK 500 ND2 ASN A 93 O HOH A 603 3655 1.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG C 89 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLU A 40 -144.02 -87.07 REMARK 500 ASN A 115 19.45 55.57 REMARK 500 LEU A 169 10.77 84.95 REMARK 500 LYS B 2 115.67 -178.28 REMARK 500 GLU B 40 -148.59 -85.55 REMARK 500 ASN B 115 16.54 57.40 REMARK 500 LYS C 2 117.07 -165.67 REMARK 500 GLU C 40 -148.70 -81.95 REMARK 500 GLN C 59 121.22 -39.60 REMARK 500 SER C 234 -16.47 -141.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 168 LEU A 169 140.32 REMARK 500 ALA C 233 SER C 234 -53.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE U22 A 901 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE U22 B 901 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE U22 C 901 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3I3A RELATED DB: PDB REMARK 900 L. INTERROGANS LPXA DONOR COMPLEX REMARK 900 RELATED ID: 3HSQ RELATED DB: PDB REMARK 900 L. INTERROGANS LPXA APO-ENZYME DBREF 3I3X A 1 259 UNP Q8EZA6 Q8EZA6_LEPIN 1 259 DBREF 3I3X B 1 259 UNP Q8EZA6 Q8EZA6_LEPIN 1 259 DBREF 3I3X C 1 259 UNP Q8EZA6 Q8EZA6_LEPIN 1 259 SEQRES 1 A 259 MET LYS ILE HIS PRO THR ALA ILE ILE ASP PRO LYS ALA SEQRES 2 A 259 GLU LEU HIS GLU SER VAL GLU VAL GLY PRO TYR SER ILE SEQRES 3 A 259 ILE GLU GLY ASN VAL SER ILE GLN GLU GLY THR ILE ILE SEQRES 4 A 259 GLU GLY HIS VAL LYS ILE CYS ALA GLY SER GLU ILE GLY SEQRES 5 A 259 LYS PHE ASN ARG PHE HIS GLN GLY ALA VAL ILE GLY VAL SEQRES 6 A 259 MET PRO GLN ASP LEU GLY PHE ASN GLN GLN LEU LEU THR SEQRES 7 A 259 LYS THR VAL ILE GLY ASP HIS ASN ILE PHE ARG GLU TYR SEQRES 8 A 259 SER ASN ILE HIS LYS GLY THR LYS GLU ASP SER PRO THR SEQRES 9 A 259 VAL ILE GLY ASN LYS ASN TYR PHE MET GLY ASN SER HIS SEQRES 10 A 259 VAL GLY HIS ASP CYS ILE LEU GLY ASN ASN ASN ILE LEU SEQRES 11 A 259 THR HIS GLY ALA VAL LEU ALA GLY HIS VAL THR LEU GLY SEQRES 12 A 259 ASN PHE ALA PHE ILE SER GLY LEU VAL ALA VAL HIS GLN SEQRES 13 A 259 PHE CYS PHE VAL GLY ASP TYR SER MET VAL ALA GLY LEU SEQRES 14 A 259 ALA LYS VAL VAL GLN ASP VAL PRO PRO TYR SER THR VAL SEQRES 15 A 259 ASP GLY ASN PRO SER THR VAL VAL GLY LEU ASN SER VAL SEQRES 16 A 259 GLY MET LYS ARG ALA GLY PHE SER PRO GLU VAL ARG ASN SEQRES 17 A 259 ALA ILE LYS HIS ALA TYR LYS VAL ILE TYR HIS SER GLY SEQRES 18 A 259 ILE SER THR ARG LYS ALA LEU ASP GLU LEU GLU ALA SER SEQRES 19 A 259 GLY ASN LEU ILE GLU GLN VAL LYS TYR ILE ILE LYS PHE SEQRES 20 A 259 PHE ARG ASP SER ASP ARG GLY VAL THR ASN HIS ARG SEQRES 1 B 259 MET LYS ILE HIS PRO THR ALA ILE ILE ASP PRO LYS ALA SEQRES 2 B 259 GLU LEU HIS GLU SER VAL GLU VAL GLY PRO TYR SER ILE SEQRES 3 B 259 ILE GLU GLY ASN VAL SER ILE GLN GLU GLY THR ILE ILE SEQRES 4 B 259 GLU GLY HIS VAL LYS ILE CYS ALA GLY SER GLU ILE GLY SEQRES 5 B 259 LYS PHE ASN ARG PHE HIS GLN GLY ALA VAL ILE GLY VAL SEQRES 6 B 259 MET PRO GLN ASP LEU GLY PHE ASN GLN GLN LEU LEU THR SEQRES 7 B 259 LYS THR VAL ILE GLY ASP HIS ASN ILE PHE ARG GLU TYR SEQRES 8 B 259 SER ASN ILE HIS LYS GLY THR LYS GLU ASP SER PRO THR SEQRES 9 B 259 VAL ILE GLY ASN LYS ASN TYR PHE MET GLY ASN SER HIS SEQRES 10 B 259 VAL GLY HIS ASP CYS ILE LEU GLY ASN ASN ASN ILE LEU SEQRES 11 B 259 THR HIS GLY ALA VAL LEU ALA GLY HIS VAL THR LEU GLY SEQRES 12 B 259 ASN PHE ALA PHE ILE SER GLY LEU VAL ALA VAL HIS GLN SEQRES 13 B 259 PHE CYS PHE VAL GLY ASP TYR SER MET VAL ALA GLY LEU SEQRES 14 B 259 ALA LYS VAL VAL GLN ASP VAL PRO PRO TYR SER THR VAL SEQRES 15 B 259 ASP GLY ASN PRO SER THR VAL VAL GLY LEU ASN SER VAL SEQRES 16 B 259 GLY MET LYS ARG ALA GLY PHE SER PRO GLU VAL ARG ASN SEQRES 17 B 259 ALA ILE LYS HIS ALA TYR LYS VAL ILE TYR HIS SER GLY SEQRES 18 B 259 ILE SER THR ARG LYS ALA LEU ASP GLU LEU GLU ALA SER SEQRES 19 B 259 GLY ASN LEU ILE GLU GLN VAL LYS TYR ILE ILE LYS PHE SEQRES 20 B 259 PHE ARG ASP SER ASP ARG GLY VAL THR ASN HIS ARG SEQRES 1 C 259 MET LYS ILE HIS PRO THR ALA ILE ILE ASP PRO LYS ALA SEQRES 2 C 259 GLU LEU HIS GLU SER VAL GLU VAL GLY PRO TYR SER ILE SEQRES 3 C 259 ILE GLU GLY ASN VAL SER ILE GLN GLU GLY THR ILE ILE SEQRES 4 C 259 GLU GLY HIS VAL LYS ILE CYS ALA GLY SER GLU ILE GLY SEQRES 5 C 259 LYS PHE ASN ARG PHE HIS GLN GLY ALA VAL ILE GLY VAL SEQRES 6 C 259 MET PRO GLN ASP LEU GLY PHE ASN GLN GLN LEU LEU THR SEQRES 7 C 259 LYS THR VAL ILE GLY ASP HIS ASN ILE PHE ARG GLU TYR SEQRES 8 C 259 SER ASN ILE HIS LYS GLY THR LYS GLU ASP SER PRO THR SEQRES 9 C 259 VAL ILE GLY ASN LYS ASN TYR PHE MET GLY ASN SER HIS SEQRES 10 C 259 VAL GLY HIS ASP CYS ILE LEU GLY ASN ASN ASN ILE LEU SEQRES 11 C 259 THR HIS GLY ALA VAL LEU ALA GLY HIS VAL THR LEU GLY SEQRES 12 C 259 ASN PHE ALA PHE ILE SER GLY LEU VAL ALA VAL HIS GLN SEQRES 13 C 259 PHE CYS PHE VAL GLY ASP TYR SER MET VAL ALA GLY LEU SEQRES 14 C 259 ALA LYS VAL VAL GLN ASP VAL PRO PRO TYR SER THR VAL SEQRES 15 C 259 ASP GLY ASN PRO SER THR VAL VAL GLY LEU ASN SER VAL SEQRES 16 C 259 GLY MET LYS ARG ALA GLY PHE SER PRO GLU VAL ARG ASN SEQRES 17 C 259 ALA ILE LYS HIS ALA TYR LYS VAL ILE TYR HIS SER GLY SEQRES 18 C 259 ILE SER THR ARG LYS ALA LEU ASP GLU LEU GLU ALA SER SEQRES 19 C 259 GLY ASN LEU ILE GLU GLN VAL LYS TYR ILE ILE LYS PHE SEQRES 20 C 259 PHE ARG ASP SER ASP ARG GLY VAL THR ASN HIS ARG HET U22 A 901 53 HET U22 B 901 53 HET U22 C 901 53 HETNAM U22 URIDINE-5'-DIPHOSPHATE-3-N-(R-3-HYDROXYLAUROYL)-N- HETNAM 2 U22 ACETYL-D-GLUCOSAMINE HETSYN U22 (2R,3R,4R,5S,6R)-3-(ACETYLAMINO)-5-HYDROXY-4-{[(3R)-3- HETSYN 2 U22 HYDROXYDODECANOYL]AMINO}-6-(HYDROXYMETHYL)TETRAHYDRO- HETSYN 3 U22 2H-PYRAN-2-YL [(2R,3S,4R,5R)-5-(2,4-DIOXO-3,4- HETSYN 4 U22 DIHYDROPYRIMIDIN-1(2H)-YL)-3,4- HETSYN 5 U22 DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN HETSYN 6 U22 DIPHOSPHATE FORMUL 4 U22 3(C29 H50 N4 O18 P2) FORMUL 7 HOH *315(H2 O) HELIX 1 1 ASN A 193 ALA A 200 1 8 HELIX 2 2 SER A 203 HIS A 219 1 17 HELIX 3 3 SER A 223 SER A 234 1 12 HELIX 4 4 ILE A 238 SER A 251 1 14 HELIX 5 5 ASN B 193 GLY B 201 1 9 HELIX 6 6 SER B 203 HIS B 219 1 17 HELIX 7 7 SER B 223 GLU B 232 1 10 HELIX 8 8 ILE B 238 SER B 251 1 14 HELIX 9 9 ASN C 193 ALA C 200 1 8 HELIX 10 10 SER C 203 SER C 220 1 18 HELIX 11 11 SER C 223 SER C 234 1 12 HELIX 12 12 ILE C 238 SER C 251 1 14 SHEET 1 A 9 ILE A 8 ILE A 9 0 SHEET 2 A 9 ILE A 26 ILE A 27 1 O ILE A 27 N ILE A 8 SHEET 3 A 9 LYS A 44 ILE A 45 1 O ILE A 45 N ILE A 26 SHEET 4 A 9 VAL A 62 VAL A 65 1 O ILE A 63 N LYS A 44 SHEET 5 A 9 ASN A 93 HIS A 95 1 O ILE A 94 N VAL A 62 SHEET 6 A 9 HIS A 117 VAL A 118 1 O VAL A 118 N HIS A 95 SHEET 7 A 9 VAL A 135 LEU A 136 1 O LEU A 136 N HIS A 117 SHEET 8 A 9 ALA A 153 VAL A 154 1 O VAL A 154 N VAL A 135 SHEET 9 A 9 LYS A 171 VAL A 172 1 O VAL A 172 N ALA A 153 SHEET 1 B 8 GLU A 14 LEU A 15 0 SHEET 2 B 8 SER A 32 ILE A 33 1 O ILE A 33 N GLU A 14 SHEET 3 B 8 SER A 49 ILE A 51 1 O ILE A 51 N SER A 32 SHEET 4 B 8 THR A 80 ILE A 82 1 O THR A 80 N GLU A 50 SHEET 5 B 8 THR A 104 ILE A 106 1 O THR A 104 N VAL A 81 SHEET 6 B 8 ILE A 123 LEU A 124 1 O LEU A 124 N VAL A 105 SHEET 7 B 8 THR A 141 LEU A 142 1 O LEU A 142 N ILE A 123 SHEET 8 B 8 PHE A 159 VAL A 160 1 O VAL A 160 N THR A 141 SHEET 1 C10 GLU A 20 VAL A 21 0 SHEET 2 C10 ILE A 38 ILE A 39 1 O ILE A 39 N GLU A 20 SHEET 3 C10 ARG A 56 PHE A 57 1 O PHE A 57 N ILE A 38 SHEET 4 C10 ILE A 87 PHE A 88 1 O PHE A 88 N ARG A 56 SHEET 5 C10 TYR A 111 PHE A 112 1 O PHE A 112 N ILE A 87 SHEET 6 C10 ILE A 129 LEU A 130 1 O LEU A 130 N TYR A 111 SHEET 7 C10 PHE A 147 ILE A 148 1 O ILE A 148 N ILE A 129 SHEET 8 C10 MET A 165 VAL A 166 1 O VAL A 166 N PHE A 147 SHEET 9 C10 SER A 180 ASP A 183 1 O SER A 180 N MET A 165 SHEET 10 C10 THR A 188 LEU A 192 -1 O VAL A 190 N THR A 181 SHEET 1 D11 LYS B 2 ILE B 3 0 SHEET 2 D11 GLU B 20 VAL B 21 1 O VAL B 21 N LYS B 2 SHEET 3 D11 ILE B 38 ILE B 39 1 O ILE B 39 N GLU B 20 SHEET 4 D11 ARG B 56 PHE B 57 1 O PHE B 57 N ILE B 38 SHEET 5 D11 ILE B 87 PHE B 88 1 O PHE B 88 N ARG B 56 SHEET 6 D11 TYR B 111 PHE B 112 1 O PHE B 112 N ILE B 87 SHEET 7 D11 ILE B 129 LEU B 130 1 O LEU B 130 N TYR B 111 SHEET 8 D11 PHE B 147 ILE B 148 1 O ILE B 148 N ILE B 129 SHEET 9 D11 MET B 165 VAL B 166 1 O VAL B 166 N PHE B 147 SHEET 10 D11 SER B 180 ASP B 183 1 O SER B 180 N MET B 165 SHEET 11 D11 THR B 188 LEU B 192 -1 O VAL B 190 N THR B 181 SHEET 1 E 9 ILE B 8 ILE B 9 0 SHEET 2 E 9 ILE B 26 ILE B 27 1 O ILE B 27 N ILE B 8 SHEET 3 E 9 LYS B 44 ILE B 45 1 O ILE B 45 N ILE B 26 SHEET 4 E 9 VAL B 62 VAL B 65 1 O ILE B 63 N LYS B 44 SHEET 5 E 9 ASN B 93 HIS B 95 1 O ILE B 94 N VAL B 62 SHEET 6 E 9 HIS B 117 VAL B 118 1 O VAL B 118 N ASN B 93 SHEET 7 E 9 VAL B 135 LEU B 136 1 O LEU B 136 N HIS B 117 SHEET 8 E 9 ALA B 153 VAL B 154 1 O VAL B 154 N VAL B 135 SHEET 9 E 9 LYS B 171 VAL B 172 1 O VAL B 172 N ALA B 153 SHEET 1 F 8 GLU B 14 LEU B 15 0 SHEET 2 F 8 SER B 32 ILE B 33 1 O ILE B 33 N GLU B 14 SHEET 3 F 8 SER B 49 ILE B 51 1 O ILE B 51 N SER B 32 SHEET 4 F 8 THR B 80 ILE B 82 1 O THR B 80 N GLU B 50 SHEET 5 F 8 THR B 104 ILE B 106 1 O THR B 104 N VAL B 81 SHEET 6 F 8 ILE B 123 LEU B 124 1 O LEU B 124 N VAL B 105 SHEET 7 F 8 THR B 141 LEU B 142 1 O LEU B 142 N ILE B 123 SHEET 8 F 8 PHE B 159 VAL B 160 1 O VAL B 160 N THR B 141 SHEET 1 G11 LYS C 2 ILE C 3 0 SHEET 2 G11 GLU C 20 VAL C 21 1 O VAL C 21 N LYS C 2 SHEET 3 G11 ILE C 38 ILE C 39 1 O ILE C 39 N GLU C 20 SHEET 4 G11 ARG C 56 PHE C 57 1 O PHE C 57 N ILE C 38 SHEET 5 G11 ILE C 87 PHE C 88 1 O PHE C 88 N ARG C 56 SHEET 6 G11 TYR C 111 PHE C 112 1 O PHE C 112 N ILE C 87 SHEET 7 G11 ILE C 129 LEU C 130 1 O LEU C 130 N TYR C 111 SHEET 8 G11 PHE C 147 ILE C 148 1 O ILE C 148 N ILE C 129 SHEET 9 G11 MET C 165 VAL C 166 1 O VAL C 166 N PHE C 147 SHEET 10 G11 SER C 180 ASP C 183 1 O VAL C 182 N MET C 165 SHEET 11 G11 THR C 188 LEU C 192 -1 O VAL C 190 N THR C 181 SHEET 1 H 9 ILE C 8 ILE C 9 0 SHEET 2 H 9 ILE C 26 ILE C 27 1 O ILE C 27 N ILE C 8 SHEET 3 H 9 LYS C 44 ILE C 45 1 O ILE C 45 N ILE C 26 SHEET 4 H 9 VAL C 62 VAL C 65 1 O ILE C 63 N LYS C 44 SHEET 5 H 9 ASN C 93 HIS C 95 1 O ILE C 94 N VAL C 62 SHEET 6 H 9 HIS C 117 VAL C 118 1 O VAL C 118 N HIS C 95 SHEET 7 H 9 VAL C 135 LEU C 136 1 O LEU C 136 N HIS C 117 SHEET 8 H 9 ALA C 153 VAL C 154 1 O VAL C 154 N VAL C 135 SHEET 9 H 9 LYS C 171 VAL C 172 1 O VAL C 172 N ALA C 153 SHEET 1 I 8 GLU C 14 LEU C 15 0 SHEET 2 I 8 SER C 32 ILE C 33 1 O ILE C 33 N GLU C 14 SHEET 3 I 8 SER C 49 ILE C 51 1 O ILE C 51 N SER C 32 SHEET 4 I 8 THR C 80 ILE C 82 1 O THR C 80 N GLU C 50 SHEET 5 I 8 THR C 104 ILE C 106 1 O THR C 104 N VAL C 81 SHEET 6 I 8 ILE C 123 LEU C 124 1 O LEU C 124 N VAL C 105 SHEET 7 I 8 THR C 141 LEU C 142 1 O LEU C 142 N ILE C 123 SHEET 8 I 8 PHE C 159 VAL C 160 1 O VAL C 160 N THR C 141 CISPEP 1 ASN A 185 PRO A 186 0 4.23 CISPEP 2 ASN B 185 PRO B 186 0 6.81 CISPEP 3 ASN C 185 PRO C 186 0 -0.40 SITE 1 AC1 19 GLN A 68 MET A 113 HIS A 117 GLY A 119 SITE 2 AC1 19 HIS A 120 THR A 131 ALA A 137 GLY A 138 SITE 3 AC1 19 PHE A 147 VAL A 154 HIS A 155 GLN A 156 SITE 4 AC1 19 PHE A 157 MET A 165 ASN A 193 VAL A 195 SITE 5 AC1 19 GLY A 196 ARG A 199 HOH A 260 SITE 1 AC2 18 GLN B 68 ASP B 69 MET B 113 HIS B 117 SITE 2 AC2 18 HIS B 120 HIS B 132 ALA B 137 GLY B 138 SITE 3 AC2 18 PHE B 147 ALA B 153 HIS B 155 GLN B 156 SITE 4 AC2 18 MET B 165 ASN B 193 VAL B 195 GLY B 196 SITE 5 AC2 18 ARG B 199 HOH B 260 SITE 1 AC3 21 GLN C 68 LEU C 70 MET C 113 HIS C 117 SITE 2 AC3 21 HIS C 120 THR C 131 HIS C 132 ALA C 137 SITE 3 AC3 21 GLY C 138 HIS C 139 VAL C 154 HIS C 155 SITE 4 AC3 21 GLN C 156 PHE C 157 MET C 165 ASN C 193 SITE 5 AC3 21 VAL C 195 GLY C 196 ARG C 199 HOH C 424 SITE 6 AC3 21 HOH C 594 CRYST1 106.953 106.953 116.536 90.00 90.00 120.00 P 3 2 1 18 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.009350 0.005398 0.000000 0.00000 SCALE2 0.000000 0.010796 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008581 0.00000 MASTER 400 0 3 12 83 0 16 6 0 0 0 60 END