HEADER TRANSFERASE/DNA 27-MAR-12 4ED8
TITLE HUMAN DNA POLYMERASE ETA - DNA TERNARY COMPLEX: REACTION IN THE TG
TITLE 2 CRYSTAL AT PH 7.0, NORMAL TRANSLOCATION
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA POLYMERASE ETA;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: CATALYTIC CORE (UNP RESIDUES 1-432);
COMPND 5 SYNONYM: RAD30 HOMOLOG A, XERODERMA PIGMENTOSUM VARIANT TYPE PROTEIN;
COMPND 6 EC: 2.7.7.7;
COMPND 7 ENGINEERED: YES;
COMPND 8 MOL_ID: 2;
COMPND 9 MOLECULE: DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*G)-3');
COMPND 10 CHAIN: T;
COMPND 11 ENGINEERED: YES;
COMPND 12 MOL_ID: 3;
COMPND 13 MOLECULE: DNA (5'-D(*TP*GP*CP*GP*TP*CP*AP*TP*A)-3');
COMPND 14 CHAIN: P;
COMPND 15 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: POLH, RAD30, RAD30A, XPV;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28;
SOURCE 11 MOL_ID: 2;
SOURCE 12 SYNTHETIC: YES;
SOURCE 13 MOL_ID: 3;
SOURCE 14 SYNTHETIC: YES
KEYWDS TRANSFERASE-DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR T.NAKAMURA,Y.ZHAO,W.YANG
REVDAT 3 20-MAR-24 4ED8 1 REMARK SEQADV LINK
REVDAT 2 25-JUL-12 4ED8 1 JRNL
REVDAT 1 11-JUL-12 4ED8 0
JRNL AUTH T.NAKAMURA,Y.ZHAO,Y.YAMAGATA,Y.J.HUA,W.YANG
JRNL TITL WATCHING DNA POLYMERASE ETA MAKE A PHOSPHODIESTER BOND
JRNL REF NATURE V. 487 196 2012
JRNL REFN ISSN 0028-0836
JRNL PMID 22785315
JRNL DOI 10.1038/NATURE11181
REMARK 2
REMARK 2 RESOLUTION. 1.52 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.1_357)
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.52
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.52
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360
REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0
REMARK 3 NUMBER OF REFLECTIONS : 67241
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.173
REMARK 3 R VALUE (WORKING SET) : 0.171
REMARK 3 FREE R VALUE : 0.200
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050
REMARK 3 FREE R VALUE TEST SET COUNT : 3397
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 28.5221 - 4.3821 0.97 2777 141 0.1643 0.1795
REMARK 3 2 4.3821 - 3.4802 1.00 2753 181 0.1415 0.1732
REMARK 3 3 3.4802 - 3.0408 1.00 2776 144 0.1585 0.1865
REMARK 3 4 3.0408 - 2.7631 1.00 2790 140 0.1777 0.2150
REMARK 3 5 2.7631 - 2.5652 0.99 2748 145 0.1707 0.1947
REMARK 3 6 2.5652 - 2.4140 0.99 2765 137 0.1724 0.1920
REMARK 3 7 2.4140 - 2.2932 0.99 2738 140 0.1602 0.1847
REMARK 3 8 2.2932 - 2.1934 0.99 2738 167 0.1552 0.2026
REMARK 3 9 2.1934 - 2.1090 0.99 2717 147 0.1590 0.1952
REMARK 3 10 2.1090 - 2.0362 0.98 2754 150 0.1621 0.1947
REMARK 3 11 2.0362 - 1.9726 0.99 2722 152 0.1617 0.2123
REMARK 3 12 1.9726 - 1.9162 0.99 2731 140 0.1656 0.2143
REMARK 3 13 1.9162 - 1.8658 0.98 2709 132 0.1723 0.2096
REMARK 3 14 1.8658 - 1.8202 0.98 2770 139 0.1806 0.2017
REMARK 3 15 1.8202 - 1.7789 0.98 2680 157 0.1813 0.2293
REMARK 3 16 1.7789 - 1.7410 0.98 2716 137 0.1890 0.2398
REMARK 3 17 1.7410 - 1.7062 0.98 2706 141 0.1883 0.2060
REMARK 3 18 1.7062 - 1.6740 0.98 2640 160 0.1944 0.2375
REMARK 3 19 1.6740 - 1.6441 0.98 2694 156 0.2014 0.2194
REMARK 3 20 1.6441 - 1.6162 0.98 2697 154 0.2057 0.2350
REMARK 3 21 1.6162 - 1.5902 0.96 2685 117 0.2254 0.2497
REMARK 3 22 1.5902 - 1.5657 0.93 2572 118 0.2291 0.2552
REMARK 3 23 1.5657 - 1.5427 0.80 2227 118 0.2390 0.2831
REMARK 3 24 1.5427 - 1.5210 0.63 1739 84 0.2544 0.2674
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : 0.34
REMARK 3 B_SOL : 42.00
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.180
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 15.60
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.41
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -1.59060
REMARK 3 B22 (A**2) : -1.59060
REMARK 3 B33 (A**2) : 3.18110
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.023 3996
REMARK 3 ANGLE : 1.133 5476
REMARK 3 CHIRALITY : 0.066 613
REMARK 3 PLANARITY : 0.005 629
REMARK 3 DIHEDRAL : 17.904 1559
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 6
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: ( CHAIN A AND ( RESID -2:15 OR RESID 88:239 ) )
REMARK 3 ORIGIN FOR THE GROUP (A): 67.1441 -4.7428 -1.6629
REMARK 3 T TENSOR
REMARK 3 T11: 0.0807 T22: 0.0571
REMARK 3 T33: 0.0864 T12: 0.0052
REMARK 3 T13: 0.0003 T23: 0.0197
REMARK 3 L TENSOR
REMARK 3 L11: 0.9302 L22: 1.5677
REMARK 3 L33: 0.7600 L12: -0.5991
REMARK 3 L13: -0.0271 L23: -0.2931
REMARK 3 S TENSOR
REMARK 3 S11: 0.0260 S12: 0.0413 S13: 0.0155
REMARK 3 S21: -0.0806 S22: -0.0893 S23: -0.2398
REMARK 3 S31: 0.0420 S32: 0.0585 S33: 0.0698
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: ( CHAIN A AND RESID 16:87 )
REMARK 3 ORIGIN FOR THE GROUP (A): 48.7041 13.4468 11.4125
REMARK 3 T TENSOR
REMARK 3 T11: 0.1164 T22: 0.0807
REMARK 3 T33: 0.0620 T12: 0.0087
REMARK 3 T13: 0.0087 T23: -0.0006
REMARK 3 L TENSOR
REMARK 3 L11: 0.5874 L22: 0.6168
REMARK 3 L33: 0.6304 L12: 0.0253
REMARK 3 L13: 0.1548 L23: -0.1665
REMARK 3 S TENSOR
REMARK 3 S11: 0.0230 S12: -0.1051 S13: 0.0274
REMARK 3 S21: 0.0644 S22: -0.0696 S23: 0.0533
REMARK 3 S31: -0.1343 S32: -0.0108 S33: 0.0350
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: ( CHAIN A AND RESID 240:306 )
REMARK 3 ORIGIN FOR THE GROUP (A): 51.5573 -22.0455 6.3147
REMARK 3 T TENSOR
REMARK 3 T11: 0.1185 T22: 0.1094
REMARK 3 T33: 0.1045 T12: 0.0071
REMARK 3 T13: -0.0168 T23: 0.0049
REMARK 3 L TENSOR
REMARK 3 L11: 0.6124 L22: 0.6645
REMARK 3 L33: 0.6956 L12: 0.3305
REMARK 3 L13: -0.0034 L23: -0.1600
REMARK 3 S TENSOR
REMARK 3 S11: -0.0781 S12: -0.0597 S13: 0.0368
REMARK 3 S21: -0.0276 S22: 0.0291 S23: 0.0797
REMARK 3 S31: 0.0939 S32: -0.1263 S33: 0.0281
REMARK 3 TLS GROUP : 4
REMARK 3 SELECTION: ( CHAIN A AND RESID 307:432 )
REMARK 3 ORIGIN FOR THE GROUP (A): 30.5922 5.7223 -7.5675
REMARK 3 T TENSOR
REMARK 3 T11: 0.1115 T22: 0.2456
REMARK 3 T33: 0.2207 T12: -0.0179
REMARK 3 T13: -0.0015 T23: -0.0630
REMARK 3 L TENSOR
REMARK 3 L11: 0.1939 L22: 2.2139
REMARK 3 L33: 1.7752 L12: 0.1263
REMARK 3 L13: 0.4191 L23: 0.9425
REMARK 3 S TENSOR
REMARK 3 S11: 0.0839 S12: -0.0130 S13: 0.1557
REMARK 3 S21: -0.0746 S22: -0.3226 S23: 0.5256
REMARK 3 S31: 0.0581 S32: -0.5674 S33: 0.2362
REMARK 3 TLS GROUP : 5
REMARK 3 SELECTION: ( CHAIN T AND RESID 2:12 )
REMARK 3 ORIGIN FOR THE GROUP (A): 37.8078 -5.9506 -1.6874
REMARK 3 T TENSOR
REMARK 3 T11: 0.2535 T22: 0.1889
REMARK 3 T33: 0.1928 T12: -0.0004
REMARK 3 T13: -0.0316 T23: 0.0064
REMARK 3 L TENSOR
REMARK 3 L11: 0.6145 L22: 3.3597
REMARK 3 L33: 0.2608 L12: 1.0857
REMARK 3 L13: 0.1220 L23: 0.9650
REMARK 3 S TENSOR
REMARK 3 S11: 0.1818 S12: -0.0618 S13: -0.1480
REMARK 3 S21: -0.2722 S22: -0.2216 S23: 0.0852
REMARK 3 S31: 0.0036 S32: -0.3246 S33: -0.0066
REMARK 3 TLS GROUP : 6
REMARK 3 SELECTION: ( CHAIN P AND RESID 1:9 )
REMARK 3 ORIGIN FOR THE GROUP (A): 36.5835 -8.2310 -3.3064
REMARK 3 T TENSOR
REMARK 3 T11: 0.3100 T22: 0.1757
REMARK 3 T33: 0.1758 T12: 0.0434
REMARK 3 T13: -0.0328 T23: -0.0224
REMARK 3 L TENSOR
REMARK 3 L11: 3.0800 L22: 3.9728
REMARK 3 L33: 1.5121 L12: 1.2940
REMARK 3 L13: 2.0749 L23: 0.9937
REMARK 3 S TENSOR
REMARK 3 S11: -0.1762 S12: -0.0856 S13: -0.0104
REMARK 3 S21: -0.9156 S22: -0.0135 S23: -0.1686
REMARK 3 S31: -0.4671 S32: -0.1474 S33: 0.1487
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 4ED8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-APR-12.
REMARK 100 THE DEPOSITION ID IS D_1000071470.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 04-AUG-11
REMARK 200 TEMPERATURE (KELVIN) : 95
REMARK 200 PH : 6.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 22-BM
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 67307
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.520
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4
REMARK 200 DATA REDUNDANCY : 3.100
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.06100
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.7000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.52
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55
REMARK 200 COMPLETENESS FOR SHELL (%) : 71.8
REMARK 200 DATA REDUNDANCY IN SHELL : 2.80
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.63100
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.600
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 41.72
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES, 6-17%(W/V) PEG 2K-MME, VAPOR
REMARK 280 DIFFUSION, TEMPERATURE 293K, PH 6.0
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+1/3
REMARK 290 3555 -X+Y,-X,Z+2/3
REMARK 290 4555 -X,-Y,Z+1/2
REMARK 290 5555 Y,-X+Y,Z+5/6
REMARK 290 6555 X-Y,X,Z+1/6
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 27.47700
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 54.95400
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 41.21550
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 68.69250
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 13.73850
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: 5430 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 22640 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -59.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P
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 155
REMARK 465 THR A 156
REMARK 465 ALA A 157
REMARK 465 GLU A 158
REMARK 465 GLU A 159
REMARK 465 DC T 1
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 10 O4' - C1' - N9 ANGL. DEV. = -5.4 DEGREES
REMARK 500 DT P 8 O4' - C4' - C3' ANGL. DEV. = -3.5 DEGREES
REMARK 500 DT P 8 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES
REMARK 500 DT P 8 O4' - C1' - N1 ANGL. DEV. = 3.7 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 16 66.49 24.43
REMARK 500 TYR A 39 -176.50 68.97
REMARK 500 LYS A 40 -27.18 -155.07
REMARK 500 SER A 62 -14.22 83.74
REMARK 500 SER A 217 -158.43 -157.51
REMARK 500 SER A 257 -11.58 97.30
REMARK 500
REMARK 500 REMARK: NULL
REMARK 600
REMARK 600 HETEROGEN
REMARK 600
REMARK 600 CA A 503 AND MG A 504 ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER.
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 MG A 502 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 13 OD2
REMARK 620 2 ASP A 115 OD2 97.8
REMARK 620 3 GLU A 116 OE2 102.8 102.0
REMARK 620 4 HOH A 601 O 79.7 162.7 95.2
REMARK 620 5 DA P 9 O3' 173.4 77.3 82.6 103.6
REMARK 620 6 DTP P 501 O2A 96.0 87.4 157.5 75.9 79.5
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 503 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 13 OD1
REMARK 620 2 ASP A 13 OD2 45.8
REMARK 620 3 MET A 14 O 75.9 109.0
REMARK 620 4 ASP A 115 OD1 115.5 88.2 83.8
REMARK 620 5 DTP P 501 O3G 78.0 103.7 98.3 166.3
REMARK 620 6 DTP P 501 O1B 152.5 158.6 91.0 86.3 80.2
REMARK 620 7 DTP P 501 O2A 111.5 76.1 172.1 90.4 86.1 83.3
REMARK 620 N 1 2 3 4 5 6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG A 504 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 13 OD1
REMARK 620 2 MET A 14 O 83.9
REMARK 620 3 ASP A 115 OD1 92.2 82.9
REMARK 620 4 DTP P 501 O3G 102.9 98.0 164.9
REMARK 620 5 DTP P 501 O1B 173.3 89.7 85.1 79.8
REMARK 620 6 DTP P 501 O2A 103.1 170.5 90.4 86.8 83.0
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 DTP P 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 502
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 503
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 504
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 505
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 506
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4ECQ RELATED DB: PDB
REMARK 900 RELATED ID: 4ECR RELATED DB: PDB
REMARK 900 RELATED ID: 4ECS RELATED DB: PDB
REMARK 900 RELATED ID: 4ECT RELATED DB: PDB
REMARK 900 RELATED ID: 4ECU RELATED DB: PDB
REMARK 900 RELATED ID: 4ECV RELATED DB: PDB
REMARK 900 RELATED ID: 4ECW RELATED DB: PDB
REMARK 900 RELATED ID: 4ECX RELATED DB: PDB
REMARK 900 RELATED ID: 4ECY RELATED DB: PDB
REMARK 900 RELATED ID: 4ECZ RELATED DB: PDB
REMARK 900 RELATED ID: 4ED0 RELATED DB: PDB
REMARK 900 RELATED ID: 4ED1 RELATED DB: PDB
REMARK 900 RELATED ID: 4ED2 RELATED DB: PDB
REMARK 900 RELATED ID: 4ED3 RELATED DB: PDB
REMARK 900 RELATED ID: 4ED6 RELATED DB: PDB
REMARK 900 RELATED ID: 4ED7 RELATED DB: PDB
DBREF 4ED8 A 1 432 UNP Q9Y253 POLH_HUMAN 1 432
DBREF 4ED8 T 1 12 PDB 4ED8 4ED8 1 12
DBREF 4ED8 P 1 9 PDB 4ED8 4ED8 1 9
SEQADV 4ED8 GLY A -2 UNP Q9Y253 EXPRESSION TAG
SEQADV 4ED8 PRO A -1 UNP Q9Y253 EXPRESSION TAG
SEQADV 4ED8 HIS A 0 UNP Q9Y253 EXPRESSION TAG
SEQRES 1 A 435 GLY PRO HIS MET ALA THR GLY GLN ASP ARG VAL VAL ALA
SEQRES 2 A 435 LEU VAL ASP MET ASP CYS PHE PHE VAL GLN VAL GLU GLN
SEQRES 3 A 435 ARG GLN ASN PRO HIS LEU ARG ASN LYS PRO CYS ALA VAL
SEQRES 4 A 435 VAL GLN TYR LYS SER TRP LYS GLY GLY GLY ILE ILE ALA
SEQRES 5 A 435 VAL SER TYR GLU ALA ARG ALA PHE GLY VAL THR ARG SER
SEQRES 6 A 435 MET TRP ALA ASP ASP ALA LYS LYS LEU CYS PRO ASP LEU
SEQRES 7 A 435 LEU LEU ALA GLN VAL ARG GLU SER ARG GLY LYS ALA ASN
SEQRES 8 A 435 LEU THR LYS TYR ARG GLU ALA SER VAL GLU VAL MET GLU
SEQRES 9 A 435 ILE MET SER ARG PHE ALA VAL ILE GLU ARG ALA SER ILE
SEQRES 10 A 435 ASP GLU ALA TYR VAL ASP LEU THR SER ALA VAL GLN GLU
SEQRES 11 A 435 ARG LEU GLN LYS LEU GLN GLY GLN PRO ILE SER ALA ASP
SEQRES 12 A 435 LEU LEU PRO SER THR TYR ILE GLU GLY LEU PRO GLN GLY
SEQRES 13 A 435 PRO THR THR ALA GLU GLU THR VAL GLN LYS GLU GLY MET
SEQRES 14 A 435 ARG LYS GLN GLY LEU PHE GLN TRP LEU ASP SER LEU GLN
SEQRES 15 A 435 ILE ASP ASN LEU THR SER PRO ASP LEU GLN LEU THR VAL
SEQRES 16 A 435 GLY ALA VAL ILE VAL GLU GLU MET ARG ALA ALA ILE GLU
SEQRES 17 A 435 ARG GLU THR GLY PHE GLN CYS SER ALA GLY ILE SER HIS
SEQRES 18 A 435 ASN LYS VAL LEU ALA LYS LEU ALA CYS GLY LEU ASN LYS
SEQRES 19 A 435 PRO ASN ARG GLN THR LEU VAL SER HIS GLY SER VAL PRO
SEQRES 20 A 435 GLN LEU PHE SER GLN MET PRO ILE ARG LYS ILE ARG SER
SEQRES 21 A 435 LEU GLY GLY LYS LEU GLY ALA SER VAL ILE GLU ILE LEU
SEQRES 22 A 435 GLY ILE GLU TYR MET GLY GLU LEU THR GLN PHE THR GLU
SEQRES 23 A 435 SER GLN LEU GLN SER HIS PHE GLY GLU LYS ASN GLY SER
SEQRES 24 A 435 TRP LEU TYR ALA MET CYS ARG GLY ILE GLU HIS ASP PRO
SEQRES 25 A 435 VAL LYS PRO ARG GLN LEU PRO LYS THR ILE GLY CYS SER
SEQRES 26 A 435 LYS ASN PHE PRO GLY LYS THR ALA LEU ALA THR ARG GLU
SEQRES 27 A 435 GLN VAL GLN TRP TRP LEU LEU GLN LEU ALA GLN GLU LEU
SEQRES 28 A 435 GLU GLU ARG LEU THR LYS ASP ARG ASN ASP ASN ASP ARG
SEQRES 29 A 435 VAL ALA THR GLN LEU VAL VAL SER ILE ARG VAL GLN GLY
SEQRES 30 A 435 ASP LYS ARG LEU SER SER LEU ARG ARG CYS CYS ALA LEU
SEQRES 31 A 435 THR ARG TYR ASP ALA HIS LYS MET SER HIS ASP ALA PHE
SEQRES 32 A 435 THR VAL ILE LYS ASN CYS ASN THR SER GLY ILE GLN THR
SEQRES 33 A 435 GLU TRP SER PRO PRO LEU THR MET LEU PHE LEU CYS ALA
SEQRES 34 A 435 THR LYS PHE SER ALA SER
SEQRES 1 T 12 DC DA DT DT DA DT DG DA DC DG DC DG
SEQRES 1 P 9 DT DG DC DG DT DC DA DT DA
HET MG A 502 1
HET CA A 503 1
HET MG A 504 1
HET GOL A 505 6
HET GOL A 506 6
HET DTP P 501 30
HETNAM MG MAGNESIUM ION
HETNAM CA CALCIUM ION
HETNAM GOL GLYCEROL
HETNAM DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 4 MG 2(MG 2+)
FORMUL 5 CA CA 2+
FORMUL 7 GOL 2(C3 H8 O3)
FORMUL 9 DTP C10 H16 N5 O12 P3
FORMUL 10 HOH *479(H2 O)
HELIX 1 1 CYS A 16 ASN A 26 1 11
HELIX 2 2 PRO A 27 ARG A 30 5 4
HELIX 3 3 SER A 51 ALA A 56 1 6
HELIX 4 4 TRP A 64 CYS A 72 1 9
HELIX 5 5 LEU A 89 SER A 104 1 16
HELIX 6 6 LEU A 121 GLN A 133 1 13
HELIX 7 7 SER A 138 LEU A 142 5 5
HELIX 8 8 GLN A 162 LEU A 178 1 17
HELIX 9 9 SER A 185 GLY A 209 1 25
HELIX 10 10 ASN A 219 ASN A 230 1 12
HELIX 11 11 SER A 239 GLY A 241 5 3
HELIX 12 12 SER A 242 GLN A 249 1 8
HELIX 13 13 MET A 250 ILE A 255 5 6
HELIX 14 14 GLY A 260 GLY A 271 1 12
HELIX 15 15 TYR A 274 PHE A 281 5 8
HELIX 16 16 THR A 282 GLY A 291 1 10
HELIX 17 17 GLY A 291 CYS A 302 1 12
HELIX 18 18 PRO A 326 ALA A 330 5 5
HELIX 19 19 ARG A 334 ASP A 360 1 27
HELIX 20 20 ASP A 391 LYS A 404 1 14
HELIX 21 21 ASN A 405 ASN A 407 5 3
SHEET 1 A 6 ILE A 109 SER A 113 0
SHEET 2 A 6 GLU A 116 ASP A 120 -1 O TYR A 118 N GLU A 110
SHEET 3 A 6 VAL A 9 MET A 14 -1 N ALA A 10 O VAL A 119
SHEET 4 A 6 CYS A 212 SER A 217 -1 O SER A 217 N VAL A 9
SHEET 5 A 6 GLN A 235 LEU A 237 1 O THR A 236 N ILE A 216
SHEET 6 A 6 THR A 145 ILE A 147 1 N TYR A 146 O LEU A 237
SHEET 1 B 3 GLY A 46 VAL A 50 0
SHEET 2 B 3 CYS A 34 GLN A 38 -1 N VAL A 36 O ILE A 48
SHEET 3 B 3 LEU A 76 GLN A 79 1 O ALA A 78 N VAL A 37
SHEET 1 C 2 GLU A 82 SER A 83 0
SHEET 2 C 2 LYS A 86 ALA A 87 -1 O LYS A 86 N SER A 83
SHEET 1 D 3 ILE A 319 ASN A 324 0
SHEET 2 D 3 GLU A 414 ALA A 431 -1 O ALA A 426 N ILE A 319
SHEET 3 D 3 LEU A 331 THR A 333 -1 N ALA A 332 O TRP A 415
SHEET 1 E 4 ILE A 319 ASN A 324 0
SHEET 2 E 4 GLU A 414 ALA A 431 -1 O ALA A 426 N ILE A 319
SHEET 3 E 4 ARG A 361 VAL A 372 -1 N VAL A 367 O CYS A 425
SHEET 4 E 4 LEU A 381 ALA A 386 -1 O ARG A 383 N VAL A 368
LINK OD2AASP A 13 MG MG A 502 1555 1555 2.21
LINK OD1AASP A 13 CA A CA A 503 1555 1555 2.39
LINK OD2AASP A 13 CA A CA A 503 1555 1555 3.02
LINK OD1BASP A 13 MG B MG A 504 1555 1555 2.12
LINK O MET A 14 CA A CA A 503 1555 1555 2.29
LINK O MET A 14 MG B MG A 504 1555 1555 2.31
LINK OD2 ASP A 115 MG MG A 502 1555 1555 2.43
LINK OD1 ASP A 115 CA A CA A 503 1555 1555 2.24
LINK OD1 ASP A 115 MG B MG A 504 1555 1555 2.26
LINK OE2 GLU A 116 MG MG A 502 1555 1555 2.11
LINK MG MG A 502 O HOH A 601 1555 1555 2.17
LINK MG MG A 502 O3' DA P 9 1555 1555 2.32
LINK MG MG A 502 O2A DTP P 501 1555 1555 2.31
LINK CA A CA A 503 O3G DTP P 501 1555 1555 2.27
LINK CA A CA A 503 O1B DTP P 501 1555 1555 2.28
LINK CA A CA A 503 O2A DTP P 501 1555 1555 2.36
LINK MG B MG A 504 O3G DTP P 501 1555 1555 2.26
LINK MG B MG A 504 O1B DTP P 501 1555 1555 2.31
LINK MG B MG A 504 O2A DTP P 501 1555 1555 2.35
CISPEP 1 LEU A 150 PRO A 151 0 1.15
CISPEP 2 LYS A 231 PRO A 232 0 -1.65
CISPEP 3 SER A 416 PRO A 417 0 -6.79
SITE 1 AC1 26 ASP A 13 MET A 14 ASP A 15 CYS A 16
SITE 2 AC1 26 PHE A 17 PHE A 18 ILE A 48 ALA A 49
SITE 3 AC1 26 TYR A 52 ARG A 55 ARG A 61 ASP A 115
SITE 4 AC1 26 LYS A 231 MG A 502 CA A 503 MG A 504
SITE 5 AC1 26 HOH A 601 HOH A 612 HOH A 641 HOH A 646
SITE 6 AC1 26 HOH A 726 HOH A 905 DA P 9 DA T 2
SITE 7 AC1 26 DT T 3 DT T 4
SITE 1 AC2 8 ASP A 13 ASP A 115 GLU A 116 CA A 503
SITE 2 AC2 8 MG A 504 HOH A 601 DA P 9 DTP P 501
SITE 1 AC3 5 ASP A 13 MET A 14 ASP A 115 MG A 502
SITE 2 AC3 5 DTP P 501
SITE 1 AC4 5 ASP A 13 MET A 14 ASP A 115 MG A 502
SITE 2 AC4 5 DTP P 501
SITE 1 AC5 9 ARG A 24 PRO A 244 SER A 248 GLY A 276
SITE 2 AC5 9 GLU A 277 HOH A 606 HOH A 636 HOH A 705
SITE 3 AC5 9 HOH A 899
SITE 1 AC6 9 ASN A 26 PRO A 27 HIS A 28 GLY A 271
SITE 2 AC6 9 GLU A 273 TYR A 274 GLU A 277 HOH A 742
SITE 3 AC6 9 HOH A 868
CRYST1 98.786 98.786 82.431 90.00 90.00 120.00 P 61 6
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 0.010123 0.005844 0.000000 0.00000
SCALE2 0.000000 0.011689 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012131 0.00000
(ATOM LINES ARE NOT SHOWN.)
END