PDB Short entry for 3H4D HEADER REPLICATION/DNA 18-APR-09 3H4D TITLE TERNARY COMPLEX OF HUMAN DNA POLYMERASE IOTA WITH TEMPLATE U/T AND TITLE 2 INCOMING DGTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE IOTA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: POLYMERASE IOTA; COMPND 5 SYNONYM: RAD30 HOMOLOG B, ETA2; COMPND 6 EC: 2.7.7.7; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 5'-D(*AP*GP*GP*AP*CP*CP*(DOC)); COMPND 10 CHAIN: P; COMPND 11 FRAGMENT: PRIMER DNA STRAND; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: PRIMER DNA STRAND; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: 5'-D(*TP*(BRU)P*GP*GP*GP*TP*CP*CP*T); COMPND 16 CHAIN: T; COMPND 17 FRAGMENT: TEMPLATE DNA STRAND; COMPND 18 ENGINEERED: YES; COMPND 19 OTHER_DETAILS: TEMPLATE DNA STRAND SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: POLI, RAD30B; SOURCE 6 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4932; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 MOL_ID: 3; SOURCE 11 SYNTHETIC: YES KEYWDS DNA POLYMERASE IOTA, REPLICATION, DNA DAMAGE, DNA REPAIR, DNA KEYWDS 2 REPLICATION, DNA SYNTHESIS, DNA-BINDING, DNA-DIRECTED DNA KEYWDS 3 POLYMERASE, MAGNESIUM, METAL-BINDING, MUTATOR PROTEIN, KEYWDS 4 NUCLEOTIDYLTRANSFERASE, NUCLEUS, SCHIFF BASE, TRANSFERASE, KEYWDS 5 REPLICATION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.JAIN,D.T.NAIR,R.E.JOHNSON,L.PRAKASH,S.PRAKASH,A.K.AGGARWAL REVDAT 3 06-SEP-23 3H4D 1 REMARK LINK REVDAT 2 08-SEP-10 3H4D 1 JRNL REVDAT 1 21-JUL-09 3H4D 0 JRNL AUTH R.JAIN,D.T.NAIR,R.E.JOHNSON,L.PRAKASH,S.PRAKASH,A.K.AGGARWAL JRNL TITL REPLICATION ACROSS TEMPLATE T/U BY HUMAN DNA JRNL TITL 2 POLYMERASE-IOTA. JRNL REF STRUCTURE V. 17 974 2009 JRNL REFN ISSN 0969-2126 JRNL PMID 19604477 JRNL DOI 10.1016/J.STR.2009.04.011 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.68 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 54308.560 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 28795 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 SET) : 0.254 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2306 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4031 REMARK 3 BIN R VALUE (WORKING SET) : 0.2730 REMARK 3 BIN FREE R VALUE : 0.3010 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 381 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.015 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2838 REMARK 3 NUCLEIC ACID ATOMS : 320 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 272 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.63000 REMARK 3 B22 (A**2) : 1.63000 REMARK 3 B33 (A**2) : -3.26000 REMARK 3 B12 (A**2) : -0.80000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.32 REMARK 3 ESD FROM SIGMAA (A) : 0.23 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.36 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.26 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.100 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.430 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.410 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.250 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.300 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 50.52 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : LIG.PAR REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA_REP.TOP REMARK 3 TOPOLOGY FILE 3 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : LIG.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3H4D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-MAY-09. REMARK 100 THE DEPOSITION ID IS D_1000052676. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-AUG-06 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92017 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30091 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 14.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 31.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.43300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2ALZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10-15% PEG 5K MME, 0.2-0.4 M AMMONIUM REMARK 280 SULFATE, 0.1 M MES , PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 135.59467 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 67.79733 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 101.69600 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 33.89867 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 169.49333 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 135.59467 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 67.79733 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 33.89867 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 101.69600 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 169.49333 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: 5050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 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 LYS A 371 REMARK 465 LEU A 372 REMARK 465 GLY A 373 REMARK 465 THR A 374 REMARK 465 GLY A 375 REMARK 465 ASN A 376 REMARK 465 TYR A 377 REMARK 465 ASP A 378 REMARK 465 VAL A 395 REMARK 465 ASN A 396 REMARK 465 VAL A 397 REMARK 465 LYS A 398 REMARK 465 MET A 399 REMARK 465 PRO A 400 REMARK 465 PHE A 401 REMARK 465 HIS A 402 REMARK 465 LEU A 403 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 49 CG CD OE1 OE2 REMARK 470 LYS A 76 CG CD CE NZ REMARK 470 ARG A 82 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 146 CG OD1 OD2 REMARK 470 LYS A 245 CG CD CE NZ REMARK 470 LYS A 248 CD CE NZ REMARK 470 LYS A 267 CE NZ REMARK 470 LYS A 271 CG CD CE NZ REMARK 470 GLN A 279 CD OE1 NE2 REMARK 470 LYS A 309 CG CD CE NZ REMARK 470 LYS A 310 CD CE NZ REMARK 470 VAL A 315 CG1 CG2 REMARK 470 GLU A 316 CG CD OE1 OE2 REMARK 470 LYS A 318 CG CD CE NZ REMARK 470 LYS A 338 CG CD CE NZ REMARK 470 TYR A 349 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 SER A 350 OG REMARK 470 SER A 351 OG REMARK 470 GLU A 352 CG CD OE1 OE2 REMARK 470 LYS A 353 CG CD CE NZ REMARK 470 HIS A 354 CG ND1 CD2 CE1 NE2 REMARK 470 TYR A 355 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG A 357 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 367 CG ND1 CD2 CE1 NE2 REMARK 470 VAL A 379 CG1 CG2 REMARK 470 ILE A 386 CG1 CG2 CD1 REMARK 470 LYS A 389 CG CD CE NZ REMARK 470 LEU A 405 CG CD1 CD2 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 DG T 841 O4' - C1' - N9 ANGL. DEV. = 1.9 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 SER A 26 -72.43 -173.68 REMARK 500 CYS A 37 64.16 20.39 REMARK 500 LYS A 51 170.53 -58.67 REMARK 500 ASP A 52 -14.61 50.19 REMARK 500 LYS A 60 -120.89 58.58 REMARK 500 CYS A 88 73.91 -153.75 REMARK 500 PRO A 89 41.17 -62.66 REMARK 500 GLN A 90 -8.72 -157.39 REMARK 500 SER A 117 112.94 -174.15 REMARK 500 SER A 145 58.53 -64.51 REMARK 500 ASP A 146 -61.94 -169.19 REMARK 500 LYS A 245 -70.25 -65.12 REMARK 500 ALA A 252 -9.14 -53.41 REMARK 500 SER A 276 -75.42 -76.33 REMARK 500 ASP A 289 110.85 -165.33 REMARK 500 ASP A 306 97.92 -172.55 REMARK 500 LYS A 309 78.55 -44.09 REMARK 500 LYS A 310 48.99 25.84 REMARK 500 CYS A 311 74.13 -108.83 REMARK 500 GLU A 314 -9.30 76.14 REMARK 500 GLU A 316 -26.01 65.39 REMARK 500 CYS A 333 -81.97 -65.80 REMARK 500 GLN A 334 -52.75 -22.91 REMARK 500 SER A 350 -117.06 -177.78 REMARK 500 SER A 351 -144.58 -78.55 REMARK 500 GLU A 352 64.37 -101.74 REMARK 500 LYS A 353 91.08 -64.99 REMARK 500 TYR A 355 103.20 -169.30 REMARK 500 THR A 381 -60.77 -22.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DC P 871 0.06 SIDE CHAIN REMARK 500 DC P 872 0.07 SIDE CHAIN REMARK 500 DG T 842 0.07 SIDE CHAIN REMARK 500 DG T 843 0.07 SIDE CHAIN REMARK 500 DT T 844 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL 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 871 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 872 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DGT T 875 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3H40 RELATED DB: PDB REMARK 900 RELATED ID: 3H4B RELATED DB: PDB DBREF 3H4D A 25 414 UNP Q9UNA4 POLI_HUMAN 25 414 DBREF 3H4D T 839 847 PDB 3H4D 3H4D 839 847 DBREF 3H4D P 867 873 PDB 3H4D 3H4D 867 873 SEQRES 1 A 390 ALA SER SER ARG VAL ILE VAL HIS VAL ASP LEU ASP CYS SEQRES 2 A 390 PHE TYR ALA GLN VAL GLU MET ILE SER ASN PRO GLU LEU SEQRES 3 A 390 LYS ASP LYS PRO LEU GLY VAL GLN GLN LYS TYR LEU VAL SEQRES 4 A 390 VAL THR CYS ASN TYR GLU ALA ARG LYS LEU GLY VAL LYS SEQRES 5 A 390 LYS LEU MET ASN VAL ARG ASP ALA LYS GLU LYS CYS PRO SEQRES 6 A 390 GLN LEU VAL LEU VAL ASN GLY GLU ASP LEU THR ARG TYR SEQRES 7 A 390 ARG GLU MET SER TYR LYS VAL THR GLU LEU LEU GLU GLU SEQRES 8 A 390 PHE SER PRO VAL VAL GLU ARG LEU GLY PHE ASP GLU ASN SEQRES 9 A 390 PHE VAL ASP LEU THR GLU MET VAL GLU LYS ARG LEU GLN SEQRES 10 A 390 GLN LEU GLN SER ASP GLU LEU SER ALA VAL THR VAL SER SEQRES 11 A 390 GLY HIS VAL TYR ASN ASN GLN SER ILE ASN LEU LEU ASP SEQRES 12 A 390 VAL LEU HIS ILE ARG LEU LEU VAL GLY SER GLN ILE ALA SEQRES 13 A 390 ALA GLU MET ARG GLU ALA MET TYR ASN GLN LEU GLY LEU SEQRES 14 A 390 THR GLY CYS ALA GLY VAL ALA SER ASN LYS LEU LEU ALA SEQRES 15 A 390 LYS LEU VAL SER GLY VAL PHE LYS PRO ASN GLN GLN THR SEQRES 16 A 390 VAL LEU LEU PRO GLU SER CYS GLN HIS LEU ILE HIS SER SEQRES 17 A 390 LEU ASN HIS ILE LYS GLU ILE PRO GLY ILE GLY TYR LYS SEQRES 18 A 390 THR ALA LYS CYS LEU GLU ALA LEU GLY ILE ASN SER VAL SEQRES 19 A 390 ARG ASP LEU GLN THR PHE SER PRO LYS ILE LEU GLU LYS SEQRES 20 A 390 GLU LEU GLY ILE SER VAL ALA GLN ARG ILE GLN LYS LEU SEQRES 21 A 390 SER PHE GLY GLU ASP ASN SER PRO VAL ILE LEU SER GLY SEQRES 22 A 390 PRO PRO GLN SER PHE SER GLU GLU ASP SER PHE LYS LYS SEQRES 23 A 390 CYS SER SER GLU VAL GLU ALA LYS ASN LYS ILE GLU GLU SEQRES 24 A 390 LEU LEU ALA SER LEU LEU ASN ARG VAL CYS GLN ASP GLY SEQRES 25 A 390 ARG LYS PRO HIS THR VAL ARG LEU ILE ILE ARG ARG TYR SEQRES 26 A 390 SER SER GLU LYS HIS TYR GLY ARG GLU SER ARG GLN CYS SEQRES 27 A 390 PRO ILE PRO SER HIS VAL ILE GLN LYS LEU GLY THR GLY SEQRES 28 A 390 ASN TYR ASP VAL MET THR PRO MET VAL ASP ILE LEU MET SEQRES 29 A 390 LYS LEU PHE ARG ASN MET VAL ASN VAL LYS MET PRO PHE SEQRES 30 A 390 HIS LEU THR LEU LEU SER VAL CYS PHE CYS ASN LEU LYS SEQRES 1 P 7 DA DG DG DA DC DC DOC SEQRES 1 T 9 DT BRU DG DG DG DT DC DC DT MODRES 3H4D DOC P 873 DC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE MODRES 3H4D BRU T 840 DU HET DOC P 873 18 HET BRU T 840 40 HET MG A 871 1 HET MG A 872 1 HET DGT T 875 31 HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM BRU 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE FORMUL 2 DOC C9 H14 N3 O6 P FORMUL 3 BRU C9 H12 BR N2 O8 P FORMUL 4 MG 2(MG 2+) FORMUL 6 DGT C10 H16 N5 O13 P3 FORMUL 7 HOH *272(H2 O) HELIX 1 1 CYS A 37 ASN A 47 1 11 HELIX 2 2 PRO A 48 LYS A 51 5 4 HELIX 3 3 ASN A 67 LEU A 73 1 7 HELIX 4 4 VAL A 81 GLU A 86 1 6 HELIX 5 5 LEU A 99 SER A 117 1 19 HELIX 6 6 LEU A 132 LEU A 143 1 12 HELIX 7 8 ASN A 159 GLN A 161 5 3 HELIX 8 9 ASP A 167 GLY A 192 1 26 HELIX 9 10 ASN A 202 GLY A 211 1 10 HELIX 10 11 LEU A 222 GLU A 224 5 3 HELIX 11 12 SER A 225 SER A 232 1 8 HELIX 12 13 HIS A 235 ILE A 239 5 5 HELIX 13 14 GLY A 243 ALA A 252 1 10 HELIX 14 15 SER A 257 PHE A 264 1 8 HELIX 15 16 SER A 265 GLY A 274 1 10 HELIX 16 17 GLY A 274 PHE A 286 1 13 HELIX 17 18 LYS A 318 GLY A 336 1 19 HELIX 18 19 PRO A 365 GLN A 370 1 6 SHEET 1 A 6 VAL A 120 LEU A 123 0 SHEET 2 A 6 GLU A 127 ASP A 131 -1 O GLU A 127 N LEU A 123 SHEET 3 A 6 ILE A 30 LEU A 35 -1 N VAL A 33 O ASN A 128 SHEET 4 A 6 GLY A 195 ALA A 200 -1 O CYS A 196 N ASP A 34 SHEET 5 A 6 GLN A 218 VAL A 220 1 O THR A 219 N VAL A 199 SHEET 6 A 6 HIS A 156 VAL A 157 1 N HIS A 156 O GLN A 218 SHEET 1 B 4 MET A 79 ASN A 80 0 SHEET 2 B 4 LEU A 62 CYS A 66 -1 N VAL A 63 O MET A 79 SHEET 3 B 4 LEU A 55 GLN A 59 -1 N VAL A 57 O THR A 65 SHEET 4 B 4 VAL A 92 ASN A 95 1 O VAL A 94 N GLN A 58 SHEET 1 C 4 SER A 301 GLU A 304 0 SHEET 2 C 4 LEU A 406 LYS A 414 -1 O PHE A 410 N PHE A 302 SHEET 3 C 4 LYS A 338 ILE A 346 -1 N LYS A 338 O LYS A 414 SHEET 4 C 4 GLU A 358 PRO A 363 -1 O CYS A 362 N VAL A 342 LINK O3' DC P 872 P DOC P 873 1555 1555 1.61 LINK O3' DT T 839 P ABRU T 840 1555 1555 1.61 LINK O3' DT T 839 P BBRU T 840 1555 1555 1.61 LINK O3'ABRU T 840 P DG T 841 1555 1555 1.61 LINK O3'BBRU T 840 P DG T 841 1555 1555 1.61 SITE 1 AC1 5 ASP A 34 LEU A 35 ASP A 126 MG A 872 SITE 2 AC1 5 DGT T 875 SITE 1 AC2 6 ASP A 34 ASP A 126 GLU A 127 MG A 871 SITE 2 AC2 6 DOC P 873 DGT T 875 SITE 1 AC3 26 ASP A 34 LEU A 35 ASP A 36 CYS A 37 SITE 2 AC3 26 PHE A 38 TYR A 39 GLN A 59 VAL A 64 SITE 3 AC3 26 THR A 65 TYR A 68 ARG A 71 LYS A 77 SITE 4 AC3 26 ASP A 126 LYS A 214 HOH A 452 HOH A 475 SITE 5 AC3 26 HOH A 557 HOH A 577 MG A 871 MG A 872 SITE 6 AC3 26 DOC P 873 HOH T 19 HOH T 173 HOH T 234 SITE 7 AC3 26 BRU T 840 DG T 841 CRYST1 97.915 97.915 203.392 90.00 90.00 120.00 P 65 2 2 12 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 0.010213 0.005896 0.000000 0.00000 SCALE2 0.000000 0.011793 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004917 0.00000