HEADER HYDROLASE 07-NOV-13 3WL3 TITLE N,N'-DIACETYLCHITOBIOSE DEACETYLASE FROM PYROCOCCUS HORIKOSHII COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE UNCHARACTERIZED PROTEIN PH0499; COMPND 3 CHAIN: A, B, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 70601; SOURCE 4 STRAIN: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3; SOURCE 5 GENE: PH0499; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ZN-DEPENDENT DEACETYLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.NAKAMURA,M.NIIYAMA,W.HASHIMOTO,K.UEGAKI REVDAT 4 03-APR-24 3WL3 1 REMARK REVDAT 3 20-MAR-24 3WL3 1 REMARK LINK REVDAT 2 20-AUG-14 3WL3 1 JRNL REVDAT 1 07-MAY-14 3WL3 0 JRNL AUTH S.MINE,M.NIIYAMA,W.HASHIMOTO,T.IKEGAMI,D.KOMA,T.OHMOTO, JRNL AUTH 2 Y.FUKUDA,T.INOUE,Y.ABE,T.UEDA,J.MORITA,K.UEGAKI,T.NAKAMURA JRNL TITL EXPRESSION FROM ENGINEERED ESCHERICHIA COLI CHROMOSOME AND JRNL TITL 2 CRYSTALLOGRAPHIC STUDY OF ARCHAEAL N,N'-DIACETYLCHITOBIOSE JRNL TITL 3 DEACETYLASE JRNL REF FEBS J. V. 281 2584 2014 JRNL REFN ISSN 1742-464X JRNL PMID 24702737 JRNL DOI 10.1111/FEBS.12805 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.24 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 50436 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) : 0.223 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2698 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3741 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.07 REMARK 3 BIN R VALUE (WORKING SET) : 0.3950 REMARK 3 BIN FREE R VALUE SET COUNT : 182 REMARK 3 BIN FREE R VALUE : 0.4170 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6550 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 51 REMARK 3 SOLVENT ATOMS : 129 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.01000 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): 0.243 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.206 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.170 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.388 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6765 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9161 ; 1.878 ; 1.976 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 796 ; 6.824 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 331 ;34.615 ;23.686 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1170 ;16.661 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 45 ;18.697 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 967 ; 0.131 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5168 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL 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): 3992 ; 0.959 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6488 ; 1.604 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2773 ; 2.732 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2673 ; 3.924 ; 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3WL3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-NOV-13. REMARK 100 THE DEPOSITION ID IS D_1000096470. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53336 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 5.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 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) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 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: N,N'-DIACETYLCHITOBIOSE DEACETYLASE FROM REMARK 200 PYROCOCCUS FURIOSUS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.4 M AMMONIUM PHOSPHATE, PH 8.1, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 152.74267 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 76.37133 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 76.37133 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 152.74267 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 34110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 51650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -456.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 VAL A 2 REMARK 465 VAL A 3 REMARK 465 ASN A 4 REMARK 465 MET A 5 REMARK 465 MET B 1 REMARK 465 VAL B 2 REMARK 465 VAL B 3 REMARK 465 ASN B 4 REMARK 465 MET B 5 REMARK 465 PHE B 6 REMARK 465 GLU B 7 REMARK 465 MET C 1 REMARK 465 VAL C 2 REMARK 465 VAL C 3 REMARK 465 ASN C 4 REMARK 465 MET C 5 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 OD1 ASP B 205 OG1 THR B 207 2.03 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 VAL A 69 CB VAL A 69 CG2 0.136 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 LEU A 147 CB - CG - CD2 ANGL. DEV. = 10.2 DEGREES REMARK 500 PRO B 43 C - N - CA ANGL. DEV. = -9.6 DEGREES REMARK 500 ARG B 157 NE - CZ - NH1 ANGL. DEV. = 3.4 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 8 71.33 -119.91 REMARK 500 ASP A 46 -24.73 97.28 REMARK 500 MET A 52 33.61 -148.01 REMARK 500 ASP A 115 126.68 -39.05 REMARK 500 THR A 116 -3.42 78.42 REMARK 500 GLN A 136 65.57 37.31 REMARK 500 ASP B 34 78.34 -111.94 REMARK 500 ASP B 46 -16.66 110.27 REMARK 500 MET B 52 28.70 -148.28 REMARK 500 ASP B 80 99.72 -69.96 REMARK 500 LYS B 106 -80.23 -57.68 REMARK 500 PRO B 225 -169.02 -57.83 REMARK 500 GLU C 7 -16.06 34.26 REMARK 500 ASN C 30 74.43 -151.25 REMARK 500 ALA C 35 116.04 -37.81 REMARK 500 ASP C 46 -11.29 120.04 REMARK 500 LYS C 107 141.91 -178.14 REMARK 500 ASP C 115 124.36 -37.81 REMARK 500 THR C 116 2.31 87.07 REMARK 500 GLU C 117 29.06 -140.67 REMARK 500 ILE C 265 17.82 52.68 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 LYS C 106 LYS C 107 -137.54 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 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 44 ND1 REMARK 620 2 ASP A 47 OD2 105.9 REMARK 620 3 HIS A 155 NE2 112.1 94.2 REMARK 620 4 PO4 A 302 O1 118.9 122.9 99.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 44 ND1 REMARK 620 2 ASP B 47 OD2 100.7 REMARK 620 3 HIS B 155 NE2 102.9 94.2 REMARK 620 4 PO4 B 302 O2 116.0 136.0 100.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 44 ND1 REMARK 620 2 ASP C 47 OD2 104.5 REMARK 620 3 HIS C 155 NE2 110.4 101.6 REMARK 620 4 PO4 C 302 O3 113.8 126.7 98.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 C 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WL4 RELATED DB: PDB REMARK 900 RELATED ID: 3WE7 RELATED DB: PDB DBREF 3WL3 A 1 272 UNP O58235 O58235_PYRHO 1 272 DBREF 3WL3 B 1 272 UNP O58235 O58235_PYRHO 1 272 DBREF 3WL3 C 1 272 UNP O58235 O58235_PYRHO 1 272 SEQRES 1 A 272 MET VAL VAL ASN MET PHE GLU ASP ILE ASP THR PHE GLU SEQRES 2 A 272 GLU ALA PHE ASN LYS LEU LEU ARG GLU VAL LEU GLU PHE SEQRES 3 A 272 ASP LEU GLN ASN PRO PHE LYS ASP ALA LYS LYS VAL LEU SEQRES 4 A 272 CYS ILE GLU PRO HIS PRO ASP ASP CYS VAL ILE GLY MET SEQRES 5 A 272 GLY GLY THR ILE LYS LYS LEU SER ASP MET GLY VAL GLU SEQRES 6 A 272 VAL ILE TYR VAL CYS MET THR ASP GLY TYR MET GLY THR SEQRES 7 A 272 THR ASP GLU SER LEU SER GLY HIS GLU LEU ALA ALA ILE SEQRES 8 A 272 ARG ARG LYS GLU GLU GLU GLU SER ALA ARG LEU LEU GLY SEQRES 9 A 272 VAL LYS LYS ILE TYR TRP LEU ASN TYR ARG ASP THR GLU SEQRES 10 A 272 LEU PRO TYR SER ARG GLU VAL ARG LYS ASP LEU THR LYS SEQRES 11 A 272 ILE LEU ARG LYS GLU GLN PRO ASP GLY VAL PHE ALA PRO SEQRES 12 A 272 ASP PRO TRP LEU PRO TYR GLU SER HIS PRO ASP HIS ARG SEQRES 13 A 272 ARG THR GLY PHE LEU ALA ILE GLU SER VAL ALA PHE SER SEQRES 14 A 272 GLN LEU PRO ASN PHE SER ASN THR ASP LEU ASP ILE GLY SEQRES 15 A 272 LEU ASN PRO TYR ASN SER GLY SER PHE ILE ALA LEU TYR SEQRES 16 A 272 TYR THR HIS LYS PRO ASN TYR ILE VAL ASP ILE THR ASP SEQRES 17 A 272 LEU MET GLU LEU LYS LEU LYS ALA ILE ARG VAL HIS ARG SEQRES 18 A 272 SER GLN PHE PRO ASP ASP ILE TRP GLU LYS TRP GLU PRO SEQRES 19 A 272 PHE LEU ARG THR ILE ALA MET PHE TYR GLY GLU LYS ILE SEQRES 20 A 272 GLY VAL ARG TYR GLY GLU GLY PHE ARG ILE MET PRO GLY SEQRES 21 A 272 LEU PHE TYR HIS ILE THR PRO PHE THR ASP LEU ILE SEQRES 1 B 272 MET VAL VAL ASN MET PHE GLU ASP ILE ASP THR PHE GLU SEQRES 2 B 272 GLU ALA PHE ASN LYS LEU LEU ARG GLU VAL LEU GLU PHE SEQRES 3 B 272 ASP LEU GLN ASN PRO PHE LYS ASP ALA LYS LYS VAL LEU SEQRES 4 B 272 CYS ILE GLU PRO HIS PRO ASP ASP CYS VAL ILE GLY MET SEQRES 5 B 272 GLY GLY THR ILE LYS LYS LEU SER ASP MET GLY VAL GLU SEQRES 6 B 272 VAL ILE TYR VAL CYS MET THR ASP GLY TYR MET GLY THR SEQRES 7 B 272 THR ASP GLU SER LEU SER GLY HIS GLU LEU ALA ALA ILE SEQRES 8 B 272 ARG ARG LYS GLU GLU GLU GLU SER ALA ARG LEU LEU GLY SEQRES 9 B 272 VAL LYS LYS ILE TYR TRP LEU ASN TYR ARG ASP THR GLU SEQRES 10 B 272 LEU PRO TYR SER ARG GLU VAL ARG LYS ASP LEU THR LYS SEQRES 11 B 272 ILE LEU ARG LYS GLU GLN PRO ASP GLY VAL PHE ALA PRO SEQRES 12 B 272 ASP PRO TRP LEU PRO TYR GLU SER HIS PRO ASP HIS ARG SEQRES 13 B 272 ARG THR GLY PHE LEU ALA ILE GLU SER VAL ALA PHE SER SEQRES 14 B 272 GLN LEU PRO ASN PHE SER ASN THR ASP LEU ASP ILE GLY SEQRES 15 B 272 LEU ASN PRO TYR ASN SER GLY SER PHE ILE ALA LEU TYR SEQRES 16 B 272 TYR THR HIS LYS PRO ASN TYR ILE VAL ASP ILE THR ASP SEQRES 17 B 272 LEU MET GLU LEU LYS LEU LYS ALA ILE ARG VAL HIS ARG SEQRES 18 B 272 SER GLN PHE PRO ASP ASP ILE TRP GLU LYS TRP GLU PRO SEQRES 19 B 272 PHE LEU ARG THR ILE ALA MET PHE TYR GLY GLU LYS ILE SEQRES 20 B 272 GLY VAL ARG TYR GLY GLU GLY PHE ARG ILE MET PRO GLY SEQRES 21 B 272 LEU PHE TYR HIS ILE THR PRO PHE THR ASP LEU ILE SEQRES 1 C 272 MET VAL VAL ASN MET PHE GLU ASP ILE ASP THR PHE GLU SEQRES 2 C 272 GLU ALA PHE ASN LYS LEU LEU ARG GLU VAL LEU GLU PHE SEQRES 3 C 272 ASP LEU GLN ASN PRO PHE LYS ASP ALA LYS LYS VAL LEU SEQRES 4 C 272 CYS ILE GLU PRO HIS PRO ASP ASP CYS VAL ILE GLY MET SEQRES 5 C 272 GLY GLY THR ILE LYS LYS LEU SER ASP MET GLY VAL GLU SEQRES 6 C 272 VAL ILE TYR VAL CYS MET THR ASP GLY TYR MET GLY THR SEQRES 7 C 272 THR ASP GLU SER LEU SER GLY HIS GLU LEU ALA ALA ILE SEQRES 8 C 272 ARG ARG LYS GLU GLU GLU GLU SER ALA ARG LEU LEU GLY SEQRES 9 C 272 VAL LYS LYS ILE TYR TRP LEU ASN TYR ARG ASP THR GLU SEQRES 10 C 272 LEU PRO TYR SER ARG GLU VAL ARG LYS ASP LEU THR LYS SEQRES 11 C 272 ILE LEU ARG LYS GLU GLN PRO ASP GLY VAL PHE ALA PRO SEQRES 12 C 272 ASP PRO TRP LEU PRO TYR GLU SER HIS PRO ASP HIS ARG SEQRES 13 C 272 ARG THR GLY PHE LEU ALA ILE GLU SER VAL ALA PHE SER SEQRES 14 C 272 GLN LEU PRO ASN PHE SER ASN THR ASP LEU ASP ILE GLY SEQRES 15 C 272 LEU ASN PRO TYR ASN SER GLY SER PHE ILE ALA LEU TYR SEQRES 16 C 272 TYR THR HIS LYS PRO ASN TYR ILE VAL ASP ILE THR ASP SEQRES 17 C 272 LEU MET GLU LEU LYS LEU LYS ALA ILE ARG VAL HIS ARG SEQRES 18 C 272 SER GLN PHE PRO ASP ASP ILE TRP GLU LYS TRP GLU PRO SEQRES 19 C 272 PHE LEU ARG THR ILE ALA MET PHE TYR GLY GLU LYS ILE SEQRES 20 C 272 GLY VAL ARG TYR GLY GLU GLY PHE ARG ILE MET PRO GLY SEQRES 21 C 272 LEU PHE TYR HIS ILE THR PRO PHE THR ASP LEU ILE HET ZN A 301 1 HET PO4 A 302 5 HET PO4 A 303 5 HET PO4 A 304 5 HET GOL A 305 6 HET ZN B 301 1 HET PO4 B 302 5 HET PO4 B 303 5 HET GOL B 304 6 HET GOL B 305 6 HET ZN C 301 1 HET PO4 C 302 5 HETNAM ZN ZINC ION HETNAM PO4 PHOSPHATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 ZN 3(ZN 2+) FORMUL 5 PO4 6(O4 P 3-) FORMUL 8 GOL 3(C3 H8 O3) FORMUL 16 HOH *129(H2 O) HELIX 1 1 THR A 11 GLU A 22 1 12 HELIX 2 2 ASP A 46 MET A 62 1 17 HELIX 3 3 SER A 84 LEU A 102 1 19 HELIX 4 4 SER A 121 GLN A 136 1 16 HELIX 5 5 HIS A 152 SER A 169 1 18 HELIX 6 6 ASN A 176 ILE A 181 1 6 HELIX 7 7 LEU A 209 VAL A 219 1 11 HELIX 8 8 PRO A 225 LYS A 246 1 22 HELIX 9 9 PRO A 259 HIS A 264 5 6 HELIX 10 10 PHE A 268 ILE A 272 5 5 HELIX 11 11 THR B 11 GLU B 22 1 12 HELIX 12 12 ASP B 46 MET B 62 1 17 HELIX 13 13 SER B 84 LEU B 102 1 19 HELIX 14 14 SER B 121 GLN B 136 1 16 HELIX 15 15 HIS B 152 SER B 169 1 18 HELIX 16 16 ASN B 176 ILE B 181 1 6 HELIX 17 17 LEU B 209 VAL B 219 1 11 HELIX 18 18 PRO B 225 LYS B 246 1 22 HELIX 19 19 PRO B 259 HIS B 264 5 6 HELIX 20 20 PHE B 268 ILE B 272 5 5 HELIX 21 21 THR C 11 GLU C 22 1 12 HELIX 22 22 ASP C 46 MET C 62 1 17 HELIX 23 23 SER C 84 LEU C 103 1 20 HELIX 24 24 SER C 121 GLN C 136 1 16 HELIX 25 25 HIS C 152 SER C 169 1 18 HELIX 26 26 ASN C 176 ILE C 181 1 6 HELIX 27 27 LEU C 209 VAL C 219 1 11 HELIX 28 28 PRO C 225 LYS C 246 1 22 HELIX 29 29 PRO C 259 HIS C 264 5 6 HELIX 30 30 PHE C 268 ILE C 272 5 5 SHEET 1 A 5 LYS A 107 TYR A 113 0 SHEET 2 A 5 GLU A 65 THR A 72 1 N CYS A 70 O TYR A 109 SHEET 3 A 5 LYS A 37 GLU A 42 1 N VAL A 38 O GLU A 65 SHEET 4 A 5 GLY A 139 PRO A 143 1 O PHE A 141 N ILE A 41 SHEET 5 A 5 PHE A 191 TYR A 195 1 O ALA A 193 N VAL A 140 SHEET 1 B 2 TYR A 202 ASP A 205 0 SHEET 2 B 2 GLY A 252 PHE A 255 -1 O PHE A 255 N TYR A 202 SHEET 1 C 7 ILE B 108 TYR B 113 0 SHEET 2 C 7 GLU B 65 THR B 72 1 N TYR B 68 O TYR B 109 SHEET 3 C 7 LYS B 37 GLU B 42 1 N GLU B 42 O MET B 71 SHEET 4 C 7 GLY B 139 PRO B 143 1 O PHE B 141 N ILE B 41 SHEET 5 C 7 PHE B 191 TYR B 195 1 O ALA B 193 N VAL B 140 SHEET 6 C 7 GLY B 252 ILE B 257 -1 O ARG B 256 N LEU B 194 SHEET 7 C 7 TYR B 202 ASP B 205 -1 N TYR B 202 O PHE B 255 SHEET 1 D 5 ILE C 108 TYR C 113 0 SHEET 2 D 5 GLU C 65 THR C 72 1 N TYR C 68 O TYR C 109 SHEET 3 D 5 LYS C 37 GLU C 42 1 N CYS C 40 O ILE C 67 SHEET 4 D 5 GLY C 139 PRO C 143 1 O PHE C 141 N ILE C 41 SHEET 5 D 5 PHE C 191 TYR C 195 1 O ALA C 193 N VAL C 140 SHEET 1 E 2 TYR C 202 ASP C 205 0 SHEET 2 E 2 GLY C 252 PHE C 255 -1 O GLU C 253 N VAL C 204 LINK ND1 HIS A 44 ZN ZN A 301 1555 1555 2.07 LINK OD2 ASP A 47 ZN ZN A 301 1555 1555 2.04 LINK NE2 HIS A 155 ZN ZN A 301 1555 1555 2.06 LINK ZN ZN A 301 O1 PO4 A 302 1555 1555 1.81 LINK ND1 HIS B 44 ZN ZN B 301 1555 1555 2.25 LINK OD2 ASP B 47 ZN ZN B 301 1555 1555 1.95 LINK NE2 HIS B 155 ZN ZN B 301 1555 1555 2.27 LINK ZN ZN B 301 O2 PO4 B 302 1555 1555 1.74 LINK ND1 HIS C 44 ZN ZN C 301 1555 1555 2.03 LINK OD2 ASP C 47 ZN ZN C 301 1555 1555 2.12 LINK NE2 HIS C 155 ZN ZN C 301 1555 1555 2.19 LINK ZN ZN C 301 O3 PO4 C 302 1555 1555 2.07 SITE 1 AC1 4 HIS A 44 ASP A 47 HIS A 155 PO4 A 302 SITE 1 AC2 7 HIS A 44 ASP A 46 ASP A 47 HIS A 155 SITE 2 AC2 7 ZN A 301 GOL A 305 HIS C 264 SITE 1 AC3 4 ARG A 157 HOH A 460 ARG B 157 ARG C 157 SITE 1 AC4 3 LYS A 134 ILE A 181 LEU A 183 SITE 1 AC5 6 HIS A 44 GLY A 77 ARG A 92 ASP A 115 SITE 2 AC5 6 HIS A 152 PO4 A 302 SITE 1 AC6 4 HIS B 44 ASP B 47 HIS B 155 PO4 B 302 SITE 1 AC7 7 HIS A 264 HIS B 44 ASP B 46 ASP B 47 SITE 2 AC7 7 HIS B 155 ZN B 301 GOL B 304 SITE 1 AC8 5 ILE B 181 LEU B 183 LYS C 134 ILE C 181 SITE 2 AC8 5 LEU C 183 SITE 1 AC9 7 HIS B 44 GLY B 77 ARG B 92 ASP B 115 SITE 2 AC9 7 HIS B 152 GLN B 223 PO4 B 302 SITE 1 BC1 7 LEU A 111 TYR A 113 ARG A 122 LYS A 126 SITE 2 BC1 7 MET B 76 ARG B 114 GLU B 117 SITE 1 BC2 4 HIS C 44 ASP C 47 HIS C 155 PO4 C 302 SITE 1 BC3 6 HIS B 264 HIS C 44 ASP C 46 ASP C 47 SITE 2 BC3 6 HIS C 155 ZN C 301 CRYST1 77.561 77.561 229.114 90.00 90.00 120.00 P 32 2 1 18 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 0.012893 0.007444 0.000000 0.00000 SCALE2 0.000000 0.014888 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004365 0.00000