PDB Short entry for 5TBB HEADER TRANSFERASE/DNA 11-SEP-16 5TBB TITLE POSTCATALYTIC TERNARY COMPLEX OF HUMAN DNA POLYMERASE BETA WITH GAPPED TITLE 2 DNA SUBSTRATE, INCORPORATED (-)FTC AND PPI. 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: 5-MER PHOSPHORYLATED DOWNSTREAM PRIMER; COMPND 8 CHAIN: D; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: SYNTHETIC DNA; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: 10- MER PRIMER; COMPND 13 CHAIN: P; COMPND 14 ENGINEERED: YES; COMPND 15 OTHER_DETAILS: SYNTHETIC DNA; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: 16- MER TEMPLATE; COMPND 18 CHAIN: T; COMPND 19 ENGINEERED: YES; COMPND 20 OTHER_DETAILS: SYNTHETIC DNA 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: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630; SOURCE 19 MOL_ID: 4; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 22 ORGANISM_TAXID: 32630 KEYWDS X-FAMILY, POL BETA, DNA POLYMERASE BETA, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.VYAS,Z.SUO REVDAT 7 25-OCT-23 5TBB 1 REMARK REVDAT 6 04-OCT-23 5TBB 1 REMARK REVDAT 5 01-FEB-23 5TBB 1 SPRSDE LINK REVDAT 4 27-NOV-19 5TBB 1 REMARK REVDAT 3 13-SEP-17 5TBB 1 SPRSDE REVDAT 2 25-JAN-17 5TBB 1 JRNL REVDAT 1 11-JAN-17 5TBB 0 JRNL AUTH A.J.REED,R.VYAS,A.T.RAPER,Z.SUO JRNL TITL STRUCTURAL INSIGHTS INTO THE POST-CHEMISTRY STEPS OF JRNL TITL 2 NUCLEOTIDE INCORPORATION CATALYZED BY A DNA POLYMERASE. JRNL REF J. AM. CHEM. SOC. V. 139 465 2017 JRNL REFN ESSN 1520-5126 JRNL PMID 27959534 JRNL DOI 10.1021/JACS.6B11258 REMARK 2 REMARK 2 RESOLUTION. 2.39 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 2.39 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 17190 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) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 968 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) : 2.39 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.45 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1251 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.3010 REMARK 3 BIN FREE R VALUE SET COUNT : 63 REMARK 3 BIN FREE R VALUE : 0.3880 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2368 REMARK 3 NUCLEIC ACID ATOMS : 632 REMARK 3 HETEROGEN ATOMS : 41 REMARK 3 SOLVENT ATOMS : 35 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.67 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.21000 REMARK 3 B22 (A**2) : 0.04000 REMARK 3 B33 (A**2) : 0.15000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.411 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.277 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.219 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.473 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.931 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.877 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3157 ; 0.012 ; 0.017 REMARK 3 BOND LENGTHS OTHERS (A): 2701 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4363 ; 1.535 ; 1.783 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6262 ; 0.926 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 291 ; 5.793 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 115 ;36.126 ;24.609 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 462 ;16.301 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ; 9.361 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 449 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3064 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 694 ; 0.001 ; 0.020 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): 1181 ; 3.116 ; 4.128 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1178 ; 3.088 ; 4.120 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1465 ; 4.914 ; 6.142 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1466 ; 4.916 ; 6.148 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1976 ; 3.395 ; 4.206 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1977 ; 3.394 ; 4.208 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2899 ; 5.055 ; 6.190 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3717 ; 7.263 ;32.803 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3712 ; 7.263 ;32.780 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 ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5TBB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1000223992. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-DEC-14 REMARK 200 TEMPERATURE (KELVIN) : 193 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97931 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18179 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.390 REMARK 200 RESOLUTION RANGE LOW (A) : 44.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.39 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.47400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4RQ7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM IMIDAZOLE, 350 MM SODIUM REMARK 280 ACETATE, 17% PEG3350, PH 8.0,, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 39.66500 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: 5240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -72.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, 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 -1 REMARK 465 GLY A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 LYS 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 465 GLU A 9 REMARK 465 THR A 205 REMARK 465 LYS A 206 REMARK 465 MET A 282 REMARK 465 ARG A 283 REMARK 465 ALA A 284 REMARK 465 HIS A 285 REMARK 465 ALA A 286 REMARK 465 LEU A 287 REMARK 465 GLU A 288 REMARK 465 LYS A 289 REMARK 465 GLY A 290 REMARK 465 PHE A 291 REMARK 465 THR A 292 REMARK 465 ILE A 293 REMARK 465 ILE A 298 REMARK 465 ARG A 299 REMARK 465 PRO A 300 REMARK 465 LEU A 301 REMARK 465 GLY A 302 REMARK 465 VAL A 303 REMARK 465 THR A 304 REMARK 465 GLY A 305 REMARK 465 ILE A 323 REMARK 465 GLN A 324 REMARK 465 TRP A 325 REMARK 465 LYS A 326 REMARK 465 TYR A 327 REMARK 465 ARG A 328 REMARK 465 SER A 334 REMARK 465 GLU A 335 REMARK 465 HIS A 336 REMARK 465 HIS A 337 REMARK 465 HIS A 338 REMARK 465 HIS A 339 REMARK 465 HIS A 340 REMARK 465 HIS A 341 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 DG D 1 P DG D 1 OP3 -0.124 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 190 CB - CG - OD1 ANGL. DEV. = 6.8 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 CYS A 178 -145.06 -94.19 REMARK 500 SER A 275 -174.38 -69.10 REMARK 500 GLU A 295 -40.53 -28.55 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 406 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 28 O REMARK 620 2 GLN A 31 OE1 121.5 REMARK 620 3 PRO A 108 O 104.1 87.5 REMARK 620 N 1 2 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 LYS A 60 O REMARK 620 2 LEU A 62 O 93.8 REMARK 620 3 VAL A 65 O 83.9 86.7 REMARK 620 4 DC D 3 OP1 166.2 84.9 82.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 101 O REMARK 620 2 VAL A 103 O 86.8 REMARK 620 3 ILE A 106 O 88.2 91.8 REMARK 620 4 ACT A 405 O 77.5 88.7 165.6 REMARK 620 5 DG P 9 OP1 163.5 98.8 107.0 87.1 REMARK 620 6 HOH P 201 O 83.8 168.5 94.6 82.7 88.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 401 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 190 OD1 REMARK 620 2 ASP A 192 OD2 103.0 REMARK 620 3 PPV A 407 O11 97.9 145.9 REMARK 620 4 43X P 101 O3A 106.8 91.4 108.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 404 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 190 OD2 REMARK 620 2 ASP A 192 OD1 92.2 REMARK 620 3 ASP A 192 OD2 90.3 46.4 REMARK 620 4 ASP A 256 OD2 90.1 70.8 117.2 REMARK 620 5 DC P 10 O3' 128.2 135.3 107.5 120.3 REMARK 620 6 43X P 101 O3A 97.0 106.9 61.2 172.7 56.1 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 MN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA 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 NA A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PPV A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 43X P 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5TBC RELATED DB: PDB REMARK 900 RELATED ID: 5TBA RELATED DB: PDB REMARK 900 RELATED ID: 5TB8 RELATED DB: PDB REMARK 900 RELATED ID: 5TB9 RELATED DB: PDB DBREF 5TBB A 1 335 UNP P06746 DPOLB_HUMAN 1 335 DBREF 5TBB D 1 5 PDB 5TBB 5TBB 1 5 DBREF 5TBB P 1 10 PDB 5TBB 5TBB 1 10 DBREF 5TBB T 1 16 PDB 5TBB 5TBB 1 16 SEQADV 5TBB MET A -1 UNP P06746 INITIATING METHIONINE SEQADV 5TBB GLY A 0 UNP P06746 EXPRESSION TAG SEQADV 5TBB HIS A 336 UNP P06746 EXPRESSION TAG SEQADV 5TBB HIS A 337 UNP P06746 EXPRESSION TAG SEQADV 5TBB HIS A 338 UNP P06746 EXPRESSION TAG SEQADV 5TBB HIS A 339 UNP P06746 EXPRESSION TAG SEQADV 5TBB HIS A 340 UNP P06746 EXPRESSION TAG SEQADV 5TBB HIS A 341 UNP P06746 EXPRESSION TAG SEQRES 1 A 343 MET GLY MET SER LYS ARG LYS ALA PRO GLN GLU THR LEU SEQRES 2 A 343 ASN GLY GLY ILE THR ASP MET LEU THR GLU LEU ALA ASN SEQRES 3 A 343 PHE GLU LYS ASN VAL SER GLN ALA ILE HIS LYS TYR ASN SEQRES 4 A 343 ALA TYR ARG LYS ALA ALA SER VAL ILE ALA LYS TYR PRO SEQRES 5 A 343 HIS LYS ILE LYS SER GLY ALA GLU ALA LYS LYS LEU PRO SEQRES 6 A 343 GLY VAL GLY THR LYS ILE ALA GLU LYS ILE ASP GLU PHE SEQRES 7 A 343 LEU ALA THR GLY LYS LEU ARG LYS LEU GLU LYS ILE ARG SEQRES 8 A 343 GLN ASP ASP THR SER SER SER ILE ASN PHE LEU THR ARG SEQRES 9 A 343 VAL SER GLY ILE GLY PRO SER ALA ALA ARG LYS PHE VAL SEQRES 10 A 343 ASP GLU GLY ILE LYS THR LEU GLU ASP LEU ARG LYS ASN SEQRES 11 A 343 GLU ASP LYS LEU ASN HIS HIS GLN ARG ILE GLY LEU LYS SEQRES 12 A 343 TYR PHE GLY ASP PHE GLU LYS ARG ILE PRO ARG GLU GLU SEQRES 13 A 343 MET LEU GLN MET GLN ASP ILE VAL LEU ASN GLU VAL LYS SEQRES 14 A 343 LYS VAL ASP SER GLU TYR ILE ALA THR VAL CYS GLY SER SEQRES 15 A 343 PHE ARG ARG GLY ALA GLU SER SER GLY ASP MET ASP VAL SEQRES 16 A 343 LEU LEU THR HIS PRO SER PHE THR SER GLU SER THR LYS SEQRES 17 A 343 GLN PRO LYS LEU LEU HIS GLN VAL VAL GLU GLN LEU GLN SEQRES 18 A 343 LYS VAL HIS PHE ILE THR ASP THR LEU SER LYS GLY GLU SEQRES 19 A 343 THR LYS PHE MET GLY VAL CYS GLN LEU PRO SER LYS ASN SEQRES 20 A 343 ASP GLU LYS GLU TYR PRO HIS ARG ARG ILE ASP ILE ARG SEQRES 21 A 343 LEU ILE PRO LYS ASP GLN TYR TYR CYS GLY VAL LEU TYR SEQRES 22 A 343 PHE THR GLY SER ASP ILE PHE ASN LYS ASN MET ARG ALA SEQRES 23 A 343 HIS ALA LEU GLU LYS GLY PHE THR ILE ASN GLU TYR THR SEQRES 24 A 343 ILE ARG PRO LEU GLY VAL THR GLY VAL ALA GLY GLU PRO SEQRES 25 A 343 LEU PRO VAL ASP SER GLU LYS ASP ILE PHE ASP TYR ILE SEQRES 26 A 343 GLN TRP LYS TYR ARG GLU PRO LYS ASP ARG SER GLU HIS SEQRES 27 A 343 HIS HIS HIS HIS HIS SEQRES 1 D 5 DG DT DC DG DG SEQRES 1 P 10 DG DC DT DG DA DT DG DC DG DC SEQRES 1 T 16 DC DC DG DA DC DG DG DC DG DC DA DT DC SEQRES 2 T 16 DA DG DC HET MN A 401 1 HET NA A 402 1 HET NA A 403 1 HET NA A 404 1 HET ACT A 405 4 HET NA A 406 1 HET PPV A 407 9 HET ACT A 408 4 HET 43X P 101 19 HETNAM MN MANGANESE (II) ION HETNAM NA SODIUM ION HETNAM ACT ACETATE ION HETNAM PPV PYROPHOSPHATE HETNAM 43X [(2R,5S)-5-(4-AMINO-5-FLUORO-2-OXOPYRIMIDIN-1(2H)-YL)- HETNAM 2 43X 1,3-OXATHIOLAN-2-YL]METHYL DIHYDROGEN PHOSPHATE HETSYN 43X FTC-MP FORMUL 5 MN MN 2+ FORMUL 6 NA 4(NA 1+) FORMUL 9 ACT 2(C2 H3 O2 1-) FORMUL 11 PPV H4 O7 P2 FORMUL 13 43X C8 H11 F N3 O6 P S FORMUL 14 HOH *35(H2 O) HELIX 1 AA1 ASN A 12 VAL A 29 1 18 HELIX 2 AA2 ALA A 32 TYR A 49 1 18 HELIX 3 AA3 SER A 55 LYS A 61 1 7 HELIX 4 AA4 GLY A 66 GLY A 80 1 15 HELIX 5 AA5 LEU A 82 ASP A 91 1 10 HELIX 6 AA6 ASP A 91 THR A 101 1 11 HELIX 7 AA7 GLY A 107 GLU A 117 1 11 HELIX 8 AA8 THR A 121 ASN A 128 1 8 HELIX 9 AA9 GLU A 129 LEU A 132 5 4 HELIX 10 AB1 ASN A 133 TYR A 142 1 10 HELIX 11 AB2 TYR A 142 LYS A 148 1 7 HELIX 12 AB3 ARG A 152 ASP A 170 1 19 HELIX 13 AB4 CYS A 178 ARG A 183 1 6 HELIX 14 AB5 LYS A 209 VAL A 221 1 13 HELIX 15 AB6 PRO A 261 GLY A 274 1 14 HELIX 16 AB7 SER A 275 LYS A 280 1 6 HELIX 17 AB8 SER A 315 TYR A 322 1 8 SHEET 1 AA1 2 ILE A 150 PRO A 151 0 SHEET 2 AA1 2 SER A 187 SER A 188 -1 O SER A 188 N ILE A 150 SHEET 1 AA2 5 ILE A 174 VAL A 177 0 SHEET 2 AA2 5 MET A 191 THR A 196 -1 O LEU A 194 N THR A 176 SHEET 3 AA2 5 ARG A 253 LEU A 259 1 O ARG A 258 N LEU A 195 SHEET 4 AA2 5 LYS A 234 CYS A 239 -1 N PHE A 235 O ILE A 257 SHEET 5 AA2 5 ILE A 224 LYS A 230 -1 N SER A 229 O MET A 236 LINK O3' DC P 10 PA 43X P 101 1555 1555 1.53 LINK O ASN A 28 NA NA A 406 1555 1555 2.60 LINK OE1 GLN A 31 NA NA A 406 1555 1555 2.60 LINK O LYS A 60 NA NA A 403 1555 1555 2.36 LINK O LEU A 62 NA NA A 403 1555 1555 2.57 LINK O VAL A 65 NA NA A 403 1555 1555 2.39 LINK O THR A 101 NA NA A 402 1555 1555 2.24 LINK O VAL A 103 NA NA A 402 1555 1555 2.47 LINK O ILE A 106 NA NA A 402 1555 1555 2.43 LINK O PRO A 108 NA NA A 406 1555 1555 2.72 LINK OD1 ASP A 190 MN MN A 401 1555 1555 1.95 LINK OD2 ASP A 190 NA NA A 404 1555 1555 2.23 LINK OD2 ASP A 192 MN MN A 401 1555 1555 1.95 LINK OD1 ASP A 192 NA NA A 404 1555 1555 2.23 LINK OD2 ASP A 192 NA NA A 404 1555 1555 3.04 LINK OD2 ASP A 256 NA NA A 404 1555 1555 2.25 LINK MN MN A 401 O11 PPV A 407 1555 1555 1.93 LINK MN MN A 401 O3A 43X P 101 1555 1555 1.93 LINK NA NA A 402 O ACT A 405 1555 1555 2.67 LINK NA NA A 402 OP1 DG P 9 1555 1555 2.30 LINK NA NA A 402 O HOH P 201 1555 1555 2.38 LINK NA NA A 403 OP1 DC D 3 1555 1555 2.91 LINK NA NA A 404 O3' DC P 10 1555 1555 2.92 LINK NA NA A 404 O3A 43X P 101 1555 1555 2.25 CISPEP 1 GLY A 274 SER A 275 0 2.51 SITE 1 AC1 5 ASP A 190 ASP A 192 NA A 404 PPV A 407 SITE 2 AC1 5 43X P 101 SITE 1 AC2 6 THR A 101 VAL A 103 ILE A 106 ACT A 405 SITE 2 AC2 6 DG P 9 HOH P 201 SITE 1 AC3 4 LYS A 60 LEU A 62 VAL A 65 DC D 3 SITE 1 AC4 6 ASP A 190 ASP A 192 ASP A 256 MN A 401 SITE 2 AC4 6 DC P 10 43X P 101 SITE 1 AC5 8 THR A 101 ARG A 102 VAL A 103 SER A 104 SITE 2 AC5 8 NA A 402 HOH A 506 DG P 9 DC P 10 SITE 1 AC6 5 ASN A 28 VAL A 29 GLN A 31 PRO A 108 SITE 2 AC6 5 ARG A 112 SITE 1 AC7 8 ARG A 149 GLY A 179 SER A 180 ARG A 183 SITE 2 AC7 8 GLY A 189 ASP A 190 MN A 401 43X P 101 SITE 1 AC8 3 PHE A 320 ASP A 321 TYR A 322 SITE 1 AC9 10 ASP A 190 ASP A 192 ARG A 258 TYR A 271 SITE 2 AC9 10 MN A 401 NA A 404 PPV A 407 DC P 10 SITE 3 AC9 10 DG T 6 DG T 7 CRYST1 55.170 79.330 55.460 90.00 107.20 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 0.018126 0.000000 0.005611 0.00000 SCALE2 0.000000 0.012606 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018875 0.00000