HEADER TRANSFERASE/DNA 21-DEC-11 3V7J TITLE CO-CRYSTAL STRUCTURE OF WILD TYPE RAT POLYMERASE BETA: ENZYME-DNA TITLE 2 BINARY COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE BETA; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.7.7, 4.2.99.-; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(P*AP*TP*GP*TP*GP*AP*GP*T)-3'); COMPND 8 CHAIN: P; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (5'-D(P*CP*AP*AP*AP*CP*TP*CP*AP*CP*AP*TP*A)-3'); COMPND 12 CHAIN: T; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: POLB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES KEYWDS PROTEIN-DNA COMPLEX, REPAIR POLYMERASE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.RANGARAJAN,J.JAEGER REVDAT 2 28-FEB-24 3V7J 1 REMARK SEQADV REVDAT 1 16-JAN-13 3V7J 0 JRNL AUTH S.RANGARAJAN,C.L.GRIDLEY,S.FIRBANK,S.DALAL,J.B.SWEASY, JRNL AUTH 2 J.JAEGER JRNL TITL CRYSTALLOGRAPHIC STUDIES OF K72E MUTANT DNA POLYMERASE JRNL TITL 2 EXPLAIN LOSS OF LYASE FUNCTION AND REVEAL CHANGES IN THE JRNL TITL 3 OVERALL CONFORMATIONAL STATE OF THE POLYMERASE DOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.2_869) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.070 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 20979 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.550 REMARK 3 FREE R VALUE TEST SET COUNT : 954 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 17.0180 - 4.2844 0.99 3512 176 0.1726 0.2073 REMARK 3 2 4.2844 - 3.4096 0.94 3229 161 0.1889 0.1967 REMARK 3 3 3.4096 - 2.9813 0.95 3212 146 0.2172 0.2478 REMARK 3 4 2.9813 - 2.7099 0.92 3104 143 0.2504 0.3038 REMARK 3 5 2.7099 - 2.5163 0.87 2907 142 0.2735 0.3467 REMARK 3 6 2.5163 - 2.3684 0.79 2644 114 0.3030 0.3804 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.32 REMARK 3 B_SOL : 7.12 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.720 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.740 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 21.82610 REMARK 3 B22 (A**2) : 37.56000 REMARK 3 B33 (A**2) : 24.38960 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 3128 REMARK 3 ANGLE : 1.325 4293 REMARK 3 CHIRALITY : 0.084 470 REMARK 3 PLANARITY : 0.004 494 REMARK 3 DIHEDRAL : 18.769 1233 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN P AND ( RESID 0:7 OR RESID 31:373 ) ) OR ( REMARK 3 CHAIN T AND ( RESID 1:12 OR RESID 13:392 ) ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.0748 10.5192 -3.9569 REMARK 3 T TENSOR REMARK 3 T11: 0.0256 T22: 0.1583 REMARK 3 T33: 0.1759 T12: 0.1945 REMARK 3 T13: 0.0545 T23: 0.0651 REMARK 3 L TENSOR REMARK 3 L11: 1.4640 L22: 3.8351 REMARK 3 L33: 3.7986 L12: 1.5349 REMARK 3 L13: 1.2935 L23: -1.0800 REMARK 3 S TENSOR REMARK 3 S11: -0.0164 S12: 0.0871 S13: 0.1726 REMARK 3 S21: 0.0207 S22: -0.0230 S23: -0.3770 REMARK 3 S31: 0.0997 S32: 0.2427 S33: -0.1016 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 9:148 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.3875 2.5730 10.8390 REMARK 3 T TENSOR REMARK 3 T11: -0.0083 T22: 0.1653 REMARK 3 T33: 0.0510 T12: -0.0085 REMARK 3 T13: 0.0128 T23: 0.1096 REMARK 3 L TENSOR REMARK 3 L11: 1.6100 L22: 0.3752 REMARK 3 L33: 0.2246 L12: 0.2595 REMARK 3 L13: 0.2903 L23: 0.1728 REMARK 3 S TENSOR REMARK 3 S11: 0.0051 S12: -0.1166 S13: 0.0050 REMARK 3 S21: 0.0640 S22: 0.0339 S23: -0.0822 REMARK 3 S31: 0.0416 S32: -0.0575 S33: 0.0111 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 149:335 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.1176 -8.0894 -16.0998 REMARK 3 T TENSOR REMARK 3 T11: 0.2488 T22: 0.0875 REMARK 3 T33: 0.0602 T12: 0.0912 REMARK 3 T13: 0.0357 T23: -0.0167 REMARK 3 L TENSOR REMARK 3 L11: 2.4700 L22: 0.9535 REMARK 3 L33: 3.1840 L12: 0.1375 REMARK 3 L13: -1.2076 L23: -0.1803 REMARK 3 S TENSOR REMARK 3 S11: -0.1260 S12: 0.1460 S13: -0.2128 REMARK 3 S21: 0.0200 S22: -0.0498 S23: -0.0387 REMARK 3 S31: 0.2865 S32: 0.2122 S33: 0.1275 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3V7J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-DEC-11. REMARK 100 THE DEPOSITION ID IS D_1000069693. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUL-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97907 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL BENDER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25465 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 17.018 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.030 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.7.2_869 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, NACL, GLYCEROL, CACODYLATE, REMARK 280 PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 296K 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 28.38950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.32650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.55700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.32650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.38950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.55700 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 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: 3850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -117.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, P, T 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 -4 REMARK 465 GLY A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 HIS A 1 REMARK 465 HIS A 2 REMARK 465 HIS A 3 REMARK 465 ARG A 4 REMARK 465 LYS A 5 REMARK 465 ALA A 6 REMARK 465 PRO A 7 REMARK 465 GLN A 8 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 DT P 7 O3' REMARK 470 DA T 12 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DA T 12 N9 C8 N7 C5 C6 N6 N1 REMARK 470 DA T 12 C2 N3 C4 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 615 O HOH A 617 1.84 REMARK 500 O HOH T 298 O HOH T 314 1.85 REMARK 500 NH2 ARG A 283 O HOH A 521 1.86 REMARK 500 O HOH A 477 O HOH A 564 1.87 REMARK 500 O HOH T 58 O HOH T 59 1.88 REMARK 500 O HOH A 554 O HOH A 563 1.90 REMARK 500 O HOH A 460 O HOH T 305 1.95 REMARK 500 O HOH A 486 O HOH A 556 1.97 REMARK 500 OG1 THR A 233 O HOH A 364 2.00 REMARK 500 OD2 ASP A 91 O HOH A 624 2.02 REMARK 500 NZ LYS A 52 O HOH A 416 2.02 REMARK 500 OD1 ASP A 74 O HOH A 604 2.04 REMARK 500 N3 DA T 2 O HOH T 372 2.05 REMARK 500 O HOH A 535 O HOH A 561 2.06 REMARK 500 OP2 DT P 3 O HOH P 75 2.13 REMARK 500 O4 DT T 11 O HOH T 55 2.14 REMARK 500 O HOH A 359 O HOH A 583 2.15 REMARK 500 O HOH A 428 O HOH T 371 2.19 REMARK 500 O HOH A 436 O HOH A 457 2.19 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 O HOH A 503 O HOH A 505 1655 2.11 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 DA P 0 P DA P 0 O5' 0.070 REMARK 500 DC T 5 O3' DC T 5 C3' 0.083 REMARK 500 DA T 10 O3' DA T 10 C3' 0.084 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 DT P 1 O4' - C1' - N1 ANGL. DEV. = -4.8 DEGREES REMARK 500 DG P 4 O4' - C4' - C3' ANGL. DEV. = -4.8 DEGREES REMARK 500 DT P 7 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA T 3 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DC T 5 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT T 6 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA T 8 O4' - C1' - N9 ANGL. DEV. = -4.4 DEGREES REMARK 500 DA T 10 O4' - C1' - N9 ANGL. DEV. = 4.1 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 THR A 10 -81.14 79.81 REMARK 500 VAL A 29 -54.65 -128.23 REMARK 500 CYS A 178 -146.97 -109.63 REMARK 500 ASP A 190 -168.32 -160.51 REMARK 500 LYS A 206 109.65 60.30 REMARK 500 GLU A 244 -89.51 -57.42 REMARK 500 ASP A 246 -119.24 51.98 REMARK 500 GLU A 247 -157.63 42.52 REMARK 500 ASN A 294 -158.34 -117.68 REMARK 500 GLU A 309 102.87 59.99 REMARK 500 ASP A 314 15.98 -142.29 REMARK 500 ARG A 333 41.12 -102.95 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 NA A 343 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 229 OG REMARK 620 2 LYS A 234 O 132.3 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 336 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 337 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 338 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 340 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 342 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 343 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 344 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 345 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 346 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 347 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3V7K RELATED DB: PDB REMARK 900 RELATED ID: 3V7L RELATED DB: PDB DBREF 3V7J A 4 335 UNP P06766 DPOLB_RAT 4 335 DBREF 3V7J P 0 7 PDB 3V7J 3V7J 0 7 DBREF 3V7J T 1 12 PDB 3V7J 3V7J 1 12 SEQADV 3V7J MET A -4 UNP P06766 INITIATING METHIONINE SEQADV 3V7J GLY A -3 UNP P06766 EXPRESSION TAG SEQADV 3V7J HIS A -2 UNP P06766 EXPRESSION TAG SEQADV 3V7J HIS A -1 UNP P06766 EXPRESSION TAG SEQADV 3V7J HIS A 0 UNP P06766 EXPRESSION TAG SEQADV 3V7J HIS A 1 UNP P06766 EXPRESSION TAG SEQADV 3V7J HIS A 2 UNP P06766 EXPRESSION TAG SEQADV 3V7J HIS A 3 UNP P06766 EXPRESSION TAG SEQRES 1 A 340 MET GLY HIS HIS HIS HIS HIS HIS ARG LYS ALA PRO GLN SEQRES 2 A 340 GLU THR LEU ASN GLY GLY ILE THR ASP MET LEU VAL GLU SEQRES 3 A 340 LEU ALA ASN PHE GLU LYS ASN VAL SER GLN ALA ILE HIS SEQRES 4 A 340 LYS TYR ASN ALA TYR ARG LYS ALA ALA SER VAL ILE ALA SEQRES 5 A 340 LYS TYR PRO HIS LYS ILE LYS SER GLY ALA GLU ALA LYS SEQRES 6 A 340 LYS LEU PRO GLY VAL GLY THR LYS ILE ALA GLU LYS ILE SEQRES 7 A 340 ASP GLU PHE LEU ALA THR GLY LYS LEU ARG LYS LEU GLU SEQRES 8 A 340 LYS ILE ARG GLN ASP ASP THR SER SER SER ILE ASN PHE SEQRES 9 A 340 LEU THR ARG VAL THR GLY ILE GLY PRO SER ALA ALA ARG SEQRES 10 A 340 LYS LEU VAL ASP GLU GLY ILE LYS THR LEU GLU ASP LEU SEQRES 11 A 340 ARG LYS ASN GLU ASP LYS LEU ASN HIS HIS GLN ARG ILE SEQRES 12 A 340 GLY LEU LYS TYR PHE GLU ASP PHE GLU LYS ARG ILE PRO SEQRES 13 A 340 ARG GLU GLU MET LEU GLN MET GLN ASP ILE VAL LEU ASN SEQRES 14 A 340 GLU VAL LYS LYS LEU ASP PRO GLU TYR ILE ALA THR VAL SEQRES 15 A 340 CYS GLY SER PHE ARG ARG GLY ALA GLU SER SER GLY ASP SEQRES 16 A 340 MET ASP VAL LEU LEU THR HIS PRO ASN PHE THR SER GLU SEQRES 17 A 340 SER SER LYS GLN PRO LYS LEU LEU HIS ARG VAL VAL GLU SEQRES 18 A 340 GLN LEU GLN LYS VAL ARG PHE ILE THR ASP THR LEU SER SEQRES 19 A 340 LYS GLY GLU THR LYS PHE MET GLY VAL CYS GLN LEU PRO SEQRES 20 A 340 SER GLU ASN ASP GLU ASN GLU TYR PRO HIS ARG ARG ILE SEQRES 21 A 340 ASP ILE ARG LEU ILE PRO LYS ASP GLN TYR TYR CYS GLY SEQRES 22 A 340 VAL LEU TYR PHE THR GLY SER ASP ILE PHE ASN LYS ASN SEQRES 23 A 340 MET ARG ALA HIS ALA LEU GLU LYS GLY PHE THR ILE ASN SEQRES 24 A 340 GLU TYR THR ILE ARG PRO LEU GLY VAL THR GLY VAL ALA SEQRES 25 A 340 GLY GLU PRO LEU PRO VAL ASP SER GLU GLN ASP ILE PHE SEQRES 26 A 340 ASP TYR ILE GLN TRP ARG TYR ARG GLU PRO LYS ASP ARG SEQRES 27 A 340 SER GLU SEQRES 1 P 8 DA DT DG DT DG DA DG DT SEQRES 1 T 12 DC DA DA DA DC DT DC DA DC DA DT DA HET NA A 336 1 HET NA A 337 1 HET NA A 338 1 HET NA A 339 1 HET NA A 340 1 HET NA A 341 1 HET NA A 342 1 HET NA A 343 1 HET CL A 344 1 HET CL A 345 1 HET CL A 346 1 HET CL A 347 1 HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 4 NA 8(NA 1+) FORMUL 12 CL 4(CL 1-) FORMUL 16 HOH *356(H2 O) HELIX 1 1 ASN A 12 VAL A 29 1 18 HELIX 2 2 ALA A 32 LYS A 48 1 17 HELIX 3 3 SER A 55 LYS A 61 1 7 HELIX 4 4 GLY A 66 GLY A 80 1 15 HELIX 5 5 LEU A 82 ASP A 91 1 10 HELIX 6 6 ASP A 91 THR A 101 1 11 HELIX 7 7 GLY A 107 GLU A 117 1 11 HELIX 8 8 THR A 121 LYS A 127 1 7 HELIX 9 9 ASN A 128 LEU A 132 5 5 HELIX 10 10 ASN A 133 TYR A 142 1 10 HELIX 11 11 TYR A 142 LYS A 148 1 7 HELIX 12 12 ARG A 152 ASP A 170 1 19 HELIX 13 13 CYS A 178 ARG A 183 1 6 HELIX 14 14 PRO A 208 VAL A 221 1 14 HELIX 15 15 PRO A 261 ASP A 263 5 3 HELIX 16 16 GLN A 264 PHE A 272 1 9 HELIX 17 17 SER A 275 GLY A 290 1 16 HELIX 18 18 SER A 315 ILE A 323 1 9 HELIX 19 19 GLU A 329 ARG A 333 5 5 SHEET 1 A 2 ILE A 150 PRO A 151 0 SHEET 2 A 2 SER A 187 SER A 188 -1 O SER A 188 N ILE A 150 SHEET 1 B 5 ILE A 174 VAL A 177 0 SHEET 2 B 5 MET A 191 THR A 196 -1 O LEU A 194 N THR A 176 SHEET 3 B 5 ARG A 253 LEU A 259 1 O ARG A 258 N LEU A 195 SHEET 4 B 5 LYS A 234 CYS A 239 -1 N CYS A 239 O ARG A 253 SHEET 5 B 5 ILE A 224 LYS A 230 -1 N SER A 229 O MET A 236 SHEET 1 C 2 PHE A 291 ILE A 293 0 SHEET 2 C 2 ILE A 298 PRO A 300 -1 O ARG A 299 N THR A 292 LINK OH TYR A 39 NA NA A 340 1555 1555 3.14 LINK OG SER A 229 NA NA A 343 1555 1555 3.16 LINK O LYS A 234 NA NA A 343 1555 1555 3.19 LINK NA NA A 336 O HOH A 491 1555 1555 3.04 CISPEP 1 GLU A 9 THR A 10 0 -1.15 CISPEP 2 GLY A 274 SER A 275 0 1.91 SITE 1 AC1 2 ASP A 190 HOH A 491 SITE 1 AC2 1 ASP A 130 SITE 1 AC3 4 THR A 101 ARG A 102 THR A 104 DG P 6 SITE 1 AC4 4 TYR A 39 LYS A 68 LYS A 72 DA P 0 SITE 1 AC5 4 ASN A 28 VAL A 29 GLN A 31 PRO A 108 SITE 1 AC6 4 SER A 229 LYS A 234 MET A 236 DC T 7 SITE 1 AC7 4 LEU A 270 THR A 273 GLY A 274 ARG A 333 SITE 1 AC8 6 ARG A 152 MET A 155 PHE A 181 ALA A 185 SITE 2 AC8 6 SER A 187 SER A 188 SITE 1 AC9 1 GLU A 117 SITE 1 BC1 1 LEU A 132 CRYST1 56.779 77.114 116.653 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 0.017612 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012968 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008572 0.00000