HEADER TRANSFERASE/DNA 11-SEP-16 5TBC TITLE PRECATALYTIC TERNARY COMPLEX OF HUMAN DNA POLYMERASE BETA WITH GAPPED TITLE 2 DNA SUBSTRATE, INCORPORATED (-)3TC-MP AND AN ANOTHER INCOMING (-)3TC- TITLE 3 TP NUCLEOTIDE. 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 8 25-OCT-23 5TBC 1 REMARK REVDAT 7 04-OCT-23 5TBC 1 REMARK REVDAT 6 01-FEB-23 5TBC 1 SPRSDE LINK REVDAT 5 27-NOV-19 5TBC 1 REMARK REVDAT 4 17-JUL-19 5TBC 1 COMPND HETNAM HETSYN REVDAT 3 13-SEP-17 5TBC 1 SPRSDE REVDAT 2 25-JAN-17 5TBC 1 JRNL REVDAT 1 11-JAN-17 5TBC 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. 1.85 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.76 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 36763 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) : 0.231 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1883 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2638 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.65 REMARK 3 BIN R VALUE (WORKING SET) : 0.3330 REMARK 3 BIN FREE R VALUE SET COUNT : 149 REMARK 3 BIN FREE R VALUE : 0.4070 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2354 REMARK 3 NUCLEIC ACID ATOMS : 632 REMARK 3 HETEROGEN ATOMS : 52 REMARK 3 SOLVENT ATOMS : 252 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.36000 REMARK 3 B22 (A**2) : 0.08000 REMARK 3 B33 (A**2) : -0.30000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.21000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.161 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.158 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.110 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.632 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.937 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.908 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3175 ; 0.007 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4359 ; 1.162 ; 1.831 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 287 ; 5.035 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 116 ;37.870 ;24.224 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 465 ;14.665 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;12.188 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 446 ; 0.070 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2113 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 706 ; 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): 1163 ; 1.575 ; 3.268 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1162 ; 1.576 ; 3.265 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1445 ; 2.700 ; 4.868 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1446 ; 2.699 ; 4.872 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1990 ; 1.730 ; 3.432 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1989 ; 1.730 ; 3.432 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2914 ; 2.833 ; 5.067 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3995 ; 4.973 ;27.379 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3870 ; 4.829 ;27.260 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 : NULL 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 REMARK 4 REMARK 4 5TBC 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_1000223987. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-APR-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 : 38657 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 32.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.68600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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 (%): 48.41 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 39.76500 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: 4830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -100.0 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 GLN A 207 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 VAL A 306 REMARK 465 ALA A 307 REMARK 465 GLY A 308 REMARK 465 GLU A 309 REMARK 465 PRO A 310 REMARK 465 LEU A 311 REMARK 465 PRO A 312 REMARK 465 ILE A 323 REMARK 465 GLN A 324 REMARK 465 TRP A 325 REMARK 465 LYS A 326 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 -0.115 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 6 C3' - O3' - P ANGL. DEV. = 7.6 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 21.12 -79.47 REMARK 500 CYS A 178 -143.02 -100.99 REMARK 500 SER A 202 -16.15 -42.79 REMARK 500 SER A 243 -156.54 -105.82 REMARK 500 LYS A 244 -152.24 -136.64 REMARK 500 ASP A 321 -121.83 40.57 REMARK 500 ASP A 332 47.46 -105.62 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 405 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 30 O REMARK 620 2 SER A 171 OG 41.5 REMARK 620 3 HOH A 554 O 172.5 130.9 REMARK 620 4 HOH A 591 O 101.4 131.1 84.7 REMARK 620 5 HOH A 623 O 86.2 57.9 88.2 171.1 REMARK 620 6 HOH A 639 O 87.1 66.7 89.0 85.0 100.3 REMARK 620 N 1 2 3 4 5 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 LYS A 60 O REMARK 620 2 LEU A 62 O 85.3 REMARK 620 3 VAL A 65 O 86.5 100.3 REMARK 620 4 HOH A 618 O 80.8 165.5 82.9 REMARK 620 5 HOH A 637 O 85.3 88.9 167.0 85.9 REMARK 620 6 DC D 3 OP1 170.3 104.4 91.2 89.6 95.3 REMARK 620 N 1 2 3 4 5 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 97.6 REMARK 620 3 ILE A 106 O 95.4 88.9 REMARK 620 4 HOH A 561 O 74.4 171.3 95.1 REMARK 620 5 HOH A 572 O 75.8 95.2 170.6 79.7 REMARK 620 6 DG P 9 OP1 161.4 96.9 96.4 90.4 91.4 REMARK 620 N 1 2 3 4 5 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 THR A 101 O REMARK 620 2 HOH A 561 O 74.3 REMARK 620 3 HOH A 572 O 75.3 79.8 REMARK 620 4 HOH A 611 O 86.6 102.2 160.6 REMARK 620 5 HOH A 659 O 106.0 175.6 96.0 82.2 REMARK 620 6 HOH A 669 O 168.1 94.7 98.8 100.2 84.6 REMARK 620 N 1 2 3 4 5 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 ASP A 190 OD1 REMARK 620 2 ASP A 190 OD2 57.8 REMARK 620 3 1RZ A 401 O3G 105.7 117.5 REMARK 620 4 1RZ A 401 O2B 153.9 148.2 64.3 REMARK 620 5 42E A 408 O1A 104.8 75.2 149.0 89.9 REMARK 620 6 HOH A 521 O 71.1 110.7 119.2 92.2 76.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA T 101 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC T 10 OP2 REMARK 620 2 HOH T 238 O 128.7 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 1RZ 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 NA 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 CL A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 42E A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA T 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5TBA RELATED DB: PDB REMARK 900 RELATED ID: 5TB8 RELATED DB: PDB REMARK 900 RELATED ID: 5TBB RELATED DB: PDB REMARK 900 RELATED ID: 5TB9 RELATED DB: PDB DBREF 5TBC A 1 335 UNP P06746 DPOLB_HUMAN 1 335 DBREF 5TBC D 1 5 PDB 5TBC 5TBC 1 5 DBREF 5TBC P 1 10 PDB 5TBC 5TBC 1 10 DBREF 5TBC T 1 16 PDB 5TBC 5TBC 1 16 SEQADV 5TBC MET A -1 UNP P06746 INITIATING METHIONINE SEQADV 5TBC GLY A 0 UNP P06746 EXPRESSION TAG SEQADV 5TBC HIS A 336 UNP P06746 EXPRESSION TAG SEQADV 5TBC HIS A 337 UNP P06746 EXPRESSION TAG SEQADV 5TBC HIS A 338 UNP P06746 EXPRESSION TAG SEQADV 5TBC HIS A 339 UNP P06746 EXPRESSION TAG SEQADV 5TBC HIS A 340 UNP P06746 EXPRESSION TAG SEQADV 5TBC 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 1RZ A 401 27 HET NA A 402 1 HET NA A 403 1 HET NA A 404 1 HET NA A 405 1 HET NA A 406 1 HET CL A 407 1 HET 42E A 408 18 HET NA T 101 1 HETNAM 1RZ LAMIVUDINE TRIPHOSPHATE HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM 42E [(2R,5S)-5-(4-AMINO-2-OXOPYRIMIDIN-1(2H)-YL)-1,3- HETNAM 2 42E OXATHIOLAN-2-YL]METHYL DIHYDROGEN PHOSPHATE HETSYN 1RZ LAMIVUDINE-5'-TRIPHOSPHATE; 3TC TRIPHOSPHATE; [[(2R, HETSYN 2 1RZ 5S)-5-(4-AZANYL-2-OXIDANYLIDENE-PYRIMIDIN-1-YL)-1,3- HETSYN 3 1RZ OXATHIOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] PHOSPHONO HETSYN 4 1RZ HYDROGEN PHOSPHATE HETSYN 42E 3TC-MP FORMUL 5 1RZ C8 H14 N3 O12 P3 S FORMUL 6 NA 6(NA 1+) FORMUL 11 CL CL 1- FORMUL 12 42E C8 H12 N3 O6 P S FORMUL 14 HOH *252(H2 O) HELIX 1 AA1 ASN A 12 VAL A 29 1 18 HELIX 2 AA2 ALA A 32 LYS A 48 1 17 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 LYS A 127 1 7 HELIX 9 AA9 ASN A 128 LEU A 132 5 5 HELIX 10 AB1 ASN A 133 TYR A 142 1 10 HELIX 11 AB2 TYR A 142 GLU A 147 1 6 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 ASP A 263 5 3 HELIX 16 AB7 GLN A 264 GLY A 274 1 11 HELIX 17 AB8 SER A 275 ARG A 283 1 9 HELIX 18 AB9 SER A 315 ASP A 321 1 7 HELIX 19 AC1 GLU A 329 ARG A 333 5 5 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 CYS A 239 O ARG A 253 SHEET 5 AA2 5 ILE A 224 LYS A 230 -1 N SER A 229 O MET A 236 LINK PA 42E A 408 O3' DC P 10 1555 1555 1.50 LINK O SER A 30 NA NA A 405 1555 1555 2.26 LINK O LYS A 60 NA NA A 404 1555 1555 2.29 LINK O LEU A 62 NA NA A 404 1555 1555 2.25 LINK O VAL A 65 NA NA A 404 1555 1555 2.25 LINK O THR A 101 NA NA A 403 1555 1555 2.26 LINK O THR A 101 NA NA A 406 1555 1555 2.28 LINK O VAL A 103 NA NA A 403 1555 1555 2.30 LINK O ILE A 106 NA NA A 403 1555 1555 2.27 LINK OG SER A 171 NA NA A 405 1555 1655 2.38 LINK OD1 ASP A 190 NA NA A 402 1555 1555 2.25 LINK OD2 ASP A 190 NA NA A 402 1555 1555 2.26 LINK O3G 1RZ A 401 NA NA A 402 1555 1555 2.25 LINK O2B 1RZ A 401 NA NA A 402 1555 1555 2.25 LINK NA NA A 402 O1A 42E A 408 1555 1555 2.54 LINK NA NA A 402 O HOH A 521 1555 1555 2.24 LINK NA NA A 403 O HOH A 561 1555 1555 2.27 LINK NA NA A 403 O HOH A 572 1555 1555 2.26 LINK NA NA A 403 OP1 DG P 9 1555 1555 2.27 LINK NA NA A 404 O HOH A 618 1555 1555 2.26 LINK NA NA A 404 O HOH A 637 1555 1555 2.25 LINK NA NA A 404 OP1 DC D 3 1555 1555 2.31 LINK NA NA A 405 O HOH A 554 1555 1455 2.44 LINK NA NA A 405 O HOH A 591 1555 1455 2.48 LINK NA NA A 405 O HOH A 623 1555 1555 2.25 LINK NA NA A 405 O HOH A 639 1555 1555 2.26 LINK NA NA A 406 O HOH A 561 1555 1555 2.26 LINK NA NA A 406 O HOH A 572 1555 1555 2.27 LINK NA NA A 406 O HOH A 611 1555 1555 2.26 LINK NA NA A 406 O HOH A 659 1555 1555 2.25 LINK NA NA A 406 O HOH A 669 1555 1555 2.25 LINK OP2 DC T 10 NA NA T 101 1555 1555 2.25 LINK NA NA T 101 O HOH T 238 1555 1555 2.24 CISPEP 1 GLY A 274 SER A 275 0 -0.91 SITE 1 AC1 17 ARG A 149 GLY A 179 SER A 180 ARG A 183 SITE 2 AC1 17 SER A 188 GLY A 189 ASP A 190 TYR A 271 SITE 3 AC1 17 PHE A 272 THR A 273 GLY A 274 ASP A 276 SITE 4 AC1 17 NA A 402 42E A 408 HOH A 514 HOH A 627 SITE 5 AC1 17 HOH A 629 SITE 1 AC2 4 ASP A 190 1RZ A 401 42E A 408 HOH A 521 SITE 1 AC3 7 THR A 101 VAL A 103 ILE A 106 NA A 406 SITE 2 AC3 7 HOH A 561 HOH A 572 DG P 9 SITE 1 AC4 6 LYS A 60 LEU A 62 VAL A 65 HOH A 618 SITE 2 AC4 6 HOH A 637 DC D 3 SITE 1 AC5 6 SER A 30 SER A 171 HOH A 554 HOH A 591 SITE 2 AC5 6 HOH A 623 HOH A 639 SITE 1 AC6 7 THR A 101 NA A 403 HOH A 561 HOH A 572 SITE 2 AC6 7 HOH A 611 HOH A 659 HOH A 669 SITE 1 AC7 6 ALA A 32 ILE A 33 HIS A 34 LYS A 35 SITE 2 AC7 6 HOH A 663 HOH D 108 SITE 1 AC8 8 ASP A 190 ARG A 258 1RZ A 401 NA A 402 SITE 2 AC8 8 HOH A 521 DC P 10 DG T 6 DG T 7 SITE 1 AC9 3 DG T 9 DC T 10 HOH T 238 CRYST1 55.330 79.530 55.330 90.00 107.39 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 0.018073 0.000000 0.005660 0.00000 SCALE2 0.000000 0.012574 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018939 0.00000