HEADER HYDROLASE 18-JAN-06 2DCY TITLE CRYSTAL STRUCTURE OF BACILLUS SUBTILIS FAMILY-11 XYLANASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDO-1,4-BETA-XYLANASE A; COMPND 3 CHAIN: A, B, C, D, E; COMPND 4 SYNONYM: XYLANASE A, 1,4-BETA-D-XYLAN XYLANOHYDROLASE A; COMPND 5 EC: 3.2.1.8; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 GENE: XYNA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: JM109; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PTD-TAC KEYWDS ALL BETA, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.KONDO,K.MIYAZAKI,M.TAKENOUCHI,N.NORO,M.SUZUKI,S.TSUDA REVDAT 5 25-OCT-23 2DCY 1 REMARK REVDAT 4 10-JUL-19 2DCY 1 COMPND REMARK HET HETNAM REVDAT 4 2 1 FORMUL LINK SITE ATOM REVDAT 3 24-FEB-09 2DCY 1 VERSN REVDAT 2 25-APR-06 2DCY 1 JRNL REVDAT 1 07-FEB-06 2DCY 0 JRNL AUTH K.MIYAZAKI,M.TAKENOUCHI,H.KONDO,N.NORO,M.SUZUKI,S.TSUDA JRNL TITL THERMAL STABILIZATION OF BACILLUS SUBTILIS FAMILY-11 JRNL TITL 2 XYLANASE BY DIRECTED EVOLUTION JRNL REF J.BIOL.CHEM. V. 281 10236 2006 JRNL REFN ISSN 0021-9258 JRNL PMID 16467302 JRNL DOI 10.1074/JBC.M511948200 REMARK 2 REMARK 2 RESOLUTION. 1.40 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 169733 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) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 8929 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) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 10466 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2460 REMARK 3 BIN FREE R VALUE SET COUNT : 532 REMARK 3 BIN FREE R VALUE : 0.2610 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7235 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 88 REMARK 3 SOLVENT ATOMS : 248 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.16 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.08000 REMARK 3 B22 (A**2) : 0.13000 REMARK 3 B33 (A**2) : -0.05000 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): 0.066 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.066 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.040 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.993 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 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): 7596 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10406 ; 1.701 ; 1.883 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 920 ; 8.009 ; 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): 1071 ; 0.114 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6069 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2955 ; 0.201 ; 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): 315 ; 0.101 ; 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): 88 ; 0.220 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 21 ; 0.090 ; 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): 4543 ; 0.937 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 7323 ; 1.536 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3053 ; 2.291 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3083 ; 3.036 ; 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 2DCY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-JAN-06. REMARK 100 THE DEPOSITION ID IS D_1000025267. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-DEC-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 178663 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : 0.04400 REMARK 200 FOR THE DATA SET : 13.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.30100 REMARK 200 R SYM FOR SHELL (I) : 0.30100 REMARK 200 FOR SHELL : 2.500 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 1XNB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M IMIDAZOLE, 1.0-1.1K/NA TARTRATE, REMARK 280 PH 7.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 65.22250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 93.10450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 65.22250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 93.10450 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4, 5 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: MONOMERIC 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D 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 REMARK 350 BIOMOLECULE: 5 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E 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 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 O GLN A 175 O1 TLA B 503 2.03 REMARK 500 NH1 ARG B 112 O11 TLA B 503 2.14 REMARK 500 O1 TLA B 503 O HOH B 633 2.15 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 101 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 119 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP B 121 CB - CG - OD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 ARG B 132 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ASP C 4 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 LYS C 99 CD - CE - NZ ANGL. DEV. = 14.2 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 165 -155.28 -88.92 REMARK 500 ALA B 165 -152.60 -101.28 REMARK 500 ASN C 8 87.51 -151.16 REMARK 500 ALA C 165 -153.61 -96.46 REMARK 500 SER D 74 -4.51 124.80 REMARK 500 ALA D 165 -155.59 -82.48 REMARK 500 ALA E 165 -155.19 -95.98 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 SER D 74 PRO D 75 38.68 REMARK 500 GLY D 161 SER D 162 -137.51 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 DIO C 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DIO A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DIO B 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TAR E 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TAR B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TAR B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TAR A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TAR B 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TAR C 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TAR A 507 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2DCZ RELATED DB: PDB REMARK 900 THE SAME PROTEIN(Q7H/N8F/S179C) DBREF 2DCY A 1 185 UNP P18429 XYNA_BACSU 29 213 DBREF 2DCY B 1 185 UNP P18429 XYNA_BACSU 29 213 DBREF 2DCY C 1 185 UNP P18429 XYNA_BACSU 29 213 DBREF 2DCY D 1 185 UNP P18429 XYNA_BACSU 29 213 DBREF 2DCY E 1 185 UNP P18429 XYNA_BACSU 29 213 SEQRES 1 A 185 ALA SER THR ASP TYR TRP GLN ASN TRP THR ASP GLY GLY SEQRES 2 A 185 GLY ILE VAL ASN ALA VAL ASN GLY SER GLY GLY ASN TYR SEQRES 3 A 185 SER VAL ASN TRP SER ASN THR GLY ASN PHE VAL VAL GLY SEQRES 4 A 185 LYS GLY TRP THR THR GLY SER PRO PHE ARG THR ILE ASN SEQRES 5 A 185 TYR ASN ALA GLY VAL TRP ALA PRO ASN GLY ASN GLY TYR SEQRES 6 A 185 LEU THR LEU TYR GLY TRP THR ARG SER PRO LEU ILE GLU SEQRES 7 A 185 TYR TYR VAL VAL ASP SER TRP GLY THR TYR ARG PRO THR SEQRES 8 A 185 GLY THR TYR LYS GLY THR VAL LYS SER ASP GLY GLY THR SEQRES 9 A 185 TYR ASP ILE TYR THR THR THR ARG TYR ASN ALA PRO SER SEQRES 10 A 185 ILE ASP GLY ASP ARG THR THR PHE THR GLN TYR TRP SER SEQRES 11 A 185 VAL ARG GLN SER LYS ARG PRO THR GLY SER ASN ALA THR SEQRES 12 A 185 ILE THR PHE SER ASN HIS VAL ASN ALA TRP LYS SER HIS SEQRES 13 A 185 GLY MET ASN LEU GLY SER ASN TRP ALA TYR GLN VAL MET SEQRES 14 A 185 ALA THR GLU GLY TYR GLN SER SER GLY SER SER ASN VAL SEQRES 15 A 185 THR VAL TRP SEQRES 1 B 185 ALA SER THR ASP TYR TRP GLN ASN TRP THR ASP GLY GLY SEQRES 2 B 185 GLY ILE VAL ASN ALA VAL ASN GLY SER GLY GLY ASN TYR SEQRES 3 B 185 SER VAL ASN TRP SER ASN THR GLY ASN PHE VAL VAL GLY SEQRES 4 B 185 LYS GLY TRP THR THR GLY SER PRO PHE ARG THR ILE ASN SEQRES 5 B 185 TYR ASN ALA GLY VAL TRP ALA PRO ASN GLY ASN GLY TYR SEQRES 6 B 185 LEU THR LEU TYR GLY TRP THR ARG SER PRO LEU ILE GLU SEQRES 7 B 185 TYR TYR VAL VAL ASP SER TRP GLY THR TYR ARG PRO THR SEQRES 8 B 185 GLY THR TYR LYS GLY THR VAL LYS SER ASP GLY GLY THR SEQRES 9 B 185 TYR ASP ILE TYR THR THR THR ARG TYR ASN ALA PRO SER SEQRES 10 B 185 ILE ASP GLY ASP ARG THR THR PHE THR GLN TYR TRP SER SEQRES 11 B 185 VAL ARG GLN SER LYS ARG PRO THR GLY SER ASN ALA THR SEQRES 12 B 185 ILE THR PHE SER ASN HIS VAL ASN ALA TRP LYS SER HIS SEQRES 13 B 185 GLY MET ASN LEU GLY SER ASN TRP ALA TYR GLN VAL MET SEQRES 14 B 185 ALA THR GLU GLY TYR GLN SER SER GLY SER SER ASN VAL SEQRES 15 B 185 THR VAL TRP SEQRES 1 C 185 ALA SER THR ASP TYR TRP GLN ASN TRP THR ASP GLY GLY SEQRES 2 C 185 GLY ILE VAL ASN ALA VAL ASN GLY SER GLY GLY ASN TYR SEQRES 3 C 185 SER VAL ASN TRP SER ASN THR GLY ASN PHE VAL VAL GLY SEQRES 4 C 185 LYS GLY TRP THR THR GLY SER PRO PHE ARG THR ILE ASN SEQRES 5 C 185 TYR ASN ALA GLY VAL TRP ALA PRO ASN GLY ASN GLY TYR SEQRES 6 C 185 LEU THR LEU TYR GLY TRP THR ARG SER PRO LEU ILE GLU SEQRES 7 C 185 TYR TYR VAL VAL ASP SER TRP GLY THR TYR ARG PRO THR SEQRES 8 C 185 GLY THR TYR LYS GLY THR VAL LYS SER ASP GLY GLY THR SEQRES 9 C 185 TYR ASP ILE TYR THR THR THR ARG TYR ASN ALA PRO SER SEQRES 10 C 185 ILE ASP GLY ASP ARG THR THR PHE THR GLN TYR TRP SER SEQRES 11 C 185 VAL ARG GLN SER LYS ARG PRO THR GLY SER ASN ALA THR SEQRES 12 C 185 ILE THR PHE SER ASN HIS VAL ASN ALA TRP LYS SER HIS SEQRES 13 C 185 GLY MET ASN LEU GLY SER ASN TRP ALA TYR GLN VAL MET SEQRES 14 C 185 ALA THR GLU GLY TYR GLN SER SER GLY SER SER ASN VAL SEQRES 15 C 185 THR VAL TRP SEQRES 1 D 185 ALA SER THR ASP TYR TRP GLN ASN TRP THR ASP GLY GLY SEQRES 2 D 185 GLY ILE VAL ASN ALA VAL ASN GLY SER GLY GLY ASN TYR SEQRES 3 D 185 SER VAL ASN TRP SER ASN THR GLY ASN PHE VAL VAL GLY SEQRES 4 D 185 LYS GLY TRP THR THR GLY SER PRO PHE ARG THR ILE ASN SEQRES 5 D 185 TYR ASN ALA GLY VAL TRP ALA PRO ASN GLY ASN GLY TYR SEQRES 6 D 185 LEU THR LEU TYR GLY TRP THR ARG SER PRO LEU ILE GLU SEQRES 7 D 185 TYR TYR VAL VAL ASP SER TRP GLY THR TYR ARG PRO THR SEQRES 8 D 185 GLY THR TYR LYS GLY THR VAL LYS SER ASP GLY GLY THR SEQRES 9 D 185 TYR ASP ILE TYR THR THR THR ARG TYR ASN ALA PRO SER SEQRES 10 D 185 ILE ASP GLY ASP ARG THR THR PHE THR GLN TYR TRP SER SEQRES 11 D 185 VAL ARG GLN SER LYS ARG PRO THR GLY SER ASN ALA THR SEQRES 12 D 185 ILE THR PHE SER ASN HIS VAL ASN ALA TRP LYS SER HIS SEQRES 13 D 185 GLY MET ASN LEU GLY SER ASN TRP ALA TYR GLN VAL MET SEQRES 14 D 185 ALA THR GLU GLY TYR GLN SER SER GLY SER SER ASN VAL SEQRES 15 D 185 THR VAL TRP SEQRES 1 E 185 ALA SER THR ASP TYR TRP GLN ASN TRP THR ASP GLY GLY SEQRES 2 E 185 GLY ILE VAL ASN ALA VAL ASN GLY SER GLY GLY ASN TYR SEQRES 3 E 185 SER VAL ASN TRP SER ASN THR GLY ASN PHE VAL VAL GLY SEQRES 4 E 185 LYS GLY TRP THR THR GLY SER PRO PHE ARG THR ILE ASN SEQRES 5 E 185 TYR ASN ALA GLY VAL TRP ALA PRO ASN GLY ASN GLY TYR SEQRES 6 E 185 LEU THR LEU TYR GLY TRP THR ARG SER PRO LEU ILE GLU SEQRES 7 E 185 TYR TYR VAL VAL ASP SER TRP GLY THR TYR ARG PRO THR SEQRES 8 E 185 GLY THR TYR LYS GLY THR VAL LYS SER ASP GLY GLY THR SEQRES 9 E 185 TYR ASP ILE TYR THR THR THR ARG TYR ASN ALA PRO SER SEQRES 10 E 185 ILE ASP GLY ASP ARG THR THR PHE THR GLN TYR TRP SER SEQRES 11 E 185 VAL ARG GLN SER LYS ARG PRO THR GLY SER ASN ALA THR SEQRES 12 E 185 ILE THR PHE SER ASN HIS VAL ASN ALA TRP LYS SER HIS SEQRES 13 E 185 GLY MET ASN LEU GLY SER ASN TRP ALA TYR GLN VAL MET SEQRES 14 E 185 ALA THR GLU GLY TYR GLN SER SER GLY SER SER ASN VAL SEQRES 15 E 185 THR VAL TRP HET DIO A 602 6 HET TLA A 504 10 HET TAR A 507 10 HET DIO B 603 6 HET TLA B 502 10 HET TLA B 503 10 HET TLA B 505 10 HET DIO C 601 6 HET TLA C 506 10 HET TLA E 501 10 HETNAM DIO 1,4-DIETHYLENE DIOXIDE HETNAM TLA L(+)-TARTARIC ACID HETNAM TAR D(-)-TARTARIC ACID FORMUL 6 DIO 3(C4 H8 O2) FORMUL 7 TLA 6(C4 H6 O6) FORMUL 8 TAR C4 H6 O6 FORMUL 16 HOH *248(H2 O) HELIX 1 1 PHE A 146 HIS A 156 1 11 HELIX 2 2 PHE B 146 HIS B 156 1 11 HELIX 3 3 PHE C 146 HIS C 156 1 11 HELIX 4 4 PHE D 146 SER D 155 1 10 HELIX 5 5 PHE E 146 HIS E 156 1 11 SHEET 1 A 8 TYR A 5 THR A 10 0 SHEET 2 A 8 ASN A 35 TRP A 42 -1 O GLY A 39 N GLN A 7 SHEET 3 A 8 ASN A 163 TYR A 174 -1 O THR A 171 N VAL A 38 SHEET 4 A 8 GLY A 64 ARG A 73 -1 N THR A 67 O ALA A 170 SHEET 5 A 8 ILE A 77 TRP A 85 -1 O TYR A 79 N GLY A 70 SHEET 6 A 8 GLY A 120 ARG A 132 1 O SER A 130 N VAL A 82 SHEET 7 A 8 GLY A 103 SER A 117 -1 N THR A 110 O GLN A 127 SHEET 8 A 8 THR A 93 SER A 100 -1 N GLY A 96 O ILE A 107 SHEET 1 B 5 ILE A 15 ASN A 20 0 SHEET 2 B 5 ASN A 25 SER A 31 -1 O ASN A 29 N ASN A 17 SHEET 3 B 5 SER A 177 TRP A 185 -1 O GLY A 178 N TRP A 30 SHEET 4 B 5 THR A 50 ASN A 61 -1 N ASN A 61 O SER A 177 SHEET 5 B 5 ALA A 142 THR A 145 -1 O ALA A 142 N TYR A 53 SHEET 1 C 8 TYR B 5 THR B 10 0 SHEET 2 C 8 ASN B 35 TRP B 42 -1 O GLY B 39 N GLN B 7 SHEET 3 C 8 ASN B 163 TRP B 185 -1 O GLN B 167 N TRP B 42 SHEET 4 C 8 THR B 50 ARG B 73 -1 N ASN B 61 O SER B 177 SHEET 5 C 8 ILE B 77 TRP B 85 -1 O TYR B 79 N GLY B 70 SHEET 6 C 8 GLY B 120 ARG B 132 1 O SER B 130 N VAL B 82 SHEET 7 C 8 GLY B 103 SER B 117 -1 N THR B 110 O GLN B 127 SHEET 8 C 8 THR B 93 SER B 100 -1 N GLY B 96 O ILE B 107 SHEET 1 D 5 ILE B 15 ASN B 20 0 SHEET 2 D 5 ASN B 25 SER B 31 -1 O ASN B 29 N ASN B 17 SHEET 3 D 5 ASN B 163 TRP B 185 -1 O GLY B 178 N TRP B 30 SHEET 4 D 5 THR B 50 ARG B 73 -1 N ASN B 61 O SER B 177 SHEET 5 D 5 ALA B 142 THR B 145 -1 O ILE B 144 N ILE B 51 SHEET 1 E 8 TYR C 5 THR C 10 0 SHEET 2 E 8 ASN C 35 TRP C 42 -1 O GLY C 39 N GLN C 7 SHEET 3 E 8 ASN C 163 TYR C 174 -1 O THR C 171 N VAL C 38 SHEET 4 E 8 GLY C 64 ARG C 73 -1 N THR C 67 O ALA C 170 SHEET 5 E 8 ILE C 77 TRP C 85 -1 O VAL C 81 N LEU C 68 SHEET 6 E 8 GLY C 120 ARG C 132 1 O SER C 130 N VAL C 82 SHEET 7 E 8 GLY C 103 SER C 117 -1 N THR C 110 O GLN C 127 SHEET 8 E 8 THR C 93 SER C 100 -1 N LYS C 95 O ILE C 107 SHEET 1 F 5 ILE C 15 ASN C 20 0 SHEET 2 F 5 ASN C 25 SER C 31 -1 O ASN C 29 N ASN C 17 SHEET 3 F 5 SER C 177 TRP C 185 -1 O GLY C 178 N TRP C 30 SHEET 4 F 5 THR C 50 ASN C 61 -1 N ASN C 61 O SER C 177 SHEET 5 F 5 ALA C 142 THR C 145 -1 O ILE C 144 N ILE C 51 SHEET 1 G 8 TYR D 5 THR D 10 0 SHEET 2 G 8 ASN D 35 TRP D 42 -1 O GLY D 39 N GLN D 7 SHEET 3 G 8 ASN D 163 TRP D 185 -1 O THR D 171 N VAL D 38 SHEET 4 G 8 THR D 50 ARG D 73 -1 N ASN D 61 O SER D 177 SHEET 5 G 8 ILE D 77 TRP D 85 -1 O ILE D 77 N THR D 72 SHEET 6 G 8 GLY D 120 ARG D 132 1 O SER D 130 N VAL D 82 SHEET 7 G 8 GLY D 103 SER D 117 -1 N ARG D 112 O PHE D 125 SHEET 8 G 8 THR D 93 SER D 100 -1 N VAL D 98 O TYR D 105 SHEET 1 H 5 ILE D 15 ASN D 20 0 SHEET 2 H 5 ASN D 25 SER D 31 -1 O ASN D 29 N ASN D 17 SHEET 3 H 5 ASN D 163 TRP D 185 -1 O SER D 180 N VAL D 28 SHEET 4 H 5 THR D 50 ARG D 73 -1 N ASN D 61 O SER D 177 SHEET 5 H 5 ALA D 142 THR D 145 -1 O ILE D 144 N ILE D 51 SHEET 1 I 8 TYR E 5 THR E 10 0 SHEET 2 I 8 ASN E 35 TRP E 42 -1 O GLY E 39 N GLN E 7 SHEET 3 I 8 ASN E 163 TRP E 185 -1 O GLN E 167 N TRP E 42 SHEET 4 I 8 THR E 50 ARG E 73 -1 N THR E 67 O ALA E 170 SHEET 5 I 8 ILE E 77 TRP E 85 -1 O TYR E 79 N GLY E 70 SHEET 6 I 8 GLY E 120 ARG E 132 1 O SER E 130 N VAL E 82 SHEET 7 I 8 GLY E 103 SER E 117 -1 N THR E 110 O GLN E 127 SHEET 8 I 8 THR E 93 SER E 100 -1 N GLY E 96 O ILE E 107 SHEET 1 J 5 ILE E 15 ASN E 20 0 SHEET 2 J 5 ASN E 25 SER E 31 -1 O ASN E 29 N ASN E 17 SHEET 3 J 5 ASN E 163 TRP E 185 -1 O GLY E 178 N TRP E 30 SHEET 4 J 5 THR E 50 ARG E 73 -1 N THR E 67 O ALA E 170 SHEET 5 J 5 ALA E 142 THR E 145 -1 O ILE E 144 N ILE E 51 CISPEP 1 SER A 74 PRO A 75 0 -1.20 CISPEP 2 SER B 74 PRO B 75 0 1.55 CISPEP 3 SER C 74 PRO C 75 0 -0.90 CISPEP 4 SER E 74 PRO E 75 0 0.58 SITE 1 AC1 6 TRP C 9 TYR C 69 PRO C 116 SER C 117 SITE 2 AC1 6 TYR C 166 HOH C 638 SITE 1 AC2 4 ASN A 29 TRP A 30 ASN B 29 TRP B 30 SITE 1 AC3 10 ILE A 15 ASN A 17 ASN A 29 TRP A 30 SITE 2 AC3 10 SER A 31 ILE B 15 ASN B 17 ASN B 29 SITE 3 AC3 10 TRP B 30 SER B 31 SITE 1 AC4 9 SER A 134 LYS A 135 SER E 74 LYS E 99 SITE 2 AC4 9 SER E 100 ASP E 101 GLY E 102 GLY E 103 SITE 3 AC4 9 HOH E 528 SITE 1 AC5 6 ASN B 8 VAL B 16 ASN B 17 ALA B 18 SITE 2 AC5 6 TYR B 113 TLA B 505 SITE 1 AC6 14 GLN A 175 SER A 176 HOH A 610 TYR B 65 SITE 2 AC6 14 TYR B 88 PRO B 90 THR B 91 THR B 110 SITE 3 AC6 14 ARG B 112 GLN B 127 TRP B 129 HOH B 630 SITE 4 AC6 14 HOH B 633 HOH B 639 SITE 1 AC7 4 SER A 100 ASP A 101 GLY A 102 ASN A 148 SITE 1 AC8 8 TRP B 6 ASN B 8 ALA B 18 TYR B 113 SITE 2 AC8 8 TLA B 502 SER C 134 LYS C 135 HOH C 644 SITE 1 AC9 10 ALA A 1 THR C 3 ASP C 4 TYR C 5 SITE 2 AC9 10 ASN C 20 SER C 22 GLY C 23 GLY C 24 SITE 3 AC9 10 LYS C 40 HOH C 634 SITE 1 BC1 11 TRP A 58 SER A 84 TRP A 85 LYS A 135 SITE 2 BC1 11 HOH A 607 HOH A 619 HOH A 626 VAL E 98 SITE 3 BC1 11 ASN E 148 ASN E 151 ALA E 152 CRYST1 130.445 186.209 37.979 90.00 90.00 90.00 P 21 21 2 20 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 0.007666 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005370 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026330 0.00000