HEADER LIGAND BINDING PROTEIN 11-FEB-04 1SBR TITLE THE STRUCTURE AND FUNCTION OF B. SUBTILIS YKOF GENE PRODUCT: THE TITLE 2 COMPLEX WITH THIAMIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: YKOF; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES 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 6 30-OCT-24 1SBR 1 REMARK REVDAT 5 15-NOV-23 1SBR 1 REMARK REVDAT 4 23-AUG-23 1SBR 1 REMARK REVDAT 3 27-OCT-21 1SBR 1 REMARK SEQADV HETSYN LINK REVDAT 2 24-FEB-09 1SBR 1 VERSN REVDAT 1 05-OCT-04 1SBR 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. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 15723 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) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 836 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 632 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2620 REMARK 3 BIN FREE R VALUE SET COUNT : 32 REMARK 3 BIN FREE R VALUE : 0.3340 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2788 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 73 REMARK 3 SOLVENT ATOMS : 77 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 10.65000 REMARK 3 B22 (A**2) : -4.17000 REMARK 3 B33 (A**2) : -6.48000 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): 0.415 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.272 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.214 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.208 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.908 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2920 ; 0.019 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3962 ; 1.669 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 360 ; 6.971 ; 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): 444 ; 0.186 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2234 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1461 ; 0.230 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 153 ; 0.152 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.141 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 21 ; 0.200 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1806 ; 0.883 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2903 ; 1.663 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1114 ; 2.637 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1059 ; 3.861 ; 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): 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 : 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: NULL REMARK 4 REMARK 4 1SBR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-FEB-04. REMARK 100 THE DEPOSITION ID IS D_1000021583. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-SEP-03 REMARK 200 TEMPERATURE (KELVIN) : 120.0 REMARK 200 PH : 6.50 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 : ENRAF-NONIUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : PURPLE CONFOCAL MIRRORS, MSC REMARK 200 OPTICS : MIRRORS 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 : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16658 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 49.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.30600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1S99 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 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, PH 6.50 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 29.41000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.05500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.24500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.05500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.41000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.24500 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: 6500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 ASP A 100 REMARK 465 LYS A 195 REMARK 465 ASN A 196 REMARK 465 ARG A 197 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 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 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 ARG A 194 CD NE CZ NH1 NH2 REMARK 470 GLU B 73 CG CD OE1 OE2 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 MSE A 20 SE MSE A 20 CE -0.544 REMARK 500 MSE B 20 SE MSE B 20 CE -0.366 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 128 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP B 23 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP B 56 CB - CG - OD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 ASP B 159 CB - CG - OD2 ANGL. DEV. = 12.0 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 ASP A 23 37.91 -85.85 REMARK 500 GLU A 73 14.38 59.72 REMARK 500 ARG A 102 85.05 -69.83 REMARK 500 TYR A 152 -1.07 79.05 REMARK 500 GLU B 73 -8.43 76.22 REMARK 500 ASP B 89 104.91 69.38 REMARK 500 ASP B 128 40.43 -101.76 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 B 92 ASP B 93 148.93 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 89.2 REMARK 620 3 HOH A 802 O 91.8 77.9 REMARK 620 4 ALA B 33 O 173.4 90.0 94.4 REMARK 620 5 THR B 35 O 79.6 109.2 168.6 94.5 REMARK 620 6 HOH B 803 O 81.6 167.5 93.7 100.1 77.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE VIB A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE VIB A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE VIB B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE VIB B 504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1S99 RELATED DB: PDB REMARK 900 THE SAME PROTEIN, LIGAND FREE REMARK 900 RELATED ID: 1LXJ RELATED DB: PDB REMARK 900 SHARES SIMILAR FOLD REMARK 900 RELATED ID: 1LXN RELATED DB: PDB REMARK 900 SHARES SIMILAR FOLD DBREF 1SBR A 1 200 UNP O34911 O34911_BACSU 1 200 DBREF 1SBR B 1 200 UNP O34911 O34911_BACSU 1 200 SEQADV 1SBR ALA A 33 UNP O34911 LYS 33 ENGINEERED MUTATION SEQADV 1SBR ALA A 34 UNP O34911 LYS 34 ENGINEERED MUTATION SEQADV 1SBR ALA B 33 UNP O34911 LYS 33 ENGINEERED MUTATION SEQADV 1SBR ALA B 34 UNP O34911 LYS 34 ENGINEERED MUTATION 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 1SBR MSE A 20 MET SELENOMETHIONINE MODRES 1SBR MSE A 78 MET SELENOMETHIONINE MODRES 1SBR MSE A 124 MET SELENOMETHIONINE MODRES 1SBR MSE A 130 MET SELENOMETHIONINE MODRES 1SBR MSE A 134 MET SELENOMETHIONINE MODRES 1SBR MSE A 173 MET SELENOMETHIONINE MODRES 1SBR MSE A 183 MET SELENOMETHIONINE MODRES 1SBR MSE B 20 MET SELENOMETHIONINE MODRES 1SBR MSE B 78 MET SELENOMETHIONINE MODRES 1SBR MSE B 124 MET SELENOMETHIONINE MODRES 1SBR MSE B 130 MET SELENOMETHIONINE MODRES 1SBR MSE B 134 MET SELENOMETHIONINE MODRES 1SBR MSE B 173 MET SELENOMETHIONINE MODRES 1SBR 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 CA A 801 1 HET VIB A 501 18 HET VIB A 502 18 HET VIB B 503 18 HET VIB B 504 18 HETNAM MSE SELENOMETHIONINE HETNAM CA CALCIUM ION HETNAM VIB 3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY- HETNAM 2 VIB ETHYL)-4-METHYL-THIAZOL-3-IUM HETSYN VIB THIAMIN; VITAMIN B1 FORMUL 1 MSE 14(C5 H11 N O2 SE) FORMUL 3 CA CA 2+ FORMUL 4 VIB 4(C12 H17 N4 O S 1+) FORMUL 8 HOH *77(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 TYR A 129 5 2 HELIX 4 4 GLY A 131 ILE A 133 5 3 HELIX 5 5 GLU A 135 GLN A 143 1 9 HELIX 6 6 ASP A 159 ARG A 172 1 14 HELIX 7 7 ALA A 174 GLN A 177 5 4 HELIX 8 8 ASP B 23 THR B 35 1 13 HELIX 9 9 SER B 54 SER B 72 1 19 HELIX 10 10 GLU B 105 ARG B 109 5 5 HELIX 11 11 ASP B 128 TYR B 129 5 2 HELIX 12 12 GLY B 131 ILE B 133 5 3 HELIX 13 13 GLU B 135 GLN B 143 1 9 HELIX 14 14 ASP B 159 ARG B 172 1 14 HELIX 15 15 ALA B 174 GLN B 176 5 3 SHEET 1 A 4 TRP A 41 THR A 44 0 SHEET 2 A 4 THR A 49 GLY A 53 -1 O ARG A 52 N TRP A 41 SHEET 3 A 4 ALA A 11 TYR A 18 -1 N PHE A 15 O THR A 49 SHEET 4 A 4 VAL A 77 SER A 83 -1 O ASN A 79 N SER A 16 SHEET 1 B 4 PHE A 146 VAL A 150 0 SHEET 2 B 4 ALA A 153 LEU A 156 -1 O GLU A 155 N VAL A 147 SHEET 3 B 4 CYS A 117 TYR A 122 -1 N PHE A 119 O SER A 154 SHEET 4 B 4 THR A 182 LEU A 187 -1 O THR A 182 N TYR A 122 SHEET 1 C 8 TRP B 41 THR B 44 0 SHEET 2 C 8 THR B 49 GLY B 53 -1 O ARG B 52 N TRP B 41 SHEET 3 C 8 ALA B 11 TYR B 18 -1 N ALA B 11 O GLY B 53 SHEET 4 C 8 VAL B 77 ILE B 84 -1 O SER B 83 N GLY B 12 SHEET 5 C 8 ILE B 181 LEU B 187 -1 O VAL B 185 N GLY B 80 SHEET 6 C 8 CYS B 117 PHE B 119 -1 N GLN B 118 O ASN B 186 SHEET 7 C 8 ALA B 153 LEU B 156 -1 O LEU B 156 N CYS B 117 SHEET 8 C 8 PHE B 146 VAL B 150 -1 N GLN B 148 O GLU B 155 LINK C PRO A 19 N MSE A 20 1555 1555 1.33 LINK C MSE A 20 N THR A 21 1555 1555 1.33 LINK C VAL A 77 N MSE A 78 1555 1555 1.34 LINK C MSE A 78 N ASN A 79 1555 1555 1.32 LINK C PRO A 123 N MSE A 124 1555 1555 1.33 LINK C MSE A 124 N ASN A 125 1555 1555 1.33 LINK C TYR A 129 N MSE A 130 1555 1555 1.32 LINK C MSE A 130 N GLY A 131 1555 1555 1.33 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 1.33 LINK C MSE A 173 N ALA A 174 1555 1555 1.33 LINK C THR A 182 N MSE A 183 1555 1555 1.31 LINK C MSE A 183 N THR A 184 1555 1555 1.32 LINK C PRO B 19 N MSE B 20 1555 1555 1.33 LINK C MSE B 20 N THR B 21 1555 1555 1.33 LINK C VAL B 77 N MSE B 78 1555 1555 1.33 LINK C MSE B 78 N ASN B 79 1555 1555 1.33 LINK C PRO B 123 N MSE B 124 1555 1555 1.33 LINK C MSE B 124 N ASN B 125 1555 1555 1.33 LINK C TYR B 129 N MSE B 130 1555 1555 1.33 LINK C MSE B 130 N GLY B 131 1555 1555 1.34 LINK C ILE B 133 N MSE B 134 1555 1555 1.33 LINK C MSE B 134 N GLU B 135 1555 1555 1.33 LINK C ARG B 172 N MSE B 173 1555 1555 1.33 LINK C MSE B 173 N ALA B 174 1555 1555 1.33 LINK C THR B 182 N MSE B 183 1555 1555 1.32 LINK C MSE B 183 N THR B 184 1555 1555 1.34 LINK O ALA A 33 CA CA A 801 1555 1555 2.71 LINK O THR A 35 CA CA A 801 1555 1555 2.28 LINK CA CA A 801 O HOH A 802 1555 1555 2.52 LINK CA CA A 801 O ALA B 33 1555 2564 2.47 LINK CA CA A 801 O THR B 35 1555 2564 2.45 LINK CA CA A 801 O HOH B 803 1555 2564 2.72 SITE 1 AC1 6 ALA A 33 THR A 35 HOH A 802 ALA B 33 SITE 2 AC1 6 THR B 35 HOH B 803 SITE 1 AC2 10 PHE A 15 SER A 16 LEU A 17 ILE A 28 SITE 2 AC2 10 THR A 44 ASP A 45 HIS A 46 ILE A 47 SITE 3 AC2 10 SER A 48 THR A 49 SITE 1 AC3 7 PHE A 119 ALA A 120 LEU A 121 MSE A 130 SITE 2 AC3 7 ILE A 133 SER A 154 HOH A 828 SITE 1 AC4 10 PHE B 15 SER B 16 LEU B 17 ILE B 25 SITE 2 AC4 10 THR B 44 ASP B 45 HIS B 46 ILE B 47 SITE 3 AC4 10 SER B 48 THR B 49 SITE 1 AC5 9 PRO A 87 HIS A 180 PHE B 119 ALA B 120 SITE 2 AC5 9 LEU B 121 MSE B 130 ILE B 133 ALA B 153 SITE 3 AC5 9 SER B 154 CRYST1 58.820 82.490 86.110 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 0.017001 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012123 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011613 0.00000