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 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 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