HEADER TRANSFERASE/TRANSFERASE INHIBITOR 17-AUG-05 2AQ9 TITLE STRUCTURE OF E. COLI LPXA WITH A BOUND PEPTIDE THAT IS COMPETITIVE TITLE 2 WITH ACYL-ACP COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACYL-[ACYL-CARRIER-PROTEIN]--UDP-N-ACETYLGLUCOSAMINE O- COMPND 3 ACYLTRANSFERASE; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: UDP-N-ACETYLGLUCOSAMINE ACYLTRANSFERASE; COMPND 6 EC: 2.3.1.129; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: PEPTIDE INHIBITOR; COMPND 10 CHAIN: X; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: LPXA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSE; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PPET23C-LPXA(1-262) PT01; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES KEYWDS LPXA, PEPTIDE INHIBITOR, ACYL ACP, ACP, UDP-GLCNAC, LIPID A, KEYWDS 2 TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.H.WILLIAMS,R.M.IMMORMINO,D.T.GEWIRTH,C.R.RAETZ REVDAT 5 13-JUL-11 2AQ9 1 VERSN REVDAT 4 30-JUN-09 2AQ9 1 HELIX SHEET REVDAT 3 24-FEB-09 2AQ9 1 VERSN REVDAT 2 01-AUG-06 2AQ9 1 JRNL REVDAT 1 27-JUN-06 2AQ9 0 JRNL AUTH A.H.WILLIAMS,R.M.IMMORMINO,D.T.GEWIRTH,C.R.RAETZ JRNL TITL STRUCTURE OF UDP-N-ACETYLGLUCOSAMINE ACYLTRANSFERASE WITH A JRNL TITL 2 BOUND ANTIBACTERIAL PENTADECAPEPTIDE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 103 10877 2006 JRNL REFN ISSN 0027-8424 JRNL PMID 16835299 JRNL DOI 10.1073/PNAS.0604465103 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 354940.880 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 26451 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 SET) : 0.194 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.600 REMARK 3 FREE R VALUE TEST SET COUNT : 2283 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.86 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2188 REMARK 3 BIN R VALUE (WORKING SET) : 0.3210 REMARK 3 BIN FREE R VALUE : 0.3210 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 221 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.022 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2062 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 113 REMARK 3 SOLVENT ATOMS : 297 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.20 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.20 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.60 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 3.42 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.100 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.660 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.770 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.510 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 80.69 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER.PARAM REMARK 3 PARAMETER FILE 4 : PO4.PARAM REMARK 3 PARAMETER FILE 5 : DMSO.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : PO4.TOP REMARK 3 TOPOLOGY FILE 5 : DMSO.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2AQ9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 42 REMARK 42 MOLPROBITY STRUCTURE VALIDATION REMARK 42 PROGRAMS : MOLPROBITY (KING, REDUCE, AND PROBE) REMARK 42 AUTHORS : I.W.DAVIS,J.M.WORD REMARK 42 URL : HTTP://KINEMAGE.BIOCHEM.DUKE.EDU/MOLPROBITY/ REMARK 42 AUTHORS : J.S.RICHARDSON,W.B.ARENDALL,D.C.RICHARDSON REMARK 42 REFERENCE : NEW TOOLS AND DATA FOR IMPROVING REMARK 42 : STRUCTURES, USING ALL-ATOM CONTACTS REMARK 42 : METHODS IN ENZYMOLOGY. 2003;374:385-412. REMARK 42 MOLPROBITY OUTPUT SCORES: REMARK 42 ALL-ATOM CLASHSCORE : 6.42 (4.23 B<40) REMARK 42 LPXA (PROTEIN CHAIN) REMARK 42 BAD ROTAMERS : 0.5% 1/204 (TARGET 0-1%) REMARK 42 RAMACHANDRAN OUTLIERS : 0.0% 0/260 (TARGET 0.2%) REMARK 42 RAMACHANDRAN FAVORED : 97.7% 254/260 (TARGET 98.0%) REMARK 42 PEPTIDE 920 (PEPTIDE INHIBITOR OF LPXA) REMARK 42 BAD ROTAMERS : 0.0% 0/9 (TARGET 0-1%) REMARK 42 RAMACHANDRAN OUTLIERS : 0.0% 0/10 (TARGET 0.2%) REMARK 42 RAMACHANDRAN FAVORED :100.0% 10/10 (TARGET 98.0%) REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-SEP-05. REMARK 100 THE RCSB ID CODE IS RCSB034185. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JAN-05 REMARK 200 TEMPERATURE (KELVIN) : 105 REMARK 200 PH : 6.3 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 RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : COPPER KALPHA REMARK 200 OPTICS : YALE MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28264 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 18.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 10.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07300 REMARK 200 FOR THE DATA SET : 25.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.75700 REMARK 200 FOR SHELL : 3.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1LXA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: DMSO, SODIUM POTASSIUM PHOSPHATE, PH REMARK 280 6.3-6.9, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+1/2 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 -1.000000 0.000000 0.000000 48.36700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.36700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.36700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.36700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 48.36700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.36700 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 48.36700 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 48.36700 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 48.36700 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 48.36700 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 48.36700 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 48.36700 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 48.36700 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 48.36700 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 48.36700 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 48.36700 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 48.36700 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 48.36700 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 2 CHAIN(S). THERE IS ONE COPY OF THE REMARK 300 LPXA MONOMER BOUND TO ONE INHIBITORY PEPTIDE PER REMARK 300 ASYMMETRIC UNIT. THE BIOLOGICALLY ACTIVE LPXA MOLECULE, REMARK 300 WHICH IS A HOMO-TRIMER, SITS ON A CRYSTALLOGRAPHIC REMARK 300 THREE-FOLD AXIS. SWITCHING THE INDEX OF THE LPXA-PEPTIDE REMARK 300 COMPLEX FROM THE CUBIC P2(1)3 TO THE ORTHORHOMBIC REMARK 300 P2(1)2(1)2(1), WHICH IS THE MAXIMAL NON-ISOMORPHIC REMARK 300 SUBGROUP LACKING THE THREE-FOLD AXIS, RESULTS IN A REMARK 300 TRIPLING OF MOLECULES IN THE ASYMMETRIC UNIT, AND THE REMARK 300 FORMATION OF THE BIOLOGICALLY ACTIVE TRIMER. 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 24900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, X 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 0.000000 0.000000 -1.000000 96.73400 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 48.36700 REMARK 350 BIOMT3 2 0.000000 -1.000000 0.000000 145.10100 REMARK 350 BIOMT1 3 0.000000 1.000000 0.000000 -48.36700 REMARK 350 BIOMT2 3 0.000000 0.000000 -1.000000 145.10100 REMARK 350 BIOMT3 3 -1.000000 0.000000 0.000000 96.73400 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 637 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 639 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 617 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER X 1 REMARK 465 SER X 2 REMARK 465 GLY X 3 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 ARG A 224 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 241 CG CD OE1 OE2 REMARK 470 MET X 5 CG SD CE REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ASN A 190 C HIS A 191 N -0.164 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 ASN A 190 O - C - N ANGL. DEV. = -9.9 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 ASN A 23 19.32 58.03 REMARK 500 ILE A 119 126.57 -39.58 REMARK 500 PHE A 150 -0.31 66.58 REMARK 500 PHE A 162 -0.80 70.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 637 DISTANCE = 5.28 ANGSTROMS REMARK 525 HOH A 652 DISTANCE = 5.07 ANGSTROMS REMARK 525 HOH A 668 DISTANCE = 5.44 ANGSTROMS REMARK 525 HOH A 702 DISTANCE = 5.37 ANGSTROMS REMARK 650 REMARK 650 HELIX REMARK 650 REMARK 650 DETERMINATION METHOD: AUTHOR DETERMINED REMARK 700 REMARK 700 SHEET REMARK 700 REMARK 700 DETERMINATION METHOD: AUTHOR DETERMINED REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 414 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 415 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 416 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 417 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 418 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 419 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 420 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 421 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 422 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 X 305 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LXA RELATED DB: PDB REMARK 900 UDP N-ACETYLGLUCOSAMINE ACYLTRANSFERASE (STRUCTURE OF APO REMARK 900 LPXA) DBREF 2AQ9 A 1 262 UNP P0A722 LPXA_ECOLI 1 262 DBREF 2AQ9 X 1 15 PDB 2AQ9 2AQ9 1 15 SEQRES 1 A 262 MET ILE ASP LYS SER ALA PHE VAL HIS PRO THR ALA ILE SEQRES 2 A 262 VAL GLU GLU GLY ALA SER ILE GLY ALA ASN ALA HIS ILE SEQRES 3 A 262 GLY PRO PHE CYS ILE VAL GLY PRO HIS VAL GLU ILE GLY SEQRES 4 A 262 GLU GLY THR VAL LEU LYS SER HIS VAL VAL VAL ASN GLY SEQRES 5 A 262 HIS THR LYS ILE GLY ARG ASP ASN GLU ILE TYR GLN PHE SEQRES 6 A 262 ALA SER ILE GLY GLU VAL ASN GLN ASP LEU LYS TYR ALA SEQRES 7 A 262 GLY GLU PRO THR ARG VAL GLU ILE GLY ASP ARG ASN ARG SEQRES 8 A 262 ILE ARG GLU SER VAL THR ILE HIS ARG GLY THR VAL GLN SEQRES 9 A 262 GLY GLY GLY LEU THR LYS VAL GLY SER ASP ASN LEU LEU SEQRES 10 A 262 MET ILE ASN ALA HIS ILE ALA HIS ASP CYS THR VAL GLY SEQRES 11 A 262 ASN ARG CYS ILE LEU ALA ASN ASN ALA THR LEU ALA GLY SEQRES 12 A 262 HIS VAL SER VAL ASP ASP PHE ALA ILE ILE GLY GLY MET SEQRES 13 A 262 THR ALA VAL HIS GLN PHE CYS ILE ILE GLY ALA HIS VAL SEQRES 14 A 262 MET VAL GLY GLY CYS SER GLY VAL ALA GLN ASP VAL PRO SEQRES 15 A 262 PRO TYR VAL ILE ALA GLN GLY ASN HIS ALA THR PRO PHE SEQRES 16 A 262 GLY VAL ASN ILE GLU GLY LEU LYS ARG ARG GLY PHE SER SEQRES 17 A 262 ARG GLU ALA ILE THR ALA ILE ARG ASN ALA TYR LYS LEU SEQRES 18 A 262 ILE TYR ARG SER GLY LYS THR LEU ASP GLU VAL LYS PRO SEQRES 19 A 262 GLU ILE ALA GLU LEU ALA GLU THR TYR PRO GLU VAL LYS SEQRES 20 A 262 ALA PHE THR ASP PHE PHE ALA ARG SER THR ARG GLY LEU SEQRES 21 A 262 ILE ARG SEQRES 1 X 15 SER SER GLY TRP MET LEU ASP PRO ILE ALA GLY LYS TRP SEQRES 2 X 15 SER ARG HET PO4 A 301 5 HET PO4 A 302 5 HET PO4 A 303 5 HET PO4 A 304 5 HET DMS A 401 4 HET DMS A 402 4 HET DMS A 403 4 HET DMS A 404 4 HET DMS A 405 4 HET DMS A 406 4 HET DMS A 407 4 HET DMS A 408 4 HET DMS A 409 4 HET DMS A 410 4 HET DMS A 411 4 HET DMS A 412 4 HET DMS A 413 4 HET DMS A 414 4 HET DMS A 415 4 HET DMS A 416 4 HET DMS A 417 4 HET DMS A 418 4 HET DMS A 419 4 HET DMS A 420 4 HET DMS A 421 4 HET DMS A 422 4 HET PO4 X 305 5 HETNAM PO4 PHOSPHATE ION HETNAM DMS DIMETHYL SULFOXIDE FORMUL 3 PO4 5(O4 P 3-) FORMUL 7 DMS 22(C2 H6 O S) FORMUL 30 HOH *297(H2 O) HELIX 1 HA ASN A 198 ARG A 205 1 8 HELIX 2 HB ARG A 209 TYR A 223 1 15 HELIX 3 HC LEU A 229 THR A 242 1 14 HELIX 4 HD VAL A 246 SER A 256 1 11 SHEET 1 BS1 9 MET A 1 ASP A 3 0 SHEET 2 BS1 9 ALA A 18 GLY A 21 1 N ILE A 20 O MET A 1 SHEET 3 BS1 9 VAL A 36 GLY A 39 1 N ILE A 38 O SER A 19 SHEET 4 BS1 9 THR A 54 GLY A 57 1 N ILE A 56 O GLU A 37 SHEET 5 BS1 9 ARG A 83 GLY A 87 1 N ILE A 86 O LYS A 55 SHEET 6 BS1 9 GLY A 107 GLY A 112 1 N VAL A 111 O GLU A 85 SHEET 7 BS1 9 CYS A 127 GLY A 130 1 N VAL A 129 O LYS A 110 SHEET 8 BS1 9 VAL A 145 ASP A 148 1 N VAL A 147 O THR A 128 SHEET 9 BS1 9 CYS A 163 GLY A 166 1 N ILE A 165 O SER A 146 SHEET 1 BS211 PHE A 7 HIS A 9 0 SHEET 2 BS211 ALA A 24 GLY A 27 1 N ILE A 26 O PHE A 7 SHEET 3 BS211 THR A 42 LYS A 45 1 N LEU A 44 O HIS A 25 SHEET 4 BS211 ASN A 60 TYR A 63 1 N ILE A 62 O VAL A 43 SHEET 5 BS211 ASN A 90 ARG A 93 1 N ILE A 92 O GLU A 61 SHEET 6 BS211 ASN A 115 MET A 118 1 N LEU A 117 O ARG A 91 SHEET 7 BS211 CYS A 133 ALA A 136 1 N LEU A 135 O LEU A 116 SHEET 8 BS211 ALA A 151 GLY A 154 1 N ILE A 153 O ILE A 134 SHEET 9 BS211 VAL A 169 GLY A 172 1 N VAL A 171 O ILE A 152 SHEET 10 BS211 VAL A 185 GLN A 188 1 N ALA A 187 O MET A 170 SHEET 11 BS211 THR A 193 GLY A 196 -1 N PHE A 195 O ILE A 186 SHEET 1 BS3 9 ILE A 13 GLU A 15 0 SHEET 2 BS3 9 CYS A 30 GLY A 33 1 N VAL A 32 O ILE A 13 SHEET 3 BS3 9 VAL A 48 ASN A 51 1 N VAL A 50 O ILE A 31 SHEET 4 BS3 9 ALA A 66 GLU A 70 1 N ILE A 68 O VAL A 49 SHEET 5 BS3 9 VAL A 96 HIS A 99 1 O VAL A 96 N SER A 67 SHEET 6 BS3 9 ALA A 121 ALA A 124 1 O ALA A 121 N THR A 97 SHEET 7 BS3 9 ALA A 139 ALA A 142 1 O ALA A 139 N HIS A 122 SHEET 8 BS3 9 THR A 157 HIS A 160 1 O THR A 157 N THR A 140 SHEET 9 BS3 9 SER A 175 VAL A 177 1 O SER A 175 N ALA A 158 SHEET 1 BS4 2 MET X 5 ASP X 7 0 SHEET 2 BS4 2 LYS X 12 SER X 14 -1 O LYS X 12 N ASP X 7 CISPEP 1 ASN A 190 HIS A 191 0 -17.11 SITE 1 AC1 9 ARG A 100 ARG A 216 LYS A 220 PO4 A 302 SITE 2 AC1 9 HOH A 453 HOH A 540 HOH A 542 HOH A 613 SITE 3 AC1 9 HOH A 689 SITE 1 AC2 10 PRO A 34 ASN A 51 GLY A 52 PO4 A 301 SITE 2 AC2 10 HOH A 431 HOH A 488 HOH A 517 HOH A 518 SITE 3 AC2 10 HOH A 605 HOH A 660 SITE 1 AC3 8 LYS A 76 GLN A 104 LYS A 203 HOH A 536 SITE 2 AC3 8 HOH A 572 HOH A 598 TRP X 4 ARG X 15 SITE 1 AC4 4 LEU A 75 ASP A 114 ARG A 132 CYS A 133 SITE 1 AC5 3 ILE A 13 VAL A 14 GLU A 16 SITE 1 AC6 3 ILE A 56 ILE A 86 DMS A 405 SITE 1 AC7 5 GLY A 17 PRO A 34 HIS A 35 VAL A 36 SITE 2 AC7 5 GLU A 37 SITE 1 AC8 7 ASN A 23 HIS A 25 GLY A 41 ASN A 217 SITE 2 AC8 7 LEU A 239 TYR A 243 DMS A 408 SITE 1 AC9 2 ASP A 88 DMS A 402 SITE 1 BC1 2 ASP A 148 ARG A 255 SITE 1 BC2 2 HIS A 25 HOH A 549 SITE 1 BC3 7 GLY A 41 ASP A 59 ASN A 60 GLU A 210 SITE 2 BC3 7 THR A 213 TYR A 243 DMS A 404 SITE 1 BC4 5 HIS A 144 SER A 146 PHE A 162 THR A 257 SITE 2 BC4 5 DMS A 412 SITE 1 BC5 2 PHE A 7 VAL A 8 SITE 1 BC6 2 ASP A 148 ASP A 149 SITE 1 BC7 7 ASP A 126 THR A 128 VAL A 145 SER A 146 SITE 2 BC7 7 DMS A 409 HOH A 450 HOH A 703 SITE 1 BC8 4 LYS A 4 ALA A 6 GLU A 238 HOH A 530 SITE 1 BC9 3 MET A 1 ASP A 3 ILE A 20 SITE 1 CC1 2 ASP A 3 LYS A 4 SITE 1 CC2 4 GLU A 15 PRO A 28 HOH A 491 HOH A 549 SITE 1 CC3 4 ASN A 131 ARG A 132 PHE A 150 HOH A 625 SITE 1 CC4 2 PRO A 194 TYR A 219 SITE 1 CC5 3 ARG A 205 GLU A 245 HOH A 445 SITE 1 CC6 4 HIS A 25 VAL A 43 LYS A 45 HOH A 695 SITE 1 CC7 5 GLN A 73 ARG A 91 ARG A 93 LEU A 116 SITE 2 CC7 5 HOH A 524 SITE 1 CC8 3 ALA A 78 PHE A 207 ARG A 209 SITE 1 CC9 8 GLN A 73 ASP A 74 LEU A 75 LYS A 76 SITE 2 CC9 8 GLN A 161 LEU X 6 PRO X 8 HOH X 28 CRYST1 96.734 96.734 96.734 90.00 90.00 90.00 P 21 3 12 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 0.010338 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010338 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010338 0.00000 MASTER 515 0 27 4 31 0 39 6 0 0 0 23 END