HEADER HYDROLASE 30-AUG-12 3VWN TITLE CRYSTAL STRUCTURE OF 6-AMINOHEXANOATE-DIMER HYDROLASE TITLE 2 G181D/R187G/H266N/D370Y MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: 6-AMINOHEXANOATE-DIMER HYDROLASE; COMPND 3 CHAIN: X; COMPND 4 SYNONYM: NYLON OLIGOMERS-DEGRADING ENZYME EII, NYLON OLIGOMERS- COMPND 5 DEGRADING ENZYME EII'; COMPND 6 EC: 3.5.1.46; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 OTHER_DETAILS: THE FUSION PROTEIN OF RESIDUES 1-21 FROM NYLON COMPND 10 OLIGOMERS-DEGRADING ENZYME EII (UNP P07061) AND RESIDUES 22-392 FROM COMPND 11 NYLON OLIGOMERS-DEGRADING ENZYME EII' (UNP Q59710) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: FLAVOBACTERIUM; SOURCE 3 ORGANISM_TAXID: 261, 408956; SOURCE 4 STRAIN: K172, KI723T1; SOURCE 5 GENE: NYLB, NYLB'; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: KP3998; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PKP1500 KEYWDS HYDROLASE, NYLON DEGRADATION EXPDTA X-RAY DIFFRACTION AUTHOR Y.KAWASHIMA,N.SHIBATA,S.NEGORO,Y.HIGUCHI REVDAT 2 20-MAR-24 3VWN 1 REMARK SEQADV LINK REVDAT 1 16-OCT-13 3VWN 0 JRNL AUTH S.NEGORO,Y.KAWASHIMA,N.SHIBATA,Y.SHIGETA,T.KOBAYASHI, JRNL AUTH 2 H.NISHIGUCHI,T.MATSUI,T.BABA,Y.LEE,K.KAMIYA,D.KATO,M.TAKEO, JRNL AUTH 3 Y.HIGUCHI JRNL TITL STRUCTURAL, KINETIC AND THEORETICAL ANALYSES OF HYDROLASE JRNL TITL 2 MUTANTS ALTERING IN THE DIRECTIONALITY AND EQUILIBRIUM POINT JRNL TITL 3 OF REVERSIBLE AMIDE-SYNTHETIC/HYDROLYTIC REACTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 189172 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) : 0.130 REMARK 3 R VALUE (WORKING SET) : 0.130 REMARK 3 FREE R VALUE : 0.146 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 9503 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) : 1.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.23 REMARK 3 REFLECTION IN BIN (WORKING SET) : 13064 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.59 REMARK 3 BIN R VALUE (WORKING SET) : 0.1880 REMARK 3 BIN FREE R VALUE SET COUNT : 666 REMARK 3 BIN FREE R VALUE : 0.2020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2958 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 84 REMARK 3 SOLVENT ATOMS : 429 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.07000 REMARK 3 B22 (A**2) : 0.07000 REMARK 3 B33 (A**2) : -0.11000 REMARK 3 B12 (A**2) : 0.04000 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): 0.024 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.025 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.015 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.703 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.981 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.978 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3211 ; 0.028 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4400 ; 2.361 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 413 ; 6.061 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 155 ;32.901 ;23.097 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 471 ;11.297 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;19.257 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 472 ; 0.391 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2514 ; 0.017 ; 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): 1949 ; 3.361 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3147 ; 4.632 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1262 ; 6.034 ; 4.500 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1237 ; 8.619 ; 6.000 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): 2863 ; 3.432 ; 3.000 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 U VALUES: REFINED INDIVIDUALLY REMARK 4 REMARK 4 3VWN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1000095592. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-OCT-09 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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A 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 : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 189410 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.10 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.53600 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.2M AMMONIUM SULFATE, 0.2M LITHIUM REMARK 280 SULFATE, 0.1M MES, PH 6.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 283K 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 75.33067 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 37.66533 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 37.66533 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 75.33067 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -127.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: X 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 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 37.66533 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH X 533 LIES ON A SPECIAL POSITION. REMARK 375 HOH X 923 LIES ON A SPECIAL POSITION. REMARK 375 HOH X 924 LIES ON A SPECIAL POSITION. 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 X 1 REMARK 465 ASN X 2 REMARK 465 ALA X 3 REMARK 465 ARG X 4 REMARK 465 VAL X 53 REMARK 465 ASN X 54 REMARK 465 ALA X 55 REMARK 465 PRO X 56 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 X 5 CB SER X 5 OG 0.087 REMARK 500 GLN X 8 CG GLN X 8 CD 0.154 REMARK 500 GLU X 28 CD GLU X 28 OE2 0.083 REMARK 500 GLU X 96 CB GLU X 96 CG -0.162 REMARK 500 TYR X 97 CZ TYR X 97 CE2 0.079 REMARK 500 ASP X 127 CB ASP X 127 CG 0.129 REMARK 500 TYR X 166 CG TYR X 166 CD1 0.099 REMARK 500 TYR X 166 CD1 TYR X 166 CE1 0.146 REMARK 500 TYR X 166 CZ TYR X 166 OH 0.116 REMARK 500 GLU X 199 CG GLU X 199 CD 0.096 REMARK 500 VAL X 236 CB VAL X 236 CG2 -0.217 REMARK 500 GLU X 237 CD GLU X 237 OE1 -0.069 REMARK 500 GLU X 297 CG GLU X 297 CD -0.124 REMARK 500 GLU X 297 CD GLU X 297 OE2 0.077 REMARK 500 ARG X 301 CZ ARG X 301 NH1 0.081 REMARK 500 CYS X 332 CB CYS X 332 SG 0.103 REMARK 500 VAL X 340 CB VAL X 340 CG2 -0.134 REMARK 500 ARG X 376 CG ARG X 376 CD 0.180 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 X 51 NE - CZ - NH1 ANGL. DEV. = -3.7 DEGREES REMARK 500 LEU X 63 CB - CA - C ANGL. DEV. = 12.6 DEGREES REMARK 500 ASP X 105 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG X 107 NE - CZ - NH1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG X 107 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG X 107 NE - CZ - NH2 ANGL. DEV. = -9.9 DEGREES REMARK 500 LEU X 117 CB - CG - CD2 ANGL. DEV. = 10.9 DEGREES REMARK 500 ARG X 130 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG X 182 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG X 189 NE - CZ - NH1 ANGL. DEV. = -6.4 DEGREES REMARK 500 VAL X 236 CG1 - CB - CG2 ANGL. DEV. = -10.6 DEGREES REMARK 500 ASP X 252 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ARG X 281 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ASP X 298 CB - CG - OD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 ARG X 302 NH1 - CZ - NH2 ANGL. DEV. = 6.7 DEGREES REMARK 500 ARG X 302 NE - CZ - NH2 ANGL. DEV. = -7.5 DEGREES REMARK 500 ARG X 302 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG X 328 NE - CZ - NH2 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG X 376 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 ARG X 376 NE - CZ - NH2 ANGL. DEV. = -4.1 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 HIS X 38 37.22 -143.65 REMARK 500 MET X 111 -140.19 50.09 REMARK 500 LEU X 243 -70.69 -135.46 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 NA X 412 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY X 123 O REMARK 620 2 ASP X 127 OD2 85.2 REMARK 620 3 SER X 296 OG 168.0 91.1 REMARK 620 4 HOH X 772 O 115.3 118.9 57.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA X 413 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP X 181 OD2 REMARK 620 2 HOH X 810 O 70.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA X 414 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP X 285 O REMARK 620 2 GLU X 297 OE2 124.3 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL X 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL X 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL X 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL X 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL X 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES X 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES X 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES X 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 X 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 X 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 X 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA X 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA X 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA X 414 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WYB RELATED DB: PDB REMARK 900 RELATED ID: 3VWL RELATED DB: PDB REMARK 900 RELATED ID: 3VWM RELATED DB: PDB REMARK 900 RELATED ID: 3VWP RELATED DB: PDB REMARK 900 RELATED ID: 3VWQ RELATED DB: PDB REMARK 900 RELATED ID: 3VWR RELATED DB: PDB DBREF 3VWN X 1 21 UNP P07061 NYLB_FLASK 1 21 DBREF 3VWN X 22 392 UNP Q59710 Q59710_9FLAO 22 392 SEQADV 3VWN ASP X 181 UNP P07062 GLY 181 ENGINEERED MUTATION SEQADV 3VWN GLY X 187 UNP P07062 ARG 187 ENGINEERED MUTATION SEQADV 3VWN ASN X 266 UNP P07062 HIS 266 ENGINEERED MUTATION SEQADV 3VWN TYR X 370 UNP P07062 ASP 370 ENGINEERED MUTATION SEQRES 1 X 392 MET ASN ALA ARG SER THR GLY GLN HIS PRO ALA ARG TYR SEQRES 2 X 392 PRO GLY ALA ALA ALA GLY GLU PRO THR LEU ASP SER TRP SEQRES 3 X 392 GLN GLU PRO PRO HIS ASN ARG TRP ALA PHE ALA HIS LEU SEQRES 4 X 392 GLY GLU MET VAL PRO SER ALA ALA VAL SER ARG ARG PRO SEQRES 5 X 392 VAL ASN ALA PRO GLY HIS ALA LEU ALA ARG LEU GLY ALA SEQRES 6 X 392 ILE ALA ALA GLN LEU PRO ASP LEU GLU GLN ARG LEU GLU SEQRES 7 X 392 GLN THR TYR THR ASP ALA PHE LEU VAL LEU ARG GLY THR SEQRES 8 X 392 GLU VAL VAL ALA GLU TYR TYR ARG ALA GLY PHE ALA PRO SEQRES 9 X 392 ASP ASP ARG HIS LEU LEU MET SER VAL SER LYS SER LEU SEQRES 10 X 392 CYS GLY THR VAL VAL GLY ALA LEU VAL ASP GLU GLY ARG SEQRES 11 X 392 ILE ASP PRO ALA GLN PRO VAL THR GLU TYR VAL PRO GLU SEQRES 12 X 392 LEU ALA GLY SER VAL TYR ASP GLY PRO SER VAL LEU GLN SEQRES 13 X 392 VAL LEU ASP MET GLN ILE SER ILE ASP TYR ASN GLU ASP SEQRES 14 X 392 TYR VAL ASP PRO ALA SER GLU VAL GLN THR HIS ASP ARG SEQRES 15 X 392 SER ALA GLY TRP GLY THR ARG ARG HIS GLY ASP PRO ALA SEQRES 16 X 392 ASP THR TYR GLU PHE LEU THR THR LEU ARG GLY ASP GLY SEQRES 17 X 392 SER THR GLY GLU PHE GLN TYR CYS SER ALA ASN THR ASP SEQRES 18 X 392 VAL LEU ALA TRP ILE VAL GLU ARG VAL THR GLY LEU ARG SEQRES 19 X 392 TYR VAL GLU ALA LEU SER THR TYR LEU TRP ALA LYS LEU SEQRES 20 X 392 ASP ALA ASP ARG ASP ALA THR ILE THR VAL ASP THR THR SEQRES 21 X 392 GLY PHE GLY PHE ALA ASN GLY GLY VAL SER CYS THR ALA SEQRES 22 X 392 ARG ASP LEU ALA ARG VAL GLY ARG MET MET LEU ASP GLY SEQRES 23 X 392 GLY VAL ALA PRO GLY GLY ARG VAL VAL SER GLU ASP TRP SEQRES 24 X 392 VAL ARG ARG VAL LEU ALA GLY GLY SER HIS GLU ALA MET SEQRES 25 X 392 THR ASP LYS GLY PHE THR ASN THR PHE PRO ASP GLY SER SEQRES 26 X 392 TYR THR ARG GLN TRP TRP CYS THR GLY ASN GLU ARG GLY SEQRES 27 X 392 ASN VAL SER GLY ILE GLY ILE HIS GLY GLN ASN LEU TRP SEQRES 28 X 392 LEU ASP PRO LEU THR ASP SER VAL ILE VAL LYS LEU SER SEQRES 29 X 392 SER TRP PRO ASP PRO TYR THR GLU HIS TRP HIS ARG LEU SEQRES 30 X 392 GLN ASN GLY ILE LEU LEU ASP VAL SER ARG ALA LEU ASP SEQRES 31 X 392 ALA VAL HET GOL X 401 6 HET GOL X 402 6 HET GOL X 403 6 HET GOL X 404 6 HET GOL X 405 6 HET MES X 406 12 HET MES X 407 12 HET MES X 408 12 HET SO4 X 409 5 HET SO4 X 410 5 HET SO4 X 411 5 HET NA X 412 1 HET NA X 413 1 HET NA X 414 1 HETNAM GOL GLYCEROL HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM SO4 SULFATE ION HETNAM NA SODIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 5(C3 H8 O3) FORMUL 7 MES 3(C6 H13 N O4 S) FORMUL 10 SO4 3(O4 S 2-) FORMUL 13 NA 3(NA 1+) FORMUL 16 HOH *429(H2 O) HELIX 1 1 HIS X 31 PHE X 36 1 6 HELIX 2 2 ALA X 37 MET X 42 5 6 HELIX 3 3 ALA X 65 LEU X 70 1 6 HELIX 4 4 ASP X 72 THR X 80 1 9 HELIX 5 5 SER X 112 GLU X 128 1 17 HELIX 6 6 PRO X 136 VAL X 141 1 6 HELIX 7 7 PRO X 142 ALA X 145 5 4 HELIX 8 8 SER X 153 ASP X 159 1 7 HELIX 9 9 SER X 175 ALA X 184 1 10 HELIX 10 10 ASP X 196 THR X 203 1 8 HELIX 11 11 CYS X 216 GLY X 232 1 17 HELIX 12 12 ARG X 234 LEU X 243 1 10 HELIX 13 13 TRP X 244 LEU X 247 5 4 HELIX 14 14 THR X 272 ASP X 285 1 14 HELIX 15 15 SER X 296 GLY X 306 1 11 HELIX 16 16 SER X 308 MET X 312 5 5 HELIX 17 17 ASP X 314 ASN X 319 1 6 HELIX 18 18 PRO X 354 THR X 356 5 3 HELIX 19 19 THR X 371 LEU X 389 1 19 SHEET 1 A 8 LEU X 60 ARG X 62 0 SHEET 2 A 8 GLU X 92 TYR X 98 -1 O GLU X 96 N ARG X 62 SHEET 3 A 8 THR X 82 ARG X 89 -1 N ARG X 89 O GLU X 92 SHEET 4 A 8 SER X 358 SER X 364 -1 O LEU X 363 N ALA X 84 SHEET 5 A 8 GLN X 348 ASP X 353 -1 N ASP X 353 O SER X 358 SHEET 6 A 8 VAL X 340 GLY X 344 -1 N VAL X 340 O LEU X 352 SHEET 7 A 8 TRP X 330 CYS X 332 -1 N TRP X 331 O SER X 341 SHEET 8 A 8 SER X 325 THR X 327 -1 N SER X 325 O CYS X 332 SHEET 1 B 3 HIS X 108 LEU X 109 0 SHEET 2 B 3 VAL X 269 CYS X 271 -1 O CYS X 271 N HIS X 108 SHEET 3 B 3 THR X 254 ILE X 255 -1 N THR X 254 O SER X 270 SHEET 1 C 2 VAL X 288 ALA X 289 0 SHEET 2 C 2 GLY X 292 ARG X 293 -1 O GLY X 292 N ALA X 289 LINK O GLY X 123 NA NA X 412 1555 1555 2.73 LINK OD2BASP X 127 NA NA X 412 1555 1555 2.09 LINK OD2 ASP X 181 NA NA X 413 1555 1555 2.22 LINK O ASP X 285 NA NA X 414 1555 1555 2.78 LINK OG SER X 296 NA NA X 412 1555 1555 3.13 LINK OE2 GLU X 297 NA NA X 414 1555 1555 2.26 LINK NA NA X 412 O HOH X 772 1555 1555 2.87 LINK NA NA X 413 O HOH X 810 1555 1555 2.90 CISPEP 1 GLU X 20 PRO X 21 0 -6.52 CISPEP 2 PRO X 29 PRO X 30 0 -3.79 SITE 1 AC1 10 ASP X 159 GLN X 161 ARG X 302 GLY X 306 SITE 2 AC1 10 GLY X 307 SER X 308 THR X 327 ARG X 328 SITE 3 AC1 10 HOH X 581 HOH X 716 SITE 1 AC2 9 GLN X 79 TYR X 81 GLY X 211 GLU X 212 SITE 2 AC2 9 GLU X 310 ALA X 311 TRP X 374 HOH X 645 SITE 3 AC2 9 HOH X 899 SITE 1 AC3 7 ALA X 37 ASP X 106 ARG X 107 ARG X 251 SITE 2 AC3 7 HOH X 648 HOH X 855 HOH X 860 SITE 1 AC4 9 SER X 112 ASP X 181 TRP X 186 PHE X 264 SITE 2 AC4 9 ASN X 266 GLY X 267 GOL X 405 HOH X 745 SITE 3 AC4 9 HOH X 798 SITE 1 AC5 7 TYR X 166 GLU X 168 CYS X 216 SER X 217 SITE 2 AC5 7 ILE X 345 GOL X 404 HOH X 747 SITE 1 AC6 14 SER X 112 TYR X 215 GLY X 316 PHE X 317 SITE 2 AC6 14 TRP X 331 ILE X 343 GLY X 344 ILE X 345 SITE 3 AC6 14 TYR X 370 HOH X 749 HOH X 750 HOH X 752 SITE 4 AC6 14 HOH X 757 HOH X 794 SITE 1 AC7 10 TYR X 13 PRO X 30 TRP X 34 ARG X 99 SITE 2 AC7 10 GLY X 101 HIS X 309 GLU X 310 HOH X 690 SITE 3 AC7 10 HOH X 691 HOH X 719 SITE 1 AC8 6 LEU X 70 PRO X 71 ASP X 72 ARG X 76 SITE 2 AC8 6 ASP X 384 HOH X 773 SITE 1 AC9 2 ARG X 205 HOH X 822 SITE 1 BC1 5 ARG X 107 ARG X 251 ASP X 252 HOH X 619 SITE 2 BC1 5 HOH X 894 SITE 1 BC2 2 ARG X 293 HOH X 781 SITE 1 BC3 5 GLY X 123 ASP X 127 SER X 296 TRP X 299 SITE 2 BC3 5 HOH X 772 SITE 1 BC4 4 GLN X 27 GLN X 178 ASP X 181 HOH X 810 SITE 1 BC5 3 ASP X 285 VAL X 288 GLU X 297 CRYST1 96.640 96.640 112.996 90.00 90.00 120.00 P 32 2 1 6 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 0.010348 0.005974 0.000000 0.00000 SCALE2 0.000000 0.011948 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008850 0.00000