HEADER HYDROLASE 07-JAN-06 2DCK TITLE A TETRAGONAL-LATTICE STRUCTURE OF ALKALIPHILIC XYNJ FROM BACILLUS SP. TITLE 2 41M-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: XYLANASE J; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.8; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SP.; SOURCE 3 ORGANISM_TAXID: 98930; SOURCE 4 STRAIN: 41M-1; SOURCE 5 GENE: XYNJ; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PUC119 KEYWDS FAMILY 11, XYLAN BINDING DOMAIN (XBM), BETA-JELLY ROLL, ALKALIPHILIC KEYWDS 2 XYLANASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR G.FIBRIANSAH,IHSANAWATI,N.TANAKA,S.NAKAMURA,T.KUMASAKA REVDAT 4 25-OCT-23 2DCK 1 REMARK LINK REVDAT 3 13-JUL-11 2DCK 1 VERSN REVDAT 2 24-FEB-09 2DCK 1 VERSN REVDAT 1 20-MAR-07 2DCK 0 JRNL AUTH IHSANAWATI,N.TANAKA,S.NAKAMURA,T.KUMASAKA JRNL TITL A TWO-DOMAIN STRUCTURE OF ALKALIPHILIC XYNJ FROM BACILLUS JRNL TITL 2 SP. 41M-1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 34722 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) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1828 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2449 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2270 REMARK 3 BIN FREE R VALUE SET COUNT : 127 REMARK 3 BIN FREE R VALUE : 0.2910 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2492 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 339 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.55000 REMARK 3 B22 (A**2) : 0.55000 REMARK 3 B33 (A**2) : -1.09000 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): 0.125 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.121 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.083 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.209 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2574 ; 0.026 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2137 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3493 ; 1.985 ; 1.912 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4981 ; 0.944 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 318 ; 7.518 ; 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): 365 ; 0.148 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2944 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 556 ; 0.004 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 366 ; 0.196 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2585 ; 0.268 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1553 ; 0.096 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 265 ; 0.218 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 6 ; 0.170 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 6 ; 0.285 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 34 ; 0.332 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 23 ; 0.168 ; 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): 1571 ; 1.330 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2522 ; 2.285 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1003 ; 3.237 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 971 ; 4.705 ; 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 2DCK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-JAN-06. REMARK 100 THE DEPOSITION ID IS D_1000025253. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-OCT-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36572 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 119.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2DCJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10MM SODIUM PHOSPHATE BUFFER REMARK 280 (NA2HPO4/NAH2PO4), PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 22.95450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 34.43175 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 11.47725 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 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 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 -26 REMARK 465 LYS A -25 REMARK 465 GLN A -24 REMARK 465 VAL A -23 REMARK 465 LYS A -22 REMARK 465 ILE A -21 REMARK 465 MET A -20 REMARK 465 PHE A -19 REMARK 465 LEU A -18 REMARK 465 MET A -17 REMARK 465 THR A -16 REMARK 465 MET A -15 REMARK 465 PHE A -14 REMARK 465 LEU A -13 REMARK 465 GLY A -12 REMARK 465 ILE A -11 REMARK 465 GLY A -10 REMARK 465 LEU A -9 REMARK 465 LEU A -8 REMARK 465 PHE A -7 REMARK 465 PHE A -6 REMARK 465 SER A -5 REMARK 465 GLU A -4 REMARK 465 ASN A -3 REMARK 465 ALA A -2 REMARK 465 GLU A -1 REMARK 465 ALA A 0 REMARK 465 GLY A 202 REMARK 465 GLN A 203 REMARK 465 SER A 204 REMARK 465 GLY A 205 REMARK 465 GLY A 206 REMARK 465 GLU A 207 REMARK 465 GLN A 208 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 HOH A 2289 O HOH A 2339 1.95 REMARK 500 O HOH A 2291 O HOH A 2341 2.02 REMARK 500 O HOH A 2072 O HOH A 2251 2.05 REMARK 500 O HOH A 2075 O HOH A 2218 2.16 REMARK 500 O HOH A 2067 O HOH A 2271 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 SER A 31 CB SER A 31 OG 0.082 REMARK 500 TYR A 194 CE1 TYR A 194 CZ -0.079 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 48 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ASP A 54 CB - CG - OD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 ARG A 163 NE - CZ - NH1 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 163 NE - CZ - NH2 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 269 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 ARG A 269 NE - CZ - NH2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG A 273 NE - CZ - NH2 ANGL. DEV. = -4.9 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 GLU A 55 30.00 75.85 REMARK 500 ASN A 196 96.50 -163.16 REMARK 500 ASN A 264 -156.76 -150.65 REMARK 500 ASP A 286 -167.50 -161.47 REMARK 500 ASP A 314 19.86 -142.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 300 ILE A 301 -148.48 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 A1001 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 213 OE2 REMARK 620 2 GLU A 215 OE1 89.5 REMARK 620 3 GLU A 215 OE2 96.7 52.9 REMARK 620 4 ASN A 232 O 167.4 80.5 83.4 REMARK 620 5 ASP A 322 O 81.1 128.5 78.0 111.2 REMARK 620 6 ASP A 322 OD1 95.8 158.3 146.2 90.8 73.2 REMARK 620 7 HOH A2199 O 81.7 85.3 138.1 89.8 141.6 74.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1002 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 237 O REMARK 620 2 ASP A 313 OD1 86.3 REMARK 620 3 TRP A 317 O 123.1 78.6 REMARK 620 4 ASP A 318 OD2 94.2 152.1 77.8 REMARK 620 5 HOH A2180 O 85.6 78.3 141.4 129.6 REMARK 620 6 HOH A2267 O 85.9 138.8 137.4 68.9 60.8 REMARK 620 7 HOH A2279 O 150.7 111.2 84.4 81.1 75.7 65.3 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 CA A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 2002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 2003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 2004 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2DCJ RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITH DIFFERENT SPACE GROUP DBREF 2DCK A -26 327 GB 5381269 BAA82316 1 354 SEQRES 1 A 354 MET LYS GLN VAL LYS ILE MET PHE LEU MET THR MET PHE SEQRES 2 A 354 LEU GLY ILE GLY LEU LEU PHE PHE SER GLU ASN ALA GLU SEQRES 3 A 354 ALA ALA ILE THR SER ASN GLU ILE GLY THR HIS ASP GLY SEQRES 4 A 354 TYR ASP TYR GLU PHE TRP LYS ASP SER GLY GLY SER GLY SEQRES 5 A 354 SER MET THR LEU ASN SER GLY GLY THR PHE SER ALA GLN SEQRES 6 A 354 TRP SER ASN VAL ASN ASN ILE LEU PHE ARG LYS GLY LYS SEQRES 7 A 354 LYS PHE ASP GLU THR GLN THR HIS GLN GLN ILE GLY ASN SEQRES 8 A 354 MET SER ILE ASN TYR GLY ALA THR TYR ASN PRO ASN GLY SEQRES 9 A 354 ASN SER TYR LEU THR VAL TYR GLY TRP THR VAL ASP PRO SEQRES 10 A 354 LEU VAL GLU PHE TYR ILE VAL ASP SER TRP GLY THR TRP SEQRES 11 A 354 ARG PRO PRO GLY GLY THR PRO LYS GLY THR ILE ASN VAL SEQRES 12 A 354 ASP GLY GLY THR TYR GLN ILE TYR GLU THR THR ARG TYR SEQRES 13 A 354 ASN GLN PRO SER ILE LYS GLY THR ALA THR PHE GLN GLN SEQRES 14 A 354 TYR TRP SER VAL ARG THR SER LYS ARG THR SER GLY THR SEQRES 15 A 354 ILE SER VAL SER GLU HIS PHE ARG ALA TRP GLU SER LEU SEQRES 16 A 354 GLY MET ASN MET GLY ASN MET TYR GLU VAL ALA LEU THR SEQRES 17 A 354 VAL GLU GLY TYR GLN SER SER GLY SER ALA ASN VAL TYR SEQRES 18 A 354 SER ASN THR LEU THR ILE GLY GLY GLN SER GLY GLY GLU SEQRES 19 A 354 GLN ALA THR ARG VAL GLU ALA GLU SER MET THR LYS GLY SEQRES 20 A 354 GLY PRO TYR THR SER ASN ILE THR SER PRO PHE ASN GLY SEQRES 21 A 354 VAL ALA LEU TYR ALA ASN GLY ASP ASN VAL SER PHE ASN SEQRES 22 A 354 HIS SER PHE THR LYS ALA ASN SER SER PHE SER LEU ARG SEQRES 23 A 354 GLY ALA SER ASN ASN SER ASN MET ALA ARG VAL ASP LEU SEQRES 24 A 354 ARG ILE GLY GLY GLN ASN ARG GLY THR PHE TYR PHE GLY SEQRES 25 A 354 ASP GLN TYR PRO ALA VAL TYR THR ILE ASN ASN ILE ASN SEQRES 26 A 354 HIS GLY ILE GLY ASN GLN LEU VAL GLU LEU ILE VAL THR SEQRES 27 A 354 ALA ASP ASP GLY THR TRP ASP ALA TYR LEU ASP TYR LEU SEQRES 28 A 354 GLU ILE ARG HET CA A1001 1 HET CA A1002 1 HET GOL A2001 6 HET GOL A2002 6 HET GOL A2003 6 HET GOL A2004 6 HETNAM CA CALCIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 CA 2(CA 2+) FORMUL 4 GOL 4(C3 H8 O3) FORMUL 8 HOH *339(H2 O) HELIX 1 1 THR A 58 GLY A 63 1 6 HELIX 2 2 SER A 157 LEU A 168 1 12 HELIX 3 3 GLU A 215 MET A 217 5 3 SHEET 1 A 9 GLU A 6 HIS A 10 0 SHEET 2 A 9 TYR A 13 LYS A 19 -1 O TYR A 13 N HIS A 10 SHEET 3 A 9 PHE A 35 LYS A 52 -1 O LEU A 46 N TRP A 18 SHEET 4 A 9 ASN A 174 ILE A 200 -1 O VAL A 182 N PHE A 47 SHEET 5 A 9 MET A 65 VAL A 88 -1 N ASN A 76 O SER A 188 SHEET 6 A 9 VAL A 92 TRP A 100 -1 O ILE A 96 N VAL A 83 SHEET 7 A 9 ALA A 138 ARG A 147 1 O SER A 145 N VAL A 97 SHEET 8 A 9 GLY A 119 GLN A 131 -1 N ARG A 128 O PHE A 140 SHEET 9 A 9 GLY A 112 VAL A 116 -1 N ILE A 114 O TYR A 121 SHEET 1 B 5 SER A 24 LEU A 29 0 SHEET 2 B 5 PHE A 35 LYS A 52 -1 O SER A 36 N THR A 28 SHEET 3 B 5 ASN A 174 ILE A 200 -1 O VAL A 182 N PHE A 47 SHEET 4 B 5 MET A 65 VAL A 88 -1 N ASN A 76 O SER A 188 SHEET 5 B 5 SER A 153 ILE A 156 -1 O ILE A 156 N ILE A 67 SHEET 1 C 4 THR A 210 GLU A 213 0 SHEET 2 C 4 ALA A 319 ILE A 326 -1 O LEU A 324 N VAL A 212 SHEET 3 C 4 GLY A 233 LEU A 236 -1 N VAL A 234 O LEU A 321 SHEET 4 C 4 SER A 225 ILE A 227 -1 N SER A 225 O ALA A 235 SHEET 1 D 4 THR A 210 GLU A 213 0 SHEET 2 D 4 ALA A 319 ILE A 326 -1 O LEU A 324 N VAL A 212 SHEET 3 D 4 ASN A 253 SER A 262 -1 N ARG A 259 O ASP A 322 SHEET 4 D 4 ALA A 290 ASN A 298 -1 O TYR A 292 N LEU A 258 SHEET 1 E 5 THR A 218 GLY A 220 0 SHEET 2 E 5 ASN A 242 PHE A 249 -1 O SER A 244 N THR A 218 SHEET 3 E 5 GLY A 302 ILE A 309 -1 O VAL A 306 N PHE A 245 SHEET 4 E 5 ALA A 268 ILE A 274 -1 N ASP A 271 O ILE A 309 SHEET 5 E 5 GLN A 277 PHE A 284 -1 O PHE A 284 N ALA A 268 LINK OE2 GLU A 213 CA CA A1001 1555 1555 2.21 LINK OE1 GLU A 215 CA CA A1001 1555 1555 2.44 LINK OE2 GLU A 215 CA CA A1001 1555 1555 2.52 LINK O ASN A 232 CA CA A1001 1555 1555 2.11 LINK O TYR A 237 CA CA A1002 1555 1555 2.25 LINK OD1 ASP A 313 CA CA A1002 1555 1555 2.37 LINK O TRP A 317 CA CA A1002 1555 1555 2.45 LINK OD2 ASP A 318 CA CA A1002 1555 1555 2.39 LINK O ASP A 322 CA CA A1001 1555 1555 2.67 LINK OD1 ASP A 322 CA CA A1001 1555 1555 2.37 LINK CA CA A1001 O HOH A2199 1555 1555 2.44 LINK CA CA A1002 O HOH A2180 1555 1555 2.76 LINK CA CA A1002 O HOH A2267 1555 1555 2.67 LINK CA CA A1002 O HOH A2279 1555 1555 2.54 CISPEP 1 ASP A 89 PRO A 90 0 5.17 CISPEP 2 PRO A 105 PRO A 106 0 -2.00 CISPEP 3 SER A 229 PRO A 230 0 4.97 SITE 1 AC1 5 GLU A 213 GLU A 215 ASN A 232 ASP A 322 SITE 2 AC1 5 HOH A2199 SITE 1 AC2 7 TYR A 237 ASP A 313 TRP A 317 ASP A 318 SITE 2 AC2 7 HOH A2180 HOH A2267 HOH A2279 SITE 1 AC3 5 GLY A 12 TYR A 13 GLY A 50 LEU A 198 SITE 2 AC3 5 HOH A2101 SITE 1 AC4 3 ASN A 68 TYR A 69 SER A 195 SITE 1 AC5 3 HOH A2299 HOH A2323 HOH A2326 SITE 1 AC6 4 THR A 293 ASN A 295 HOH A2238 HOH A2280 CRYST1 116.579 116.579 45.909 90.00 90.00 90.00 P 43 4 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 0.008578 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008578 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021782 0.00000