HEADER TRANSFERASE/DNA 27-AUG-13 4MFF TITLE STRUCTURE OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH O6MG IN THE TITLE 2 TEMPLATE BASE PAIRED WITH INCOMING NON-HYDROLYZABLE TTP 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: TEMPLATE; COMPND 8 CHAIN: T; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: UP PRIMER; COMPND 12 CHAIN: P; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: DN PRIMER; COMPND 16 CHAIN: D; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: POLB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 OTHER_DETAILS: SYNTHETIC TEMPLATE; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: SYNTHETIC UP PRIMER; SOURCE 14 MOL_ID: 4; SOURCE 15 SYNTHETIC: YES; SOURCE 16 OTHER_DETAILS: SYNTHETIC DN PRIMER KEYWDS DNA POLYMERASE X FAMILY, DNA SYNTHESIS, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.C.KOAG,K.MIN,A.F.MONZINGO,S.LEE REVDAT 3 28-FEB-24 4MFF 1 REMARK LINK REVDAT 2 02-JUL-14 4MFF 1 JRNL REVDAT 1 16-APR-14 4MFF 0 JRNL AUTH M.C.KOAG,S.LEE JRNL TITL METAL-DEPENDENT CONFORMATIONAL ACTIVATION EXPLAINS HIGHLY JRNL TITL 2 PROMUTAGENIC REPLICATION ACROSS O6-METHYLGUANINE BY HUMAN JRNL TITL 3 DNA POLYMERASE BETA. JRNL REF J.AM.CHEM.SOC. V. 136 5709 2014 JRNL REFN ISSN 0002-7863 JRNL PMID 24694247 JRNL DOI 10.1021/JA500172D REMARK 2 REMARK 2 RESOLUTION. 2.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 13877 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) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.294 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 695 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) : 2.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.62 REMARK 3 REFLECTION IN BIN (WORKING SET) : 866 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.90 REMARK 3 BIN R VALUE (WORKING SET) : 0.3360 REMARK 3 BIN FREE R VALUE SET COUNT : 42 REMARK 3 BIN FREE R VALUE : 0.3630 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2559 REMARK 3 NUCLEIC ACID ATOMS : 633 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 51 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.44000 REMARK 3 B22 (A**2) : -0.04000 REMARK 3 B33 (A**2) : -0.14000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.47000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 4.417 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.388 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.273 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.781 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.899 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.816 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3350 ; 0.011 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4646 ; 1.617 ; 1.852 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 320 ; 6.015 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 120 ;36.613 ;24.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 493 ;18.357 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;12.987 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 483 ; 0.100 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2281 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4MFF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-AUG-13. REMARK 100 THE DEPOSITION ID IS D_1000081842. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14547 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : NULL 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14% - 23% PEG3400, AND 350 MM SODIUM REMARK 280 ACETATE , PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 39.41950 REMARK 290 SMTRY3 2 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -59.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P, D 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 205 REMARK 465 LYS A 206 REMARK 465 GLN A 207 REMARK 465 ASN A 245 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 GLU A 203 CG CD OE1 OE2 REMARK 470 LYS A 244 CG CD CE NZ REMARK 470 ASP A 246 CG OD1 OD2 REMARK 470 GLU A 247 CG CD OE1 OE2 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 CD LYS A 27 O HOH A 504 2.17 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 MG MG A 402 O HOH A 510 1655 1.68 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 HIS A 34 CG HIS A 34 CD2 0.060 REMARK 500 HIS A 135 CG HIS A 135 CD2 0.059 REMARK 500 HIS A 212 CG HIS A 212 CD2 0.056 REMARK 500 DG D 1 P DG D 1 OP3 -0.108 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 6OG T 6 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 DT T 12 O5' - P - OP1 ANGL. DEV. = -5.8 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 PRO A 50 43.68 -91.76 REMARK 500 GLU A 129 -34.73 -34.17 REMARK 500 LYS A 141 -47.42 -29.44 REMARK 500 ASP A 170 116.81 -170.26 REMARK 500 CYS A 178 -143.15 -100.60 REMARK 500 GLU A 247 154.76 -39.82 REMARK 500 ASN A 294 -166.00 -114.35 REMARK 500 LYS A 317 -36.82 -38.49 REMARK 500 ASP A 321 -72.32 -56.84 REMARK 500 TYR A 322 -49.00 -18.14 REMARK 500 ARG A 333 30.35 -99.87 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 D 101 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 60 O REMARK 620 2 VAL A 65 O 70.1 REMARK 620 3 DC D 3 OP1 123.3 79.5 REMARK 620 4 DC D 3 OP2 153.2 83.2 51.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 403 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 101 O REMARK 620 2 VAL A 103 O 92.3 REMARK 620 3 ILE A 106 O 104.1 91.4 REMARK 620 4 DG P 9 OP1 152.0 102.8 99.0 REMARK 620 5 HOH P 101 O 86.2 93.9 168.3 69.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 190 OD1 REMARK 620 2 1FZ A 404 O2B 175.4 REMARK 620 3 1FZ A 404 O1G 94.7 82.6 REMARK 620 4 1FZ A 404 O1A 100.1 75.7 78.0 REMARK 620 5 HOH A 538 O 80.7 100.4 159.2 82.8 REMARK 620 6 HOH A 539 O 102.3 80.9 77.4 147.9 123.4 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1FZ A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA D 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ISB RELATED DB: PDB REMARK 900 RELATED ID: 1BPX RELATED DB: PDB REMARK 900 RELATED ID: 4MF2 RELATED DB: PDB REMARK 900 RELATED ID: 4MF8 RELATED DB: PDB REMARK 900 RELATED ID: 4MFA RELATED DB: PDB REMARK 900 RELATED ID: 4MFC RELATED DB: PDB DBREF 4MFF A 11 335 UNP P06746 DPOLB_HUMAN 11 335 DBREF 4MFF T 1 16 PDB 4MFF 4MFF 1 16 DBREF 4MFF P 1 10 PDB 4MFF 4MFF 1 10 DBREF 4MFF D 1 5 PDB 4MFF 4MFF 1 5 SEQRES 1 A 325 LEU ASN GLY GLY ILE THR ASP MET LEU THR GLU LEU ALA SEQRES 2 A 325 ASN PHE GLU LYS ASN VAL SER GLN ALA ILE HIS LYS TYR SEQRES 3 A 325 ASN ALA TYR ARG LYS ALA ALA SER VAL ILE ALA LYS TYR SEQRES 4 A 325 PRO HIS LYS ILE LYS SER GLY ALA GLU ALA LYS LYS LEU SEQRES 5 A 325 PRO GLY VAL GLY THR LYS ILE ALA GLU LYS ILE ASP GLU SEQRES 6 A 325 PHE LEU ALA THR GLY LYS LEU ARG LYS LEU GLU LYS ILE SEQRES 7 A 325 ARG GLN ASP ASP THR SER SER SER ILE ASN PHE LEU THR SEQRES 8 A 325 ARG VAL SER GLY ILE GLY PRO SER ALA ALA ARG LYS PHE SEQRES 9 A 325 VAL ASP GLU GLY ILE LYS THR LEU GLU ASP LEU ARG LYS SEQRES 10 A 325 ASN GLU ASP LYS LEU ASN HIS HIS GLN ARG ILE GLY LEU SEQRES 11 A 325 LYS TYR PHE GLY ASP PHE GLU LYS ARG ILE PRO ARG GLU SEQRES 12 A 325 GLU MET LEU GLN MET GLN ASP ILE VAL LEU ASN GLU VAL SEQRES 13 A 325 LYS LYS VAL ASP SER GLU TYR ILE ALA THR VAL CYS GLY SEQRES 14 A 325 SER PHE ARG ARG GLY ALA GLU SER SER GLY ASP MET ASP SEQRES 15 A 325 VAL LEU LEU THR HIS PRO SER PHE THR SER GLU SER THR SEQRES 16 A 325 LYS GLN PRO LYS LEU LEU HIS GLN VAL VAL GLU GLN LEU SEQRES 17 A 325 GLN LYS VAL HIS PHE ILE THR ASP THR LEU SER LYS GLY SEQRES 18 A 325 GLU THR LYS PHE MET GLY VAL CYS GLN LEU PRO SER LYS SEQRES 19 A 325 ASN ASP GLU LYS GLU TYR PRO HIS ARG ARG ILE ASP ILE SEQRES 20 A 325 ARG LEU ILE PRO LYS ASP GLN TYR TYR CYS GLY VAL LEU SEQRES 21 A 325 TYR PHE THR GLY SER ASP ILE PHE ASN LYS ASN MET ARG SEQRES 22 A 325 ALA HIS ALA LEU GLU LYS GLY PHE THR ILE ASN GLU TYR SEQRES 23 A 325 THR ILE ARG PRO LEU GLY VAL THR GLY VAL ALA GLY GLU SEQRES 24 A 325 PRO LEU PRO VAL ASP SER GLU LYS ASP ILE PHE ASP TYR SEQRES 25 A 325 ILE GLN TRP LYS TYR ARG GLU PRO LYS ASP ARG SER GLU SEQRES 1 T 16 DC DC DG DA DC 6OG DT DC DG DC DA DT DC SEQRES 2 T 16 DA DG DC SEQRES 1 P 10 DG DC DT DG DA DT DG DC DG DA SEQRES 1 D 5 DG DT DC DG DG MODRES 4MFF 6OG T 6 DG 6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE HET 6OG T 6 23 HET MG A 401 1 HET MG A 402 1 HET NA A 403 1 HET 1FZ A 404 29 HET NA D 101 1 HETNAM 6OG 6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM 1FZ 5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY) HETNAM 2 1FZ PHOSPHORYL]AMINO}PHOSPHORYL]THYMIDINE FORMUL 2 6OG C11 H16 N5 O7 P FORMUL 5 MG 2(MG 2+) FORMUL 7 NA 2(NA 1+) FORMUL 8 1FZ C10 H18 N3 O13 P3 FORMUL 10 HOH *51(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 60 1 6 HELIX 4 4 GLY A 66 GLY A 80 1 15 HELIX 5 5 LEU A 82 GLN A 90 1 9 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 GLY A 144 LYS A 148 5 5 HELIX 12 12 ARG A 152 ASP A 170 1 19 HELIX 13 13 CYS A 178 GLY A 184 1 7 HELIX 14 14 LEU A 211 VAL A 221 1 11 HELIX 15 15 PRO A 261 PHE A 272 1 12 HELIX 16 16 SER A 275 LYS A 289 1 15 HELIX 17 17 SER A 315 ILE A 323 1 9 HELIX 18 18 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 THR A 196 N ILE A 174 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 O3' DC T 5 P 6OG T 6 1555 1555 1.61 LINK O3' 6OG T 6 P DT T 7 1555 1555 1.60 LINK O SER A 30 MG MG A 402 1555 1555 2.42 LINK O LYS A 60 NA NA D 101 1555 1555 2.68 LINK O VAL A 65 NA NA D 101 1555 1555 2.88 LINK O THR A 101 NA NA A 403 1555 1555 2.31 LINK O VAL A 103 NA NA A 403 1555 1555 2.35 LINK O ILE A 106 NA NA A 403 1555 1555 2.02 LINK OD1 ASP A 190 MG MG A 401 1555 1555 2.14 LINK MG MG A 401 O2B 1FZ A 404 1555 1555 2.05 LINK MG MG A 401 O1G 1FZ A 404 1555 1555 2.27 LINK MG MG A 401 O1A 1FZ A 404 1555 1555 2.35 LINK MG MG A 401 O HOH A 538 1555 1555 2.44 LINK MG MG A 401 O HOH A 539 1555 1555 2.32 LINK NA NA A 403 OP1 DG P 9 1555 1555 2.42 LINK NA NA A 403 O HOH P 101 1555 1555 3.02 LINK OP1 DC D 3 NA NA D 101 1555 1555 2.90 LINK OP2 DC D 3 NA NA D 101 1555 1555 3.04 CISPEP 1 GLY A 274 SER A 275 0 -3.11 SITE 1 AC1 4 ASP A 190 1FZ A 404 HOH A 538 HOH A 539 SITE 1 AC2 4 SER A 30 GLN A 31 SER A 171 HOH A 510 SITE 1 AC3 5 THR A 101 VAL A 103 ILE A 106 DG P 9 SITE 2 AC3 5 HOH P 101 SITE 1 AC4 16 ARG A 149 GLY A 179 SER A 180 ARG A 183 SITE 2 AC4 16 SER A 188 GLY A 189 ASP A 190 TYR A 271 SITE 3 AC4 16 PHE A 272 THR A 273 GLY A 274 ASP A 276 SITE 4 AC4 16 ASN A 279 MG A 401 HOH A 539 DA P 10 SITE 1 AC5 3 LYS A 60 VAL A 65 DC D 3 CRYST1 54.546 78.839 54.751 90.00 105.95 90.00 P 1 21 1 2 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 0.018333 0.000000 0.005239 0.00000 SCALE2 0.000000 0.012684 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018996 0.00000