HEADER HYDROLASE 11-AUG-07 2QXF TITLE PRODUCT BOUND STRUCTURE OF EXONUCLEASE I AT 1.5 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: EXODEOXYRIBONUCLEASE I; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: EXONUCLEASE I, DNA DEOXYRIBOPHOSPHODIESTERASE, DRPASE; COMPND 5 EC: 3.1.11.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: SBCB, CPEA, XONA, B2011, JW1993; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ALPHA-BETA DOMAIN, DNAQ SUPERFAMILY, SH3-LIKE DOMAIN, PRODUCT BOUND KEYWDS 2 STRUCTURE, DNA DAMAGE, DNA REPAIR, EXONUCLEASE, HYDROLASE, NUCLEASE EXPDTA X-RAY DIFFRACTION AUTHOR R.D.BUSAM REVDAT 6 21-FEB-24 2QXF 1 REMARK SEQADV LINK REVDAT 5 25-OCT-17 2QXF 1 REMARK REVDAT 4 13-JUL-11 2QXF 1 VERSN REVDAT 3 24-FEB-09 2QXF 1 VERSN REVDAT 2 10-JUN-08 2QXF 1 JRNL REVDAT 1 22-JAN-08 2QXF 0 JRNL AUTH R.D.BUSAM JRNL TITL STRUCTURE OF ESCHERICHIA COLI EXONUCLEASE I IN COMPLEX WITH JRNL TITL 2 THYMIDINE 5'-MONOPHOSPHATE. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 64 206 2008 JRNL REFN ISSN 0907-4449 JRNL PMID 18219121 JRNL DOI 10.1107/S090744490706012X REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 80202 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) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4023 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5540 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.51 REMARK 3 BIN R VALUE (WORKING SET) : 0.2410 REMARK 3 BIN FREE R VALUE SET COUNT : 296 REMARK 3 BIN FREE R VALUE : 0.2900 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3525 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 544 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.082 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.081 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.049 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.424 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3859 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5281 ; 1.759 ; 1.953 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 478 ; 5.953 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 200 ;35.582 ;23.800 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 642 ;13.997 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;18.523 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 561 ; 0.056 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3068 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1795 ; 0.161 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2672 ; 0.270 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 442 ; 0.065 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 6 ; 0.090 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 62 ; 0.118 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 40 ; 0.068 ; 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): 2315 ; 0.325 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3776 ; 0.638 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1609 ; 1.057 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1505 ; 1.736 ; 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 7 A 133 REMARK 3 ORIGIN FOR THE GROUP (A): 25.0760 26.1350 28.4110 REMARK 3 T TENSOR REMARK 3 T11: -0.0012 T22: 0.0201 REMARK 3 T33: -0.0310 T12: 0.0051 REMARK 3 T13: 0.0099 T23: -0.0052 REMARK 3 L TENSOR REMARK 3 L11: 1.1074 L22: 0.7582 REMARK 3 L33: 0.6521 L12: 0.3158 REMARK 3 L13: 0.3839 L23: 0.2205 REMARK 3 S TENSOR REMARK 3 S11: 0.0354 S12: -0.0903 S13: -0.0085 REMARK 3 S21: 0.0032 S22: -0.0245 S23: 0.0014 REMARK 3 S31: 0.0132 S32: -0.0598 S33: -0.0110 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 134 A 347 REMARK 3 ORIGIN FOR THE GROUP (A): 22.4920 12.9120 6.6330 REMARK 3 T TENSOR REMARK 3 T11: -0.0102 T22: 0.0057 REMARK 3 T33: 0.0059 T12: 0.0020 REMARK 3 T13: -0.0028 T23: 0.0131 REMARK 3 L TENSOR REMARK 3 L11: 0.5356 L22: 1.2856 REMARK 3 L33: 0.7948 L12: -0.1180 REMARK 3 L13: -0.3182 L23: 0.2139 REMARK 3 S TENSOR REMARK 3 S11: -0.0114 S12: -0.0367 S13: -0.0577 REMARK 3 S21: 0.0090 S22: -0.0343 S23: -0.1230 REMARK 3 S31: 0.0656 S32: 0.0370 S33: 0.0458 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 361 A 474 REMARK 3 ORIGIN FOR THE GROUP (A): 41.5890 27.8900 34.7550 REMARK 3 T TENSOR REMARK 3 T11: -0.0632 T22: 0.0237 REMARK 3 T33: -0.0571 T12: 0.0181 REMARK 3 T13: -0.0094 T23: -0.0094 REMARK 3 L TENSOR REMARK 3 L11: 0.9753 L22: 0.9884 REMARK 3 L33: 2.0309 L12: 0.0760 REMARK 3 L13: -0.2276 L23: -0.5554 REMARK 3 S TENSOR REMARK 3 S11: 0.0218 S12: -0.1520 S13: -0.0897 REMARK 3 S21: 0.0309 S22: -0.0728 S23: -0.1105 REMARK 3 S31: 0.0093 S32: 0.1862 S33: 0.0509 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 2QXF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-AUG-07. REMARK 100 THE DEPOSITION ID IS D_1000044165. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-MAY-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97000 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 : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 80289 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.37100 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR 2.5 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M SODIUM CHLORIDE, 0.1M TRIS-HCL, REMARK 280 20% PEG 8000, 1.5X MOLAR EXCESS SSDNA, PH 8.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 26.31500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.37600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.92450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.37600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.31500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.92450 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE PROGRAM GENERATED ASSEMBLY REMARK 300 INFORMATION FOR THE STRUCTURE IN THIS ENTRY. REMARK 300 AUTHORS STATE THAT THE INFORMATION ABOUT THE REMARK 300 BIOLOGICAL UNIT OF THIS PROTEIN IS NOT AVAILABLE. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 MET A 1 REMARK 465 MET A 2 REMARK 465 ASN A 3 REMARK 465 ASP A 4 REMARK 465 GLY A 5 REMARK 465 LYS A 6 REMARK 465 ASN A 179 REMARK 465 ALA A 180 REMARK 465 HIS A 181 REMARK 465 SER A 276 REMARK 465 ASP A 277 REMARK 465 THR A 278 REMARK 465 LEU A 279 REMARK 465 ARG A 280 REMARK 465 GLU A 281 REMARK 465 ARG A 282 REMARK 465 LEU A 283 REMARK 465 TYR A 284 REMARK 465 THR A 285 REMARK 465 ALA A 286 REMARK 465 LYS A 287 REMARK 465 THR A 288 REMARK 465 ASP A 289 REMARK 465 LEU A 290 REMARK 465 GLY A 291 REMARK 465 ASP A 292 REMARK 465 ASN A 293 REMARK 465 ALA A 294 REMARK 465 VAL A 348 REMARK 465 ALA A 349 REMARK 465 ILE A 350 REMARK 465 PHE A 351 REMARK 465 ALA A 352 REMARK 465 GLU A 353 REMARK 465 ALA A 354 REMARK 465 GLU A 355 REMARK 465 PRO A 356 REMARK 465 PHE A 357 REMARK 465 THR A 358 REMARK 465 PRO A 359 REMARK 465 SER A 360 REMARK 465 VAL A 475 REMARK 465 GLU A 476 REMARK 465 HIS A 477 REMARK 465 HIS A 478 REMARK 465 HIS A 479 REMARK 465 HIS A 480 REMARK 465 HIS A 481 REMARK 465 HIS A 482 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 CYS A 306 CB CYS A 306 SG -0.136 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 55 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 106 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 134 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 ASP A 420 CB - CG - OD1 ANGL. DEV. = 5.5 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 PHE A 107 -74.03 -112.20 REMARK 500 PHE A 107 -74.03 -125.36 REMARK 500 HIS A 177 85.37 -161.46 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 MG A2001 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 15 OD1 REMARK 620 2 TMP A3000 O1P 174.7 REMARK 620 3 HOH A3078 O 87.5 88.4 REMARK 620 4 HOH A3079 O 85.5 91.5 94.7 REMARK 620 5 HOH A3080 O 91.2 93.3 173.6 91.5 REMARK 620 6 HOH A3097 O 85.5 97.7 88.2 170.4 85.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A2000 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 17 OE2 REMARK 620 2 ASP A 186 OD2 85.4 REMARK 620 3 HOH A3111 O 83.5 87.1 REMARK 620 4 HOH A3173 O 95.1 90.7 177.4 REMARK 620 5 HOH A3251 O 170.0 90.3 87.2 94.1 REMARK 620 6 HOH A3255 O 89.5 173.8 95.9 86.2 95.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A2002 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 17 OE2 REMARK 620 2 ASP A 186 OD2 77.8 REMARK 620 3 HOH A3107 O 90.0 93.1 REMARK 620 4 HOH A3109 O 112.0 170.0 85.7 REMARK 620 5 HOH A3111 O 72.5 74.2 160.1 109.4 REMARK 620 6 HOH A3125 O 154.0 83.0 108.5 88.0 85.6 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 2000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 2002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TMP A 3000 DBREF 2QXF A 1 475 UNP P04995 EX1_ECOLI 1 475 SEQADV 2QXF ASP A 472 UNP P04995 GLU 472 CONFLICT SEQADV 2QXF GLU A 476 UNP P04995 EXPRESSION TAG SEQADV 2QXF HIS A 477 UNP P04995 EXPRESSION TAG SEQADV 2QXF HIS A 478 UNP P04995 EXPRESSION TAG SEQADV 2QXF HIS A 479 UNP P04995 EXPRESSION TAG SEQADV 2QXF HIS A 480 UNP P04995 EXPRESSION TAG SEQADV 2QXF HIS A 481 UNP P04995 EXPRESSION TAG SEQADV 2QXF HIS A 482 UNP P04995 EXPRESSION TAG SEQRES 1 A 482 MET MET ASN ASP GLY LYS GLN GLN SER THR PHE LEU PHE SEQRES 2 A 482 HIS ASP TYR GLU THR PHE GLY THR HIS PRO ALA LEU ASP SEQRES 3 A 482 ARG PRO ALA GLN PHE ALA ALA ILE ARG THR ASP SER GLU SEQRES 4 A 482 PHE ASN VAL ILE GLY GLU PRO GLU VAL PHE TYR CYS LYS SEQRES 5 A 482 PRO ALA ASP ASP TYR LEU PRO GLN PRO GLY ALA VAL LEU SEQRES 6 A 482 ILE THR GLY ILE THR PRO GLN GLU ALA ARG ALA LYS GLY SEQRES 7 A 482 GLU ASN GLU ALA ALA PHE ALA ALA ARG ILE HIS SER LEU SEQRES 8 A 482 PHE THR VAL PRO LYS THR CYS ILE LEU GLY TYR ASN ASN SEQRES 9 A 482 VAL ARG PHE ASP ASP GLU VAL THR ARG ASN ILE PHE TYR SEQRES 10 A 482 ARG ASN PHE TYR ASP PRO TYR ALA TRP SER TRP GLN HIS SEQRES 11 A 482 ASP ASN SER ARG TRP ASP LEU LEU ASP VAL MET ARG ALA SEQRES 12 A 482 CYS TYR ALA LEU ARG PRO GLU GLY ILE ASN TRP PRO GLU SEQRES 13 A 482 ASN ASP ASP GLY LEU PRO SER PHE ARG LEU GLU HIS LEU SEQRES 14 A 482 THR LYS ALA ASN GLY ILE GLU HIS SER ASN ALA HIS ASP SEQRES 15 A 482 ALA MET ALA ASP VAL TYR ALA THR ILE ALA MET ALA LYS SEQRES 16 A 482 LEU VAL LYS THR ARG GLN PRO ARG LEU PHE ASP TYR LEU SEQRES 17 A 482 PHE THR HIS ARG ASN LYS HIS LYS LEU MET ALA LEU ILE SEQRES 18 A 482 ASP VAL PRO GLN MET LYS PRO LEU VAL HIS VAL SER GLY SEQRES 19 A 482 MET PHE GLY ALA TRP ARG GLY ASN THR SER TRP VAL ALA SEQRES 20 A 482 PRO LEU ALA TRP HIS PRO GLU ASN ARG ASN ALA VAL ILE SEQRES 21 A 482 MET VAL ASP LEU ALA GLY ASP ILE SER PRO LEU LEU GLU SEQRES 22 A 482 LEU ASP SER ASP THR LEU ARG GLU ARG LEU TYR THR ALA SEQRES 23 A 482 LYS THR ASP LEU GLY ASP ASN ALA ALA VAL PRO VAL LYS SEQRES 24 A 482 LEU VAL HIS ILE ASN LYS CYS PRO VAL LEU ALA GLN ALA SEQRES 25 A 482 ASN THR LEU ARG PRO GLU ASP ALA ASP ARG LEU GLY ILE SEQRES 26 A 482 ASN ARG GLN HIS CYS LEU ASP ASN LEU LYS ILE LEU ARG SEQRES 27 A 482 GLU ASN PRO GLN VAL ARG GLU LYS VAL VAL ALA ILE PHE SEQRES 28 A 482 ALA GLU ALA GLU PRO PHE THR PRO SER ASP ASN VAL ASP SEQRES 29 A 482 ALA GLN LEU TYR ASN GLY PHE PHE SER ASP ALA ASP ARG SEQRES 30 A 482 ALA ALA MET LYS ILE VAL LEU GLU THR GLU PRO ARG ASN SEQRES 31 A 482 LEU PRO ALA LEU ASP ILE THR PHE VAL ASP LYS ARG ILE SEQRES 32 A 482 GLU LYS LEU LEU PHE ASN TYR ARG ALA ARG ASN PHE PRO SEQRES 33 A 482 GLY THR LEU ASP TYR ALA GLU GLN GLN ARG TRP LEU GLU SEQRES 34 A 482 HIS ARG ARG GLN VAL PHE THR PRO GLU PHE LEU GLN GLY SEQRES 35 A 482 TYR ALA ASP GLU LEU GLN MET LEU VAL GLN GLN TYR ALA SEQRES 36 A 482 ASP ASP LYS GLU LYS VAL ALA LEU LEU LYS ALA LEU TRP SEQRES 37 A 482 GLN TYR ALA ASP GLU ILE VAL GLU HIS HIS HIS HIS HIS SEQRES 38 A 482 HIS HET MG A2000 1 HET MG A2001 1 HET NA A2002 1 HET TMP A3000 21 HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM TMP THYMIDINE-5'-PHOSPHATE FORMUL 2 MG 2(MG 2+) FORMUL 4 NA NA 1+ FORMUL 5 TMP C10 H15 N2 O8 P FORMUL 6 HOH *544(H2 O) HELIX 1 1 GLN A 60 GLY A 68 1 9 HELIX 2 2 THR A 70 GLY A 78 1 9 HELIX 3 3 ASN A 80 THR A 93 1 14 HELIX 4 4 PHE A 107 ASN A 119 1 13 HELIX 5 5 TYR A 124 ASN A 132 5 9 HELIX 6 6 LEU A 137 ARG A 148 1 12 HELIX 7 7 ARG A 165 ASN A 173 1 9 HELIX 8 8 MET A 184 GLN A 201 1 18 HELIX 9 9 GLN A 201 HIS A 211 1 11 HELIX 10 10 ASN A 213 LEU A 220 1 8 HELIX 11 11 GLY A 234 GLY A 241 5 8 HELIX 12 12 ILE A 268 LEU A 274 1 7 HELIX 13 13 ASN A 313 LEU A 315 5 3 HELIX 14 14 ARG A 316 GLY A 324 1 9 HELIX 15 15 ASN A 326 ASN A 340 1 15 HELIX 16 16 GLN A 342 VAL A 347 1 6 HELIX 17 17 ASN A 362 GLY A 370 5 9 HELIX 18 18 SER A 373 THR A 386 1 14 HELIX 19 19 LYS A 401 PHE A 415 1 15 HELIX 20 20 PRO A 416 LEU A 419 5 4 HELIX 21 21 ASP A 420 PHE A 435 1 16 HELIX 22 22 THR A 436 TYR A 454 1 19 HELIX 23 23 ASP A 457 ILE A 474 1 18 SHEET 1 A 5 GLU A 47 TYR A 50 0 SHEET 2 A 5 PRO A 28 THR A 36 -1 N PHE A 31 O PHE A 49 SHEET 3 A 5 THR A 10 THR A 18 -1 N GLU A 17 O ALA A 29 SHEET 4 A 5 THR A 97 GLY A 101 1 O CYS A 98 N LEU A 12 SHEET 5 A 5 SER A 133 ASP A 136 1 O SER A 133 N ILE A 99 SHEET 1 B 5 VAL A 298 HIS A 302 0 SHEET 2 B 5 ALA A 258 ASP A 263 -1 N MET A 261 O LYS A 299 SHEET 3 B 5 THR A 243 TRP A 251 -1 N ALA A 250 O ILE A 260 SHEET 4 B 5 LEU A 229 VAL A 232 -1 N LEU A 229 O VAL A 246 SHEET 5 B 5 VAL A 308 GLN A 311 -1 O ALA A 310 N VAL A 230 LINK OD1 ASP A 15 MG MG A2001 1555 1555 2.09 LINK OE2 GLU A 17 MG MG A2000 1555 1555 2.26 LINK OE2 GLU A 17 NA NA A2002 1555 1555 2.41 LINK OD2 ASP A 186 MG MG A2000 1555 1555 2.18 LINK OD2 ASP A 186 NA NA A2002 1555 1555 2.39 LINK MG MG A2000 O HOH A3111 1555 1555 2.22 LINK MG MG A2000 O HOH A3173 1555 1555 1.92 LINK MG MG A2000 O HOH A3251 1555 1555 2.02 LINK MG MG A2000 O HOH A3255 1555 1555 2.18 LINK MG MG A2001 O1P TMP A3000 1555 1555 2.02 LINK MG MG A2001 O HOH A3078 1555 1555 2.18 LINK MG MG A2001 O HOH A3079 1555 1555 2.12 LINK MG MG A2001 O HOH A3080 1555 1555 2.08 LINK MG MG A2001 O HOH A3097 1555 1555 2.09 LINK NA NA A2002 O HOH A3107 1555 1555 2.33 LINK NA NA A2002 O HOH A3109 1555 1555 2.27 LINK NA NA A2002 O HOH A3111 1555 1555 2.63 LINK NA NA A2002 O HOH A3125 1555 1555 2.28 CISPEP 1 HIS A 177 SER A 178 0 -0.80 SITE 1 AC1 7 GLU A 17 ASP A 186 NA A2002 HOH A3111 SITE 2 AC1 7 HOH A3173 HOH A3251 HOH A3255 SITE 1 AC2 6 ASP A 15 TMP A3000 HOH A3078 HOH A3079 SITE 2 AC2 6 HOH A3080 HOH A3097 SITE 1 AC3 7 GLU A 17 ASP A 186 MG A2000 HOH A3107 SITE 2 AC3 7 HOH A3109 HOH A3111 HOH A3125 SITE 1 AC4 19 GLU A 17 THR A 18 THR A 21 ALA A 63 SITE 2 AC4 19 ILE A 66 THR A 67 PHE A 107 ARG A 165 SITE 3 AC4 19 MG A2001 HOH A3064 HOH A3078 HOH A3079 SITE 4 AC4 19 HOH A3080 HOH A3097 HOH A3127 HOH A3128 SITE 5 AC4 19 HOH A3290 HOH A3446 HOH A3506 CRYST1 52.630 91.849 102.752 90.00 90.00 90.00 P 21 21 21 4 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 0.019001 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010887 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009732 0.00000