HEADER HYDROLASE/HYDROLASE INHIBITOR 15-JAN-16 5B2F
TITLE N,N'-DIACETYLCHITOBIOSE DEACETYLASE FROM PYROCOCCUS HORIKOSHII
TITLE 2 COMPLEXED WITH ITS INHIBITOR MPG (PHOSPHATE-CONTAINING CONDITION)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PUTATIVE UNCHARACTERIZED PROTEIN PH0499;
COMPND 3 CHAIN: A, B, C;
COMPND 4 SYNONYM: N,N'-DIACETYLCHITOBIOSE DEACETYLASE;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII OT3;
SOURCE 3 ORGANISM_TAXID: 70601;
SOURCE 4 STRAIN: OT3;
SOURCE 5 GENE: PH0499;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS DEACETYLASE CARBOHYDRATE ESTERASE 14 INHIBITOR COMPLEX, HYDROLASE-
KEYWDS 2 HYDROLASE INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR T.NAKAMURA,M.NIIYAMA,K.IDA,K.UEGAKI
REVDAT 5 20-MAR-24 5B2F 1 HETSYN
REVDAT 4 29-JUL-20 5B2F 1 COMPND REMARK HETNAM LINK
REVDAT 4 2 1 SITE
REVDAT 3 26-FEB-20 5B2F 1 JRNL REMARK
REVDAT 2 24-AUG-16 5B2F 1 JRNL
REVDAT 1 10-AUG-16 5B2F 0
JRNL AUTH T.NAKAMURA,Y.YONEZAWA,Y.TSUCHIYA,M.NIIYAMA,K.IDA,M.OSHIMA,
JRNL AUTH 2 J.MORITA,K.UEGAKI
JRNL TITL SUBSTRATE RECOGNITION OF N,N'-DIACETYLCHITOBIOSE DEACETYLASE
JRNL TITL 2 FROM PYROCOCCUS HORIKOSHII
JRNL REF J.STRUCT.BIOL. V. 195 286 2016
JRNL REFN ESSN 1095-8657
JRNL PMID 27456364
JRNL DOI 10.1016/J.JSB.2016.07.015
REMARK 2
REMARK 2 RESOLUTION. 1.90 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) : 1.90
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.46
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 94.6
REMARK 3 NUMBER OF REFLECTIONS : 57838
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) : 0.220
REMARK 3 R VALUE (WORKING SET) : 0.218
REMARK 3 FREE R VALUE : 0.270
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 3087
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) : 1.90
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95
REMARK 3 REFLECTION IN BIN (WORKING SET) : 4136
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.68
REMARK 3 BIN R VALUE (WORKING SET) : 0.4080
REMARK 3 BIN FREE R VALUE SET COUNT : 204
REMARK 3 BIN FREE R VALUE : 0.4670
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 : 186
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.61
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.37000
REMARK 3 B22 (A**2) : 0.37000
REMARK 3 B33 (A**2) : -0.75000
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): 0.043
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.039
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.094
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.457
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.927
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6849 ; 0.023 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9287 ; 1.986 ; 1.977
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 811 ; 7.088 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 334 ;35.258 ;23.743
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1179 ;16.158 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 45 ;18.924 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 991 ; 0.144 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5240 ; 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): 4052 ; 1.124 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6584 ; 1.786 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2797 ; 3.025 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2703 ; 4.324 ; 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 5B2F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-JAN-16.
REMARK 100 THE DEPOSITION ID IS D_1300000401.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 11-OCT-15
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SPRING-8
REMARK 200 BEAMLINE : BL38B1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.90000
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 61101
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900
REMARK 200 RESOLUTION RANGE LOW (A) : 40.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 94.9
REMARK 200 DATA REDUNDANCY : 5.600
REMARK 200 R MERGE (I) : 0.06300
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.9000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93
REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5
REMARK 200 DATA REDUNDANCY IN SHELL : 4.00
REMARK 200 R MERGE FOR SHELL (I) : 0.49000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
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 (%): 41.55
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.4 M AMMONIUM PHOSPHATE, VAPOR
REMARK 280 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 152.82000
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 76.41000
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 76.41000
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 152.82000
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: TRIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 10750 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 30550 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -96.0 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 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 C 454 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 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 ASN A 17 NH1 ARG A 21 2.11
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 NZ LYS B 36 OD2 ASP B 80 4545 2.12
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 0.130
REMARK 500 PHE A 255 CZ PHE A 255 CE2 0.120
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 61 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES
REMARK 500 LEU A 147 CB - CG - CD2 ANGL. DEV. = 12.1 DEGREES
REMARK 500 ASP A 205 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES
REMARK 500 LYS A 215 CD - CE - NZ ANGL. DEV. = -15.8 DEGREES
REMARK 500 ASP B 127 CB - CG - OD1 ANGL. DEV. = 6.4 DEGREES
REMARK 500 ASP B 144 CB - CG - OD2 ANGL. DEV. = 6.7 DEGREES
REMARK 500 LEU B 147 CA - CB - CG ANGL. DEV. = 15.4 DEGREES
REMARK 500 ASP B 205 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES
REMARK 500 ARG C 21 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES
REMARK 500 ASP C 127 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES
REMARK 500 GLY C 189 N - CA - C ANGL. DEV. = -17.4 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 LYS A 33 -67.01 -20.32
REMARK 500 ASP A 46 -15.08 109.85
REMARK 500 MET A 52 33.06 -153.94
REMARK 500 LYS A 106 -105.79 114.62
REMARK 500 ASP A 115 122.51 -37.66
REMARK 500 SER A 190 116.01 45.86
REMARK 500 ILE A 265 25.02 47.86
REMARK 500 ASN B 30 72.12 -153.81
REMARK 500 ASP B 46 -15.40 101.03
REMARK 500 MET B 52 27.25 -154.19
REMARK 500 LYS B 106 -71.06 -54.17
REMARK 500 GLN B 136 61.91 36.45
REMARK 500 TYR B 149 15.93 58.84
REMARK 500 ASN B 187 -93.48 -86.93
REMARK 500 SER B 188 -68.86 141.33
REMARK 500 SER B 188 -69.78 116.49
REMARK 500 SER B 190 134.41 126.93
REMARK 500 PRO B 225 173.02 -59.81
REMARK 500 ASN C 30 73.71 -150.60
REMARK 500 ASP C 46 -7.33 113.78
REMARK 500 MET C 52 25.63 -145.73
REMARK 500 ASP C 115 128.52 -32.12
REMARK 500 THR C 116 -0.72 81.09
REMARK 500 GLN C 136 54.02 39.69
REMARK 500 TYR C 149 10.05 59.44
REMARK 500 ASN C 187 -107.15 -144.39
REMARK 500 SER C 188 -65.37 48.76
REMARK 500 SER C 190 122.41 84.37
REMARK 500 LYS C 199 60.89 -119.13
REMARK 500 ILE C 265 25.76 39.59
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 ASN A 187 SER A 188 -143.76
REMARK 500 LYS C 106 LYS C 107 -145.03
REMARK 500 TYR C 186 ASN C 187 148.77
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 103.6
REMARK 620 3 HIS A 155 NE2 112.5 101.8
REMARK 620 4 MQG A 302 O72 115.3 123.4 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 OD1 152.4
REMARK 620 3 ASP B 47 OD2 101.9 54.2
REMARK 620 4 HIS B 155 NE2 106.7 89.1 91.3
REMARK 620 5 MQG B 302 O72 110.0 88.2 140.3 101.2
REMARK 620 N 1 2 3 4
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 105.1
REMARK 620 3 HIS C 155 NE2 110.8 99.3
REMARK 620 4 MQG C 302 O72 113.0 131.5 94.1
REMARK 620 N 1 2 3
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5B2E RELATED DB: PDB
DBREF 5B2F A 1 272 UNP O58235 O58235_PYRHO 1 272
DBREF 5B2F B 1 272 UNP O58235 O58235_PYRHO 1 272
DBREF 5B2F 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 MQG A 302 16
HET ZN B 301 1
HET MQG B 302 16
HET ZN C 301 1
HET MQG C 302 16
HETNAM ZN ZINC ION
HETNAM MQG 2-DEOXY-2-{[(S)-HYDROXY(METHYL)PHOSPHORYL]AMINO}-BETA-
HETNAM 2 MQG D-GLUCOPYRANOSE
HETSYN MQG ~{N}-[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-
HETSYN 2 MQG (HYDROXYMETHYL)-2,4,5-TRIS(OXIDANYL)OXAN-3-YL]-METHYL-
HETSYN 3 MQG PHOSPHONAMIDIC ACID; 2-DEOXY-2-{[(S)-HYDROXY(METHYL)
HETSYN 4 MQG PHOSPHORYL]AMINO}-BETA-D-GLUCOSE; 2-DEOXY-2-{[(S)-
HETSYN 5 MQG HYDROXY(METHYL)PHOSPHORYL]AMINO}-D-GLUCOSE; 2-DEOXY-2-
HETSYN 6 MQG {[(S)-HYDROXY(METHYL)PHOSPHORYL]AMINO}-GLUCOSE
FORMUL 4 ZN 3(ZN 2+)
FORMUL 5 MQG 3(C7 H16 N O7 P)
FORMUL 10 HOH *186(H2 O)
HELIX 1 AA1 THR A 11 GLU A 22 1 12
HELIX 2 AA2 ASP A 46 MET A 62 1 17
HELIX 3 AA3 SER A 84 LEU A 103 1 20
HELIX 4 AA4 SER A 121 GLN A 136 1 16
HELIX 5 AA5 HIS A 152 SER A 169 1 18
HELIX 6 AA6 ASN A 176 ILE A 181 1 6
HELIX 7 AA7 LEU A 209 VAL A 219 1 11
HELIX 8 AA8 PRO A 225 LYS A 246 1 22
HELIX 9 AA9 PRO A 259 HIS A 264 5 6
HELIX 10 AB1 PHE A 268 ILE A 272 5 5
HELIX 11 AB2 THR B 11 GLU B 22 1 12
HELIX 12 AB3 ASP B 46 MET B 62 1 17
HELIX 13 AB4 SER B 84 LEU B 103 1 20
HELIX 14 AB5 SER B 121 GLN B 136 1 16
HELIX 15 AB6 HIS B 152 SER B 169 1 18
HELIX 16 AB7 ASN B 176 ILE B 181 1 6
HELIX 17 AB8 LEU B 209 VAL B 219 1 11
HELIX 18 AB9 PRO B 225 LYS B 246 1 22
HELIX 19 AC1 PRO B 259 HIS B 264 5 6
HELIX 20 AC2 PHE B 268 ILE B 272 5 5
HELIX 21 AC3 THR C 11 GLU C 22 1 12
HELIX 22 AC4 ASP C 46 MET C 62 1 17
HELIX 23 AC5 SER C 84 LEU C 103 1 20
HELIX 24 AC6 SER C 121 GLN C 136 1 16
HELIX 25 AC7 HIS C 152 SER C 169 1 18
HELIX 26 AC8 ASN C 176 ILE C 181 1 6
HELIX 27 AC9 LEU C 209 VAL C 219 1 11
HELIX 28 AD1 PRO C 225 LYS C 246 1 22
HELIX 29 AD2 PRO C 259 HIS C 264 5 6
HELIX 30 AD3 PHE C 268 ILE C 272 5 5
SHEET 1 AA1 5 LYS A 107 TYR A 113 0
SHEET 2 AA1 5 GLU A 65 THR A 72 1 N CYS A 70 O TYR A 109
SHEET 3 AA1 5 LYS A 37 GLU A 42 1 N CYS A 40 O ILE A 67
SHEET 4 AA1 5 GLY A 139 PRO A 143 1 O PHE A 141 N ILE A 41
SHEET 5 AA1 5 PHE A 191 TYR A 195 1 O ALA A 193 N VAL A 140
SHEET 1 AA2 2 TYR A 202 ASP A 205 0
SHEET 2 AA2 2 GLY A 252 PHE A 255 -1 O PHE A 255 N TYR A 202
SHEET 1 AA3 5 LYS B 107 TYR B 113 0
SHEET 2 AA3 5 GLU B 65 THR B 72 1 N TYR B 68 O TYR B 109
SHEET 3 AA3 5 LYS B 37 GLU B 42 1 N GLU B 42 O MET B 71
SHEET 4 AA3 5 GLY B 139 PRO B 143 1 O PHE B 141 N ILE B 41
SHEET 5 AA3 5 PHE B 191 TYR B 195 1 O ALA B 193 N VAL B 140
SHEET 1 AA4 2 TYR B 202 ASP B 205 0
SHEET 2 AA4 2 GLY B 252 PHE B 255 -1 O PHE B 255 N TYR B 202
SHEET 1 AA5 5 LYS C 107 TYR C 113 0
SHEET 2 AA5 5 GLU C 65 THR C 72 1 N CYS C 70 O TYR C 109
SHEET 3 AA5 5 LYS C 37 GLU C 42 1 N CYS C 40 O ILE C 67
SHEET 4 AA5 5 GLY C 139 PRO C 143 1 O PHE C 141 N ILE C 41
SHEET 5 AA5 5 PHE C 191 TYR C 195 1 O ALA C 193 N VAL C 140
SHEET 1 AA6 2 TYR C 202 ASP C 205 0
SHEET 2 AA6 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 2.01
LINK OD2 ASP A 47 ZN ZN A 301 1555 1555 2.13
LINK NE2 HIS A 155 ZN ZN A 301 1555 1555 2.09
LINK ZN ZN A 301 O72 MQG A 302 1555 1555 1.88
LINK ND1 HIS B 44 ZN ZN B 301 1555 1555 2.19
LINK OD1 ASP B 47 ZN ZN B 301 1555 1555 2.65
LINK OD2 ASP B 47 ZN ZN B 301 1555 1555 1.96
LINK NE2 HIS B 155 ZN ZN B 301 1555 1555 2.23
LINK ZN ZN B 301 O72 MQG B 302 1555 1555 1.84
LINK ND1 HIS C 44 ZN ZN C 301 1555 1555 1.94
LINK OD2 ASP C 47 ZN ZN C 301 1555 1555 2.00
LINK NE2 HIS C 155 ZN ZN C 301 1555 1555 1.99
LINK ZN ZN C 301 O72 MQG C 302 1555 1555 2.08
CISPEP 1 VAL A 105 LYS A 106 0 25.30
CISPEP 2 ASN B 187 SER B 188 0 5.82
CISPEP 3 ASN B 187 SER B 188 0 18.96
CRYST1 77.821 77.821 229.230 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 0.012850 0.007419 0.000000 0.00000
SCALE2 0.000000 0.014838 0.000000 0.00000
SCALE3 0.000000 0.000000 0.004362 0.00000