HEADER HYDROLASE/DNA 24-MAY-04 1TDZ
TITLE CRYSTAL STRUCTURE COMPLEX BETWEEN THE LACTOCOCCUS LACTIS FPG (MUTM)
TITLE 2 AND A FAPY-DG CONTAINING DNA
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*CP*TP*CP*TP*TP*TP*(FOX)P*TP*TP*TP*CP*TP*CP*G)-3';
COMPND 3 CHAIN: B;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: 5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3';
COMPND 7 CHAIN: C;
COMPND 8 ENGINEERED: YES;
COMPND 9 MOL_ID: 3;
COMPND 10 MOLECULE: FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASE;
COMPND 11 CHAIN: A;
COMPND 12 SYNONYM: FAPY-DNA GLYCOSYLASE;
COMPND 13 EC: 3.2.2.23;
COMPND 14 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 MOL_ID: 2;
SOURCE 4 SYNTHETIC: YES;
SOURCE 5 MOL_ID: 3;
SOURCE 6 ORGANISM_SCIENTIFIC: LACTOCOCCUS LACTIS;
SOURCE 7 ORGANISM_TAXID: 1358;
SOURCE 8 GENE: MUTM, FPG;
SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PMAL-C
KEYWDS DNA REPAIR; FPG; MUTM; FAPY G, HYDROLASE-DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR F.COSTE,M.OBER,T.CARELL,S.BOITEUX,C.ZELWER,B.CASTAING
REVDAT 5 23-AUG-23 1TDZ 1 REMARK LINK
REVDAT 4 13-JUL-11 1TDZ 1 VERSN
REVDAT 3 24-FEB-09 1TDZ 1 VERSN
REVDAT 2 18-APR-06 1TDZ 1 JRNL
REVDAT 1 07-SEP-04 1TDZ 0
JRNL AUTH F.COSTE,M.OBER,T.CARELL,S.BOITEUX,C.ZELWER,B.CASTAING
JRNL TITL STRUCTURAL BASIS FOR THE RECOGNITION OF THE FAPYDG LESION
JRNL TITL 2 (2,6-DIAMINO-4-HYDROXY-5-FORMAMIDOPYRIMIDINE) BY
JRNL TITL 3 FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASE
JRNL REF J.BIOL.CHEM. V. 279 44074 2004
JRNL REFN ISSN 0021-9258
JRNL PMID 15249553
JRNL DOI 10.1074/JBC.M405928200
REMARK 2
REMARK 2 RESOLUTION. 1.80 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.1.19
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1
REMARK 3 NUMBER OF REFLECTIONS : 52844
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) : 0.180
REMARK 3 R VALUE (WORKING SET) : 0.179
REMARK 3 FREE R VALUE : 0.207
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 2825
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 30
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.83
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2563
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : 0.2330
REMARK 3 BIN FREE R VALUE SET COUNT : 153
REMARK 3 BIN FREE R VALUE : 0.3000
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2110
REMARK 3 NUCLEIC ACID ATOMS : 569
REMARK 3 HETEROGEN ATOMS : 7
REMARK 3 SOLVENT ATOMS : 431
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 24.88
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.79
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.02000
REMARK 3 B22 (A**2) : -0.02000
REMARK 3 B33 (A**2) : 0.03000
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): 0.092
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.093
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.061
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.946
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2809 ; 0.018 ; 0.021
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3892 ; 1.709 ; 2.237
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 263 ; 5.737 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 413 ; 0.109 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1857 ; 0.008 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1226 ; 0.210 ; 0.200
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): 350 ; 0.143 ; 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): 40 ; 0.131 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 29 ; 0.178 ; 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): 1313 ; 0.989 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2129 ; 1.755 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1496 ; 2.620 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1763 ; 4.122 ; 4.500
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : BABINET MODEL WITH MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.40
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1TDZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUN-04.
REMARK 100 THE DEPOSITION ID IS D_1000022569.
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 : 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 : ID14-2
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9330
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA)
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55781
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800
REMARK 200 RESOLUTION RANGE LOW (A) : 76.700
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3
REMARK 200 DATA REDUNDANCY : 3.600
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.04800
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.7000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 3.60
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.23400
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.100
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 1NNJ
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 63.20
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.37
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES, SODIUM CITRATE, PH 7.0, 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 70.78750
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 45.70400
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 45.70400
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 35.39375
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 45.70400
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 45.70400
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 106.18125
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 45.70400
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.70400
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 35.39375
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 45.70400
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.70400
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 106.18125
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 70.78750
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 APPLY THE FOLLOWING TO CHAINS: B, C, 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 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 A5148 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A5326 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A5332 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 0
REMARK 465 PRO A 1
REMARK 465 ARG A 220
REMARK 465 THR A 221
REMARK 465 TYR A 222
REMARK 465 SER A 223
REMARK 465 ALA A 224
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 GLN A 50 CD OE1 NE2
REMARK 470 LYS A 78 CD CE NZ
REMARK 470 ARG A 88 CD NE CZ NH1 NH2
REMARK 470 LYS A 130 CE NZ
REMARK 470 GLU A 138 CD OE1 OE2
REMARK 470 LYS A 151 NZ
REMARK 470 LYS A 213 CD CE NZ
REMARK 470 LYS A 230 CE NZ
REMARK 470 LYS A 271 CE NZ
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 MET A 96 SD MET A 96 CE -0.342
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 DC B 1 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 DT B 2 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES
REMARK 500 DT B 6 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 DT B 9 OP1 - P - OP2 ANGL. DEV. = 14.2 DEGREES
REMARK 500 DT B 9 O5' - P - OP1 ANGL. DEV. = -11.4 DEGREES
REMARK 500 DC B 13 O4' - C1' - N1 ANGL. DEV. = -5.7 DEGREES
REMARK 500 DA C 20 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES
REMARK 500 DG C 27 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES
REMARK 500 DA C 28 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES
REMARK 500 ASP A 85 CB - CG - OD1 ANGL. DEV. = 6.6 DEGREES
REMARK 500 ASP A 107 CB - CG - OD1 ANGL. DEV. = 5.6 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 -125.96 49.01
REMARK 500 ASP A 107 101.56 -161.33
REMARK 500 GLN A 163 -0.65 80.62
REMARK 500 VAL A 166 142.59 -170.98
REMARK 500 VAL A 237 -36.74 -137.63
REMARK 500 GLN A 269 79.49 -118.17
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 A1001 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 245 SG
REMARK 620 2 CYS A 248 SG 112.1
REMARK 620 3 CYS A 265 SG 109.5 97.4
REMARK 620 4 CYS A 268 SG 108.1 114.2 115.3
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 1001
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 5001
DBREF 1TDZ A 0 271 UNP P42371 FPG_LACLC 1 273
DBREF 1TDZ B 1 14 PDB 1TDZ 1TDZ 1 14
DBREF 1TDZ C 15 28 PDB 1TDZ 1TDZ 15 28
SEQADV 1TDZ A UNP P42371 ASP 139 SEE REMARK 999
SEQRES 1 B 14 DC DT DC DT DT DT FOX DT DT DT DC DT DC
SEQRES 2 B 14 DG
SEQRES 1 C 14 DG DC DG DA DG DA DA DA DC DA DA DA DG
SEQRES 2 C 14 DA
SEQRES 1 A 272 MET PRO GLU LEU PRO GLU VAL GLU THR VAL ARG ARG GLU
SEQRES 2 A 272 LEU GLU LYS ARG ILE VAL GLY GLN LYS ILE ILE SER ILE
SEQRES 3 A 272 GLU ALA THR TYR PRO ARG MET VAL LEU THR GLY PHE GLU
SEQRES 4 A 272 GLN LEU LYS LYS GLU LEU THR GLY LYS THR ILE GLN GLY
SEQRES 5 A 272 ILE SER ARG ARG GLY LYS TYR LEU ILE PHE GLU ILE GLY
SEQRES 6 A 272 ASP ASP PHE ARG LEU ILE SER HIS LEU ARG MET GLU GLY
SEQRES 7 A 272 LYS TYR ARG LEU ALA THR LEU ASP ALA PRO ARG GLU LYS
SEQRES 8 A 272 HIS ASP HIS LEU THR MET LYS PHE ALA ASP GLY GLN LEU
SEQRES 9 A 272 ILE TYR ALA ASP VAL ARG LYS PHE GLY THR TRP GLU LEU
SEQRES 10 A 272 ILE SER THR ASP GLN VAL LEU PRO TYR PHE LEU LYS LYS
SEQRES 11 A 272 LYS ILE GLY PRO GLU PRO THR TYR GLU ASP PHE ASP GLU
SEQRES 12 A 272 LYS LEU PHE ARG GLU LYS LEU ARG LYS SER THR LYS LYS
SEQRES 13 A 272 ILE LYS PRO TYR LEU LEU GLU GLN THR LEU VAL ALA GLY
SEQRES 14 A 272 LEU GLY ASN ILE TYR VAL ASP GLU VAL LEU TRP LEU ALA
SEQRES 15 A 272 LYS ILE HIS PRO GLU LYS GLU THR ASN GLN LEU ILE GLU
SEQRES 16 A 272 SER SER ILE HIS LEU LEU HIS ASP SER ILE ILE GLU ILE
SEQRES 17 A 272 LEU GLN LYS ALA ILE LYS LEU GLY GLY SER SER ILE ARG
SEQRES 18 A 272 THR TYR SER ALA LEU GLY SER THR GLY LYS MET GLN ASN
SEQRES 19 A 272 GLU LEU GLN VAL TYR GLY LYS THR GLY GLU LYS CYS SER
SEQRES 20 A 272 ARG CYS GLY ALA GLU ILE GLN LYS ILE LYS VAL ALA GLY
SEQRES 21 A 272 ARG GLY THR HIS PHE CYS PRO VAL CYS GLN GLN LYS
MODRES 1TDZ FOX B 7 DG
HET FOX B 7 23
HET ZN A1001 1
HET GOL A5001 6
HETNAM FOX ((1R,2S,4R)-4-{[2-AMINO-5-(FORMYLAMINO)-6-OXO-3,6-
HETNAM 2 FOX DIHYDROPYRIMIDIN-4-YL]AMINO}-2-HYDROXYCYCLOPENTYL)
HETNAM 3 FOX METHYL 5'-PHOSPHATE
HETNAM ZN ZINC ION
HETNAM GOL GLYCEROL
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 1 FOX C11 H18 N5 O7 P
FORMUL 4 ZN ZN 2+
FORMUL 5 GOL C3 H8 O3
FORMUL 6 HOH *431(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 SER A 152 1 12
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 ALA A 82 O GLN A 102
SHEET 1 B 4 ILE A 49 ARG A 55 0
SHEET 2 B 4 TYR A 58 ILE A 63 -1 O GLU A 62 N GLY A 51
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 ARG A 260 N VAL A 257
LINK O3' DT B 6 P FOX B 7 1555 1555 1.59
LINK O3' FOX B 7 P DT B 8 1555 1555 1.54
LINK SG CYS A 245 ZN ZN A1001 1555 1555 2.34
LINK SG CYS A 248 ZN ZN A1001 1555 1555 2.36
LINK SG CYS A 265 ZN ZN A1001 1555 1555 2.21
LINK SG CYS A 268 ZN ZN A1001 1555 1555 2.33
SITE 1 AC1 4 CYS A 245 CYS A 248 CYS A 265 CYS A 268
SITE 1 AC2 9 TYR A 58 HIS A 72 ARG A 74 THR A 113
SITE 2 AC2 9 GLU A 115 TYR A 125 LYS A 129 DT B 9
SITE 3 AC2 9 DT B 10
CRYST1 91.408 91.408 141.575 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 0.010940 0.000000 0.000000 0.00000
SCALE2 0.000000 0.010940 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007063 0.00000