HEADER HYDROLASE/DNA 31-JAN-08 3C58
TITLE CRYSTAL STRUCTURE OF A COMPLEX BETWEEN THE WILD-TYPE LACTOCOCCUS
TITLE 2 LACTIS FPG (MUTM) AND A N7-BENZYL-FAPY-DG CONTAINING DNA
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-
COMPND 3 D(*DGP*DCP*DGP*DAP*DGP*DAP*DAP*DAP*DCP*DAP*DAP*DAP*DGP*DA)-3');
COMPND 4 CHAIN: C;
COMPND 5 ENGINEERED: YES;
COMPND 6 MOL_ID: 2;
COMPND 7 MOLECULE: DNA (5'-D(*DCP*DTP*DCP*DTP*DTP*DTP*(SOS)
COMPND 8 P*DTP*DTP*DTP*DCP*DTP*DCP*DG)-3');
COMPND 9 CHAIN: B;
COMPND 10 ENGINEERED: YES;
COMPND 11 MOL_ID: 3;
COMPND 12 MOLECULE: DNA GLYCOSYLASE;
COMPND 13 CHAIN: A;
COMPND 14 SYNONYM: FAPY-DNA GLYCOSYLASE, DNA-APURINIC OR APYRIMIDINIC SITE,
COMPND 15 LYASE MUTM, AP LYASE MUTM;
COMPND 16 EC: 4.2.99.18;
COMPND 17 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: SYNTHETIC DNA;
SOURCE 4 MOL_ID: 2;
SOURCE 5 SYNTHETIC: YES;
SOURCE 6 OTHER_DETAILS: SYNTHETIC DNA;
SOURCE 7 MOL_ID: 3;
SOURCE 8 ORGANISM_SCIENTIFIC: LACTOCOCCUS LACTIS;
SOURCE 9 ORGANISM_TAXID: 416870;
SOURCE 10 VARIANT: SUBSP. CREMORIS;
SOURCE 11 GENE: MUTM, FPG;
SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 14 EXPRESSION_SYSTEM_STRAIN: BL21;
SOURCE 15 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 16 EXPRESSION_SYSTEM_PLASMID: PMAL-C
KEYWDS PROTEIN-DNA COMPLEX, GLYCOSYLASE, BENZYL-FAPY, DNA REPAIR, HYDROLASE-
KEYWDS 2 DNA COMPLEX, DNA DAMAGE, DNA-BINDING, GLYCOSIDASE, LYASE, METAL-
KEYWDS 3 BINDING, MULTIFUNCTIONAL ENZYME, ZINC-FINGER
EXPDTA X-RAY DIFFRACTION
AUTHOR F.COSTE,B.CASTAING,T.CARELL
REVDAT 3 01-NOV-23 3C58 1 REMARK LINK
REVDAT 2 13-JUL-11 3C58 1 VERSN
REVDAT 1 16-DEC-08 3C58 0
JRNL AUTH F.COSTE,M.OBER,Y.V.LE BIHAN,M.A.IZQUIERDO,N.HERVOUET,
JRNL AUTH 2 H.MUELLER,T.CARELL,B.CASTAING
JRNL TITL BACTERIAL BASE EXCISION REPAIR ENZYME FPG RECOGNIZES BULKY
JRNL TITL 2 N7-SUBSTITUTED-FAPYDG LESION VIA UNPRODUCTIVE BINDING MODE
JRNL REF CHEM.BIOL. V. 15 706 2008
JRNL REFN ISSN 1074-5521
JRNL PMID 18635007
JRNL DOI 10.1016/J.CHEMBIOL.2008.05.014
REMARK 2
REMARK 2 RESOLUTION. 1.90 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0019
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) : 45.69
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 3 NUMBER OF REFLECTIONS : 45259
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) : 0.173
REMARK 3 R VALUE (WORKING SET) : 0.172
REMARK 3 FREE R VALUE : 0.200
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 2411
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) : 3304
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0
REMARK 3 BIN R VALUE (WORKING SET) : 0.2380
REMARK 3 BIN FREE R VALUE SET COUNT : 152
REMARK 3 BIN FREE R VALUE : 0.2700
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2126
REMARK 3 NUCLEIC ACID ATOMS : 576
REMARK 3 HETEROGEN ATOMS : 7
REMARK 3 SOLVENT ATOMS : 335
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 23.67
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.101
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.101
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.061
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2832 ; 0.018 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3924 ; 1.745 ; 2.236
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 269 ; 5.825 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 94 ;34.775 ;24.574
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 423 ;12.291 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;19.997 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1889 ; 0.007 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1250 ; 0.217 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1850 ; 0.306 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 307 ; 0.159 ; 0.200
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 45 ; 0.180 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 11 ; 0.140 ; 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): 1408 ; 1.114 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2168 ; 1.621 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1794 ; 2.602 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1756 ; 3.769 ; 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 : 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 3C58 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-FEB-08.
REMARK 100 THE DEPOSITION ID IS D_1000046356.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 21-MAR-06
REMARK 200 TEMPERATURE (KELVIN) : 100.0
REMARK 200 PH : 7.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : ID23-1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97935
REMARK 200 MONOCHROMATOR : SILICON (1 1 1) CHANNEL-CUT
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47718
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900
REMARK 200 RESOLUTION RANGE LOW (A) : 47.620
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 7.000
REMARK 200 R MERGE (I) : 0.09900
REMARK 200 R SYM (I) : 0.09900
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.0000
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) : 2.00
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 7.10
REMARK 200 R MERGE FOR SHELL (I) : 0.45100
REMARK 200 R SYM FOR SHELL (I) : 0.45100
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.300
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: AMORE
REMARK 200 STARTING MODEL: PDB ENTRY 1XC8
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 66.46
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.67
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES, SODIUM CITRATE, PH7.0, VAPOR
REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2
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+1/2,X+1/2,Z+1/4
REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4
REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4
REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4
REMARK 290 7555 Y,X,-Z
REMARK 290 8555 -Y,-X,-Z+1/2
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 70.47150
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 45.67800
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 45.67800
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 35.23575
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 45.67800
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 45.67800
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 105.70725
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 45.67800
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.67800
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 35.23575
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 45.67800
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.67800
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 105.70725
REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 70.47150
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: 4380 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 15660 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.5 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, B, 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 THR A 221
REMARK 465 TYR A 222
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 LYS A 15 CE NZ
REMARK 470 ARG A 31 CZ NH1 NH2
REMARK 470 LYS A 42 CD CE NZ
REMARK 470 ARG A 88 CG CD NE CZ NH1 NH2
REMARK 470 LYS A 130 CE NZ
REMARK 470 GLU A 138 CG CD OE1 OE2
REMARK 470 ARG A 150 CD NE CZ NH1 NH2
REMARK 470 LYS A 151 CE NZ
REMARK 470 LYS A 213 CD CE NZ
REMARK 470 ARG A 220 CG CD NE CZ NH1 NH2
REMARK 470 SER A 223 OG
REMARK 470 LYS A 230 CE NZ
REMARK 470 LYS A 244 NZ
REMARK 470 LYS A 271 CE NZ
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 484 O HOH A 669 2.01
REMARK 500 OD2 ASP A 66 O HOH A 483 2.07
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 SOS B 7 O3' DT B 8 P -0.076
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 DG C 17 O5' - C5' - C4' ANGL. DEV. = -6.1 DEGREES
REMARK 500 DA C 20 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES
REMARK 500 DG C 27 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 DA C 28 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES
REMARK 500 DT B 2 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES
REMARK 500 DT B 6 O4' - C4' - C3' ANGL. DEV. = -3.5 DEGREES
REMARK 500 DT B 6 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 DT B 6 C3' - O3' - P ANGL. DEV. = 10.8 DEGREES
REMARK 500 SOS B 7 C3' - O3' - P ANGL. DEV. = 11.5 DEGREES
REMARK 500 DT B 8 N3 - C2 - O2 ANGL. DEV. = -3.6 DEGREES
REMARK 500 LEU A 40 CA - CB - CG ANGL. DEV. = 17.8 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 ARG A 74 -124.71 49.07
REMARK 500 GLU A 76 21.54 -147.54
REMARK 500 ASP A 107 101.62 -162.57
REMARK 500 VAL A 166 143.33 -170.72
REMARK 500 VAL A 237 -39.31 -134.52
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 401 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 245 SG
REMARK 620 2 CYS A 248 SG 112.9
REMARK 620 3 CYS A 265 SG 110.9 96.4
REMARK 620 4 CYS A 268 SG 107.4 114.0 115.1
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 SOS B 7
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 401
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 402
DBREF 3C58 A 1 271 UNP P42371 A2RI84_LACLM 2 273
DBREF 3C58 B 1 14 PDB 3C58 3C58 1 14
DBREF 3C58 C 15 28 PDB 3C58 3C58 15 28
SEQRES 1 C 14 DG DC DG DA DG DA DA DA DC DA DA DA DG
SEQRES 2 C 14 DA
SEQRES 1 B 14 DC DT DC DT DT DT SOS DT DT DT DC DT DC
SEQRES 2 B 14 DG
SEQRES 1 A 271 PRO GLU LEU PRO GLU VAL GLU THR VAL ARG ARG GLU LEU
SEQRES 2 A 271 GLU LYS ARG ILE VAL GLY GLN LYS ILE ILE SER ILE GLU
SEQRES 3 A 271 ALA THR TYR PRO ARG MET VAL LEU THR GLY PHE GLU GLN
SEQRES 4 A 271 LEU LYS LYS GLU LEU THR GLY LYS THR ILE GLN GLY ILE
SEQRES 5 A 271 SER ARG ARG GLY LYS TYR LEU ILE PHE GLU ILE GLY ASP
SEQRES 6 A 271 ASP PHE ARG LEU ILE SER HIS LEU ARG MET GLU GLY LYS
SEQRES 7 A 271 TYR ARG LEU ALA THR LEU ASP ALA PRO ARG GLU LYS HIS
SEQRES 8 A 271 ASP HIS LEU THR MET LYS PHE ALA ASP GLY GLN LEU ILE
SEQRES 9 A 271 TYR ALA ASP VAL ARG LYS PHE GLY THR TRP GLU LEU ILE
SEQRES 10 A 271 SER THR ASP GLN VAL LEU PRO TYR PHE LEU LYS LYS LYS
SEQRES 11 A 271 ILE GLY PRO GLU PRO THR TYR GLU ASP PHE ASP GLU LYS
SEQRES 12 A 271 LEU PHE ARG GLU LYS LEU ARG LYS SER THR LYS LYS ILE
SEQRES 13 A 271 LYS PRO TYR LEU LEU GLU GLN THR LEU VAL ALA GLY LEU
SEQRES 14 A 271 GLY ASN ILE TYR VAL ASP GLU VAL LEU TRP LEU ALA LYS
SEQRES 15 A 271 ILE HIS PRO GLU LYS GLU THR ASN GLN LEU ILE GLU SER
SEQRES 16 A 271 SER ILE HIS LEU LEU HIS ASP SER ILE ILE GLU ILE LEU
SEQRES 17 A 271 GLN LYS ALA ILE LYS LEU GLY GLY SER SER ILE ARG THR
SEQRES 18 A 271 TYR SER ALA LEU GLY SER THR GLY LYS MET GLN ASN GLU
SEQRES 19 A 271 LEU GLN VAL TYR GLY LYS THR GLY GLU LYS CYS SER ARG
SEQRES 20 A 271 CYS GLY ALA GLU ILE GLN LYS ILE LYS VAL ALA GLY ARG
SEQRES 21 A 271 GLY THR HIS PHE CYS PRO VAL CYS GLN GLN LYS
HET SOS B 7 30
HET ZN A 401 1
HET GOL A 402 6
HETNAM SOS [(1R,2S,4R)-4-({2-AMINO-5-[BENZYL(FORMYL)AMINO]-6-OXO-
HETNAM 2 SOS 1,6-DIHYDROPYRIMIDIN-4-YL}AMINO)-2-
HETNAM 3 SOS HYDROXYCYCLOPENTYL]METHYL DIHYDROGEN PHOSPHATE
HETNAM ZN ZINC ION
HETNAM GOL GLYCEROL
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 2 SOS C18 H24 N5 O7 P
FORMUL 4 ZN ZN 2+
FORMUL 5 GOL C3 H8 O3
FORMUL 6 HOH *335(H2 O)
HELIX 1 1 GLU A 2 VAL A 18 1 17
HELIX 2 2 TYR A 29 VAL A 33 5 5
HELIX 3 3 GLY A 36 THR A 45 1 10
HELIX 4 4 GLN A 121 LYS A 130 1 10
HELIX 5 5 ASP A 141 LYS A 151 1 11
HELIX 6 6 LYS A 155 GLU A 162 1 8
HELIX 7 7 GLY A 170 ALA A 181 1 12
HELIX 8 8 GLU A 188 LEU A 192 5 5
HELIX 9 9 ILE A 193 LEU A 214 1 22
HELIX 10 10 LYS A 230 LEU A 235 5 6
SHEET 1 A 4 SER A 24 ALA A 27 0
SHEET 2 A 4 ASP A 92 LYS A 97 -1 O LYS A 97 N SER A 24
SHEET 3 A 4 GLN A 102 ALA A 106 -1 O TYR A 105 N HIS A 93
SHEET 4 A 4 LYS A 78 ALA A 82 -1 N LYS A 78 O ALA A 106
SHEET 1 B 4 ILE A 49 ARG A 55 0
SHEET 2 B 4 TYR A 58 ILE A 63 -1 O ILE A 60 N SER A 53
SHEET 3 B 4 PHE A 67 HIS A 72 -1 O SER A 71 N LEU A 59
SHEET 4 B 4 THR A 113 SER A 118 -1 O GLU A 115 N ILE A 70
SHEET 1 C 2 GLN A 253 VAL A 257 0
SHEET 2 C 2 ARG A 260 PHE A 264 -1 O PHE A 264 N GLN A 253
LINK O3' DT B 6 P SOS B 7 1555 1555 1.65
LINK O3' SOS B 7 P DT B 8 1555 1555 1.53
LINK SG CYS A 245 ZN ZN A 401 1555 1555 2.32
LINK SG CYS A 248 ZN ZN A 401 1555 1555 2.43
LINK SG CYS A 265 ZN ZN A 401 1555 1555 2.19
LINK SG CYS A 268 ZN ZN A 401 1555 1555 2.34
SITE 1 AC1 12 PRO A 1 GLU A 2 GLU A 5 MET A 75
SITE 2 AC1 12 ASN A 171 ILE A 172 SER A 217 ILE A 219
SITE 3 AC1 12 TYR A 238 ARG A 260 DT B 6 DT B 8
SITE 1 AC2 4 CYS A 245 CYS A 248 CYS A 265 CYS A 268
SITE 1 AC3 9 TYR A 58 HIS A 72 ARG A 74 THR A 113
SITE 2 AC3 9 GLU A 115 TYR A 125 LYS A 129 DT B 9
SITE 3 AC3 9 DT B 10
CRYST1 91.356 91.356 140.943 90.00 90.00 90.00 P 41 21 2 8
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 0.010946 0.000000 0.000000 0.00000
SCALE2 0.000000 0.010946 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007095 0.00000