HEADER LIGAND BINDING PROTEIN 04-FEB-04 1S99 TITLE THE STRUCTURE AND FUNCTION OF B. SUBTILIS YKOF GENE PRODUCT: LIGAND TITLE 2 FREE PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: YKOF; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 OTHER_DETAILS: THIAMIN BINDING PROTEIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 GENE: YKOF; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMCSG7 KEYWDS YKOF, THIAMIN-BINDING PROTEIN, ACT-DOMAIN FAMILY, LIGAND BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.DEVEDJIEV,Y.SURENDRANATH,U.DEREWENDA,Z.S.DEREWENDA REVDAT 4 27-OCT-21 1S99 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 1S99 1 VERSN REVDAT 2 14-DEC-04 1S99 1 HEADER REVDAT 1 05-OCT-04 1S99 0 JRNL AUTH Y.DEVEDJIEV,Y.SURENDRANATH,U.DEREWENDA,A.GABRYS,D.R.COOPER, JRNL AUTH 2 R.G.ZHANG,L.LEZONDRA,A.JOACHIMIAK,Z.S.DEREWENDA JRNL TITL THE STRUCTURE AND LIGAND BINDING PROPERTIES OF THE JRNL TITL 2 B.SUBTILIS YKOF GENE PRODUCT, A MEMBER OF A NOVEL FAMILY OF JRNL TITL 3 THIAMIN/HMP-BINDING PROTEINS JRNL REF J.MOL.BIOL. V. 343 395 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15451668 JRNL DOI 10.1016/J.JMB.2004.08.037 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 47795 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) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.600 REMARK 3 FREE R VALUE TEST SET COUNT : 1265 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2144 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2430 REMARK 3 BIN FREE R VALUE SET COUNT : 45 REMARK 3 BIN FREE R VALUE : 0.2520 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2819 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 362 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.90000 REMARK 3 B22 (A**2) : -0.89000 REMARK 3 B33 (A**2) : -2.01000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.117 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.096 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.067 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.046 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2881 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2531 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3903 ; 1.517 ; 1.927 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5884 ; 0.885 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 362 ; 6.344 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 441 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3250 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 582 ; 0.006 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 612 ; 0.234 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2873 ; 0.266 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1556 ; 0.088 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 266 ; 0.169 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.068 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 11 ; 0.209 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 42 ; 0.316 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 24 ; 0.282 ; 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): 1816 ; 1.337 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2920 ; 2.105 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1065 ; 2.911 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 983 ; 4.166 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 2881 ; 1.691 ; 2.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 363 ; 4.894 ; 2.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2827 ; 2.748 ; 2.000 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 : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1S99 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-FEB-04. REMARK 100 THE DEPOSITION ID IS D_1000021527. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-AUG-03 REMARK 200 TEMPERATURE (KELVIN) : 120.0 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9642, 0.9795, 0.9794 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51209 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 34.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.24000 REMARK 200 FOR THE DATA SET : 24.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 43.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.32200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 8000, 0.2 M CALCIUM ACETATE, REMARK 280 0.1 M MES, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 295.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 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 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 30.46500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.95000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.64000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.95000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.46500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.64000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A HOMODIMER 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 MET A 1 REMARK 465 GLU A 2 REMARK 465 HIS A 3 REMARK 465 ILE A 4 REMARK 465 CYS A 5 REMARK 465 GLY A 6 REMARK 465 THR A 7 REMARK 465 SER A 8 REMARK 465 SER A 97 REMARK 465 LYS A 98 REMARK 465 GLY A 99 REMARK 465 LYS A 198 REMARK 465 GLN A 199 REMARK 465 GLY A 200 REMARK 465 MET B 1 REMARK 465 GLU B 2 REMARK 465 HIS B 3 REMARK 465 ILE B 4 REMARK 465 CYS B 5 REMARK 465 GLY B 6 REMARK 465 THR B 7 REMARK 465 SER B 8 REMARK 465 LEU B 96 REMARK 465 SER B 97 REMARK 465 LYS B 98 REMARK 465 GLY B 99 REMARK 465 SER B 193 REMARK 465 ARG B 194 REMARK 465 LYS B 195 REMARK 465 ASN B 196 REMARK 465 ARG B 197 REMARK 465 LYS B 198 REMARK 465 GLN B 199 REMARK 465 GLY B 200 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NE2 GLN B 176 O HOH B 1179 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 OH TYR A 95 NZ LYS B 29 2564 1.94 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 ASP A 157 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP A 159 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP A 162 CB - CG - OD2 ANGL. DEV. = 7.7 DEGREES REMARK 500 ASP B 159 CB - CG - OD2 ANGL. DEV. = 5.5 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 ALA A 113 129.32 -170.11 REMARK 500 GLU B 73 -2.54 70.15 REMARK 500 VAL B 147 -63.99 -103.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 801 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 33 O REMARK 620 2 THR A 35 O 93.6 REMARK 620 3 HOH A 808 O 93.3 75.5 REMARK 620 4 HOH A 846 O 89.6 153.4 77.9 REMARK 620 5 HOH A 990 O 86.7 63.6 139.0 143.1 REMARK 620 6 ALA B 33 O 178.4 85.6 87.8 91.8 91.7 REMARK 620 7 THR B 35 O 85.1 130.6 153.9 76.0 67.0 94.3 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 801 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LXJ RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF YBL001C NORTHEAST STRUCTURAL GENOMICS (NESG) REMARK 900 CONSORTIUM TARGET YTYST72: SHARES SIMILAR FOLD REMARK 900 RELATED ID: 1LXN RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF MTH1187 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM REMARK 900 TARGET TT272: SHARES SIMILAR FOLD DBREF 1S99 A 1 200 UNP O34911 O34911_BACSU 1 200 DBREF 1S99 B 1 200 UNP O34911 O34911_BACSU 1 200 SEQADV 1S99 MSE A 20 UNP O34911 MET 20 MODIFIED RESIDUE SEQADV 1S99 ALA A 33 UNP O34911 LYS 33 ENGINEERED MUTATION SEQADV 1S99 ALA A 34 UNP O34911 LYS 34 ENGINEERED MUTATION SEQADV 1S99 MSE A 78 UNP O34911 MET 78 MODIFIED RESIDUE SEQADV 1S99 MSE A 124 UNP O34911 MET 124 MODIFIED RESIDUE SEQADV 1S99 MSE A 130 UNP O34911 MET 130 MODIFIED RESIDUE SEQADV 1S99 MSE A 134 UNP O34911 MET 134 MODIFIED RESIDUE SEQADV 1S99 MSE A 173 UNP O34911 MET 173 MODIFIED RESIDUE SEQADV 1S99 MSE A 183 UNP O34911 MET 183 MODIFIED RESIDUE SEQADV 1S99 MSE B 20 UNP O34911 MET 20 MODIFIED RESIDUE SEQADV 1S99 ALA B 33 UNP O34911 LYS 33 ENGINEERED MUTATION SEQADV 1S99 ALA B 34 UNP O34911 LYS 34 ENGINEERED MUTATION SEQADV 1S99 MSE B 78 UNP O34911 MET 78 MODIFIED RESIDUE SEQADV 1S99 MSE B 124 UNP O34911 MET 124 MODIFIED RESIDUE SEQADV 1S99 MSE B 130 UNP O34911 MET 130 MODIFIED RESIDUE SEQADV 1S99 MSE B 134 UNP O34911 MET 134 MODIFIED RESIDUE SEQADV 1S99 MSE B 173 UNP O34911 MET 173 MODIFIED RESIDUE SEQADV 1S99 MSE B 183 UNP O34911 MET 183 MODIFIED RESIDUE SEQRES 1 A 200 MET GLU HIS ILE CYS GLY THR SER ARG ILE ALA GLY PHE SEQRES 2 A 200 ARG PHE SER LEU TYR PRO MSE THR ASP ASP PHE ILE SER SEQRES 3 A 200 VAL ILE LYS SER ALA LEU ALA ALA THR ASP THR SER LYS SEQRES 4 A 200 VAL TRP THR LYS THR ASP HIS ILE SER THR VAL LEU ARG SEQRES 5 A 200 GLY SER ILE ASP HIS VAL PHE ASP ALA ALA LYS ALA ILE SEQRES 6 A 200 TYR LEU HIS ALA ALA ASN SER GLU GLN HIS ILE VAL MSE SEQRES 7 A 200 ASN GLY THR PHE SER ILE GLY CYS PRO GLY ASP THR GLN SEQRES 8 A 200 GLY ASP THR TYR LEU SER LYS GLY ASP LYS ARG VAL ASN SEQRES 9 A 200 GLU ASP ALA VAL ARG GLY LEU LYS ALA GLU ALA PRO CYS SEQRES 10 A 200 GLN PHE ALA LEU TYR PRO MSE ASN GLU PRO ASP TYR MSE SEQRES 11 A 200 GLY LEU ILE MSE GLU ALA VAL ASP ILE ALA LYS ALA GLN SEQRES 12 A 200 GLY THR PHE VAL GLN GLY VAL HIS TYR ALA SER GLU LEU SEQRES 13 A 200 ASP GLY ASP ALA HIS ASP VAL PHE SER THR LEU GLU ALA SEQRES 14 A 200 VAL PHE ARG MSE ALA GLU GLN GLN THR ASN HIS ILE THR SEQRES 15 A 200 MSE THR VAL ASN LEU SER ALA ASN SER PRO SER ARG LYS SEQRES 16 A 200 ASN ARG LYS GLN GLY SEQRES 1 B 200 MET GLU HIS ILE CYS GLY THR SER ARG ILE ALA GLY PHE SEQRES 2 B 200 ARG PHE SER LEU TYR PRO MSE THR ASP ASP PHE ILE SER SEQRES 3 B 200 VAL ILE LYS SER ALA LEU ALA ALA THR ASP THR SER LYS SEQRES 4 B 200 VAL TRP THR LYS THR ASP HIS ILE SER THR VAL LEU ARG SEQRES 5 B 200 GLY SER ILE ASP HIS VAL PHE ASP ALA ALA LYS ALA ILE SEQRES 6 B 200 TYR LEU HIS ALA ALA ASN SER GLU GLN HIS ILE VAL MSE SEQRES 7 B 200 ASN GLY THR PHE SER ILE GLY CYS PRO GLY ASP THR GLN SEQRES 8 B 200 GLY ASP THR TYR LEU SER LYS GLY ASP LYS ARG VAL ASN SEQRES 9 B 200 GLU ASP ALA VAL ARG GLY LEU LYS ALA GLU ALA PRO CYS SEQRES 10 B 200 GLN PHE ALA LEU TYR PRO MSE ASN GLU PRO ASP TYR MSE SEQRES 11 B 200 GLY LEU ILE MSE GLU ALA VAL ASP ILE ALA LYS ALA GLN SEQRES 12 B 200 GLY THR PHE VAL GLN GLY VAL HIS TYR ALA SER GLU LEU SEQRES 13 B 200 ASP GLY ASP ALA HIS ASP VAL PHE SER THR LEU GLU ALA SEQRES 14 B 200 VAL PHE ARG MSE ALA GLU GLN GLN THR ASN HIS ILE THR SEQRES 15 B 200 MSE THR VAL ASN LEU SER ALA ASN SER PRO SER ARG LYS SEQRES 16 B 200 ASN ARG LYS GLN GLY MODRES 1S99 MSE A 20 MET SELENOMETHIONINE MODRES 1S99 MSE A 78 MET SELENOMETHIONINE MODRES 1S99 MSE A 124 MET SELENOMETHIONINE MODRES 1S99 MSE A 130 MET SELENOMETHIONINE MODRES 1S99 MSE A 134 MET SELENOMETHIONINE MODRES 1S99 MSE A 173 MET SELENOMETHIONINE MODRES 1S99 MSE A 183 MET SELENOMETHIONINE MODRES 1S99 MSE B 20 MET SELENOMETHIONINE MODRES 1S99 MSE B 78 MET SELENOMETHIONINE MODRES 1S99 MSE B 124 MET SELENOMETHIONINE MODRES 1S99 MSE B 130 MET SELENOMETHIONINE MODRES 1S99 MSE B 134 MET SELENOMETHIONINE MODRES 1S99 MSE B 173 MET SELENOMETHIONINE MODRES 1S99 MSE B 183 MET SELENOMETHIONINE HET MSE A 20 8 HET MSE A 78 8 HET MSE A 124 8 HET MSE A 130 8 HET MSE A 134 8 HET MSE A 173 8 HET MSE A 183 8 HET MSE B 20 8 HET MSE B 78 8 HET MSE B 124 8 HET MSE B 130 8 HET MSE B 134 8 HET MSE B 173 8 HET MSE B 183 8 HET ACT A 201 4 HET CA A 801 1 HET ACT B 201 4 HETNAM MSE SELENOMETHIONINE HETNAM ACT ACETATE ION HETNAM CA CALCIUM ION FORMUL 1 MSE 14(C5 H11 N O2 SE) FORMUL 3 ACT 2(C2 H3 O2 1-) FORMUL 4 CA CA 2+ FORMUL 6 HOH *362(H2 O) HELIX 1 1 ASP A 23 THR A 35 1 13 HELIX 2 2 SER A 54 ASN A 71 1 18 HELIX 3 3 ASP A 128 GLN A 143 1 16 HELIX 4 4 ASP A 159 THR A 178 1 20 HELIX 5 5 ASP B 23 THR B 35 1 13 HELIX 6 6 SER B 54 ASN B 71 1 18 HELIX 7 7 ASP B 128 GLN B 143 1 16 HELIX 8 8 ASP B 159 THR B 178 1 20 SHEET 1 A 8 TRP A 41 THR A 44 0 SHEET 2 A 8 THR A 49 GLY A 53 -1 O ARG A 52 N TRP A 41 SHEET 3 A 8 ALA A 11 PRO A 19 -1 N PHE A 15 O THR A 49 SHEET 4 A 8 ILE A 76 ILE A 84 -1 O VAL A 77 N TYR A 18 SHEET 5 A 8 ILE A 181 ALA A 189 -1 O LEU A 187 N MSE A 78 SHEET 6 A 8 CYS A 117 PRO A 123 -1 N TYR A 122 O THR A 182 SHEET 7 A 8 ALA A 153 LEU A 156 -1 O LEU A 156 N CYS A 117 SHEET 8 A 8 PHE A 146 VAL A 150 -1 N GLN A 148 O GLU A 155 SHEET 1 B 8 TRP B 41 THR B 44 0 SHEET 2 B 8 THR B 49 GLY B 53 -1 O ARG B 52 N TRP B 41 SHEET 3 B 8 ALA B 11 PRO B 19 -1 N ALA B 11 O GLY B 53 SHEET 4 B 8 ILE B 76 ILE B 84 -1 O VAL B 77 N TYR B 18 SHEET 5 B 8 ILE B 181 ALA B 189 -1 O LEU B 187 N MSE B 78 SHEET 6 B 8 CYS B 117 PRO B 123 -1 N TYR B 122 O THR B 182 SHEET 7 B 8 ALA B 153 LEU B 156 -1 O SER B 154 N PHE B 119 SHEET 8 B 8 PHE B 146 VAL B 150 -1 N VAL B 147 O GLU B 155 LINK C PRO A 19 N MSE A 20 1555 1555 1.32 LINK C MSE A 20 N THR A 21 1555 1555 1.31 LINK C VAL A 77 N MSE A 78 1555 1555 1.33 LINK C MSE A 78 N ASN A 79 1555 1555 1.33 LINK C PRO A 123 N MSE A 124 1555 1555 1.32 LINK C MSE A 124 N ASN A 125 1555 1555 1.32 LINK C TYR A 129 N MSE A 130 1555 1555 1.33 LINK C MSE A 130 N GLY A 131 1555 1555 1.34 LINK C ILE A 133 N MSE A 134 1555 1555 1.33 LINK C MSE A 134 N GLU A 135 1555 1555 1.33 LINK C ARG A 172 N MSE A 173 1555 1555 1.32 LINK C MSE A 173 N ALA A 174 1555 1555 1.34 LINK C THR A 182 N MSE A 183 1555 1555 1.32 LINK C MSE A 183 N THR A 184 1555 1555 1.33 LINK C PRO B 19 N MSE B 20 1555 1555 1.33 LINK C MSE B 20 N THR B 21 1555 1555 1.32 LINK C VAL B 77 N MSE B 78 1555 1555 1.35 LINK C MSE B 78 N ASN B 79 1555 1555 1.34 LINK C PRO B 123 N MSE B 124 1555 1555 1.33 LINK C MSE B 124 N ASN B 125 1555 1555 1.32 LINK C TYR B 129 N MSE B 130 1555 1555 1.33 LINK C MSE B 130 N GLY B 131 1555 1555 1.33 LINK C ILE B 133 N MSE B 134 1555 1555 1.33 LINK C MSE B 134 N GLU B 135 1555 1555 1.34 LINK C ARG B 172 N MSE B 173 1555 1555 1.32 LINK C MSE B 173 N ALA B 174 1555 1555 1.33 LINK C THR B 182 N MSE B 183 1555 1555 1.33 LINK C MSE B 183 N THR B 184 1555 1555 1.33 LINK O ALA A 33 CA CA A 801 1555 1555 2.44 LINK O THR A 35 CA CA A 801 1555 1555 2.35 LINK CA CA A 801 O HOH A 808 1555 1555 2.49 LINK CA CA A 801 O HOH A 846 1555 1555 2.48 LINK CA CA A 801 O HOH A 990 1555 1555 2.99 LINK CA CA A 801 O ALA B 33 1555 2564 2.50 LINK CA CA A 801 O THR B 35 1555 2564 2.34 SITE 1 AC1 5 PHE A 15 SER A 16 LEU A 17 SER A 48 SITE 2 AC1 5 THR A 49 SITE 1 AC2 5 PHE B 15 SER B 16 LEU B 17 SER B 48 SITE 2 AC2 5 THR B 49 SITE 1 AC3 7 ALA A 33 THR A 35 HOH A 808 HOH A 846 SITE 2 AC3 7 HOH A 990 ALA B 33 THR B 35 CRYST1 60.930 83.280 85.900 90.00 90.00 90.00 P 21 21 21 8 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 0.016412 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012008 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011641 0.00000 MASTER 390 0 17 8 16 0 6 6 0 0 0 32 END