PDB Short entry for 5IIM HEADER TRANSFERASE/DNA 01-MAR-16 5IIM TITLE CRYSTAL STRUCTURE OF THE PRE-CATALYTIC TERNARY EXTENSION COMPLEX OF TITLE 2 DNA POLYMERASE LAMBDA WITH AN 8-OXO-DG:DA BASE-PAIR COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE LAMBDA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: POL LAMBDA,DNA POLYMERASE BETA-2,POL BETA2,DNA POLYMERASE COMPND 5 KAPPA; COMPND 6 EC: 2.7.7.7,4.2.99.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(P*GP*CP*CP*G)-3'); COMPND 10 CHAIN: D; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*CP*AP*GP*TP*AP*A)-3'); COMPND 14 CHAIN: P; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: DNA (5'-D(*CP*GP*GP*CP*AP*(8OG)P*TP*AP*CP*TP*G)-3'); COMPND 18 CHAIN: T; COMPND 19 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: POLL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 16 ORGANISM_TAXID: 32630; SOURCE 17 MOL_ID: 4; SOURCE 18 SYNTHETIC: YES; SOURCE 19 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 20 ORGANISM_TAXID: 32630 KEYWDS TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.J.BURAK,K.E.GUJA,M.GARCIA-DIAZ REVDAT 3 27-SEP-23 5IIM 1 JRNL REMARK LINK REVDAT 2 28-SEP-16 5IIM 1 JRNL REVDAT 1 07-SEP-16 5IIM 0 JRNL AUTH M.J.BURAK,K.E.GUJA,E.HAMBARDJIEVA,B.DERKUNT,M.GARCIA-DIAZ JRNL TITL A FIDELITY MECHANISM IN DNA POLYMERASE LAMBDA PROMOTES JRNL TITL 2 ERROR-FREE BYPASS OF 8-OXO-DG. JRNL REF EMBO J. V. 35 2045 2016 JRNL REFN ESSN 1460-2075 JRNL PMID 27481934 JRNL DOI 10.15252/EMBJ.201694332 REMARK 2 REMARK 2 RESOLUTION. 1.94 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 1.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 36076 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.970 REMARK 3 FREE R VALUE TEST SET COUNT : 3597 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 43.9587 - 5.7453 0.92 1352 135 0.1864 0.2125 REMARK 3 2 5.7453 - 4.5617 1.00 1385 142 0.1497 0.1544 REMARK 3 3 4.5617 - 3.9855 1.00 1351 150 0.1381 0.1554 REMARK 3 4 3.9855 - 3.6213 0.99 1342 149 0.2180 0.2624 REMARK 3 5 3.6213 - 3.3619 1.00 1344 134 0.1698 0.2097 REMARK 3 6 3.3619 - 3.1637 1.00 1316 148 0.1820 0.2274 REMARK 3 7 3.1637 - 3.0053 1.00 1347 150 0.1769 0.1897 REMARK 3 8 3.0053 - 2.8745 1.00 1328 144 0.1760 0.1853 REMARK 3 9 2.8745 - 2.7639 1.00 1311 146 0.1768 0.2215 REMARK 3 10 2.7639 - 2.6685 1.00 1323 141 0.1710 0.2034 REMARK 3 11 2.6685 - 2.5851 1.00 1336 143 0.1629 0.2193 REMARK 3 12 2.5851 - 2.5112 1.00 1296 162 0.1619 0.1997 REMARK 3 13 2.5112 - 2.4451 1.00 1290 140 0.1636 0.1907 REMARK 3 14 2.4451 - 2.3854 1.00 1332 154 0.1685 0.2183 REMARK 3 15 2.3854 - 2.3312 1.00 1298 144 0.1773 0.2077 REMARK 3 16 2.3312 - 2.2816 1.00 777 87 0.1936 0.2488 REMARK 3 17 2.2816 - 2.2360 0.57 722 77 0.4529 0.4478 REMARK 3 18 2.2360 - 2.1938 0.52 672 82 0.2543 0.3210 REMARK 3 19 2.1938 - 2.1546 1.00 1291 149 0.1919 0.2418 REMARK 3 20 2.1546 - 2.1181 1.00 1313 137 0.1761 0.2545 REMARK 3 21 2.1181 - 2.0839 1.00 1289 146 0.1763 0.2187 REMARK 3 22 2.0839 - 2.0518 1.00 1308 144 0.1770 0.2238 REMARK 3 23 2.0518 - 2.0217 1.00 1288 155 0.1795 0.2087 REMARK 3 24 2.0217 - 1.9932 1.00 1309 159 0.1940 0.2498 REMARK 3 25 1.9932 - 1.9663 1.00 1301 147 0.2200 0.2456 REMARK 3 26 1.9663 - 1.9407 0.98 1258 132 0.3648 0.3606 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.006 3055 REMARK 3 ANGLE : 0.898 4234 REMARK 3 CHIRALITY : 0.050 469 REMARK 3 PLANARITY : 0.006 472 REMARK 3 DIHEDRAL : 15.882 1740 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 250 THROUGH 575) REMARK 3 ORIGIN FOR THE GROUP (A): -13.6995 11.3666 -15.4868 REMARK 3 T TENSOR REMARK 3 T11: 0.1196 T22: 0.1397 REMARK 3 T33: 0.1135 T12: -0.0151 REMARK 3 T13: 0.0245 T23: -0.0134 REMARK 3 L TENSOR REMARK 3 L11: 1.4620 L22: 0.7767 REMARK 3 L33: 0.8797 L12: -0.1433 REMARK 3 L13: 0.6333 L23: 0.0571 REMARK 3 S TENSOR REMARK 3 S11: 0.0221 S12: 0.1798 S13: -0.0876 REMARK 3 S21: -0.0693 S22: 0.0468 S23: -0.0692 REMARK 3 S31: 0.0369 S32: 0.1134 S33: 0.0112 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'D' AND RESID 1 THROUGH 4) REMARK 3 ORIGIN FOR THE GROUP (A): -19.5118 29.1080 -29.7394 REMARK 3 T TENSOR REMARK 3 T11: 0.2894 T22: 0.3866 REMARK 3 T33: 0.1920 T12: 0.0046 REMARK 3 T13: -0.0107 T23: 0.1169 REMARK 3 L TENSOR REMARK 3 L11: 0.0300 L22: 0.0184 REMARK 3 L33: 0.0252 L12: 0.0087 REMARK 3 L13: 0.0019 L23: -0.0198 REMARK 3 S TENSOR REMARK 3 S11: 0.1155 S12: 0.0216 S13: 0.0432 REMARK 3 S21: -0.0923 S22: 0.0102 S23: 0.1599 REMARK 3 S31: -0.0703 S32: 0.1094 S33: 0.0462 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'P' AND RESID 1 THROUGH 6) REMARK 3 ORIGIN FOR THE GROUP (A): -25.0573 15.1793 -8.6927 REMARK 3 T TENSOR REMARK 3 T11: 0.1418 T22: 0.1811 REMARK 3 T33: 0.1365 T12: -0.0083 REMARK 3 T13: 0.0147 T23: -0.0258 REMARK 3 L TENSOR REMARK 3 L11: 0.0083 L22: 0.0273 REMARK 3 L33: 0.0193 L12: 0.0076 REMARK 3 L13: -0.0147 L23: -0.0210 REMARK 3 S TENSOR REMARK 3 S11: -0.0568 S12: 0.0188 S13: 0.0564 REMARK 3 S21: 0.1125 S22: -0.0065 S23: 0.0754 REMARK 3 S31: 0.1691 S32: -0.0369 S33: -0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN 'T' AND RESID 1 THROUGH 11) REMARK 3 ORIGIN FOR THE GROUP (A): -27.0152 15.5777 -17.4066 REMARK 3 T TENSOR REMARK 3 T11: 0.2085 T22: 0.1799 REMARK 3 T33: 0.1628 T12: -0.0009 REMARK 3 T13: -0.0106 T23: 0.0031 REMARK 3 L TENSOR REMARK 3 L11: 0.1979 L22: 0.0606 REMARK 3 L33: 0.1080 L12: -0.1135 REMARK 3 L13: -0.0965 L23: 0.0506 REMARK 3 S TENSOR REMARK 3 S11: -0.0547 S12: 0.1007 S13: -0.0301 REMARK 3 S21: 0.0082 S22: 0.0028 S23: 0.2511 REMARK 3 S31: -0.0543 S32: 0.0099 S33: -0.0561 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 5IIM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000218891. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JAN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36628 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.940 REMARK 200 RESOLUTION RANGE LOW (A) : 58.030 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.76600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400 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: 1XSN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM REMARK 280 CITRATE PH 4.8, AND 3-5% PEG 4000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 278K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 28.13700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.36250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.85000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.36250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.13700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.85000 REMARK 290 SMTRY3 4 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: 6100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 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 ALA A 242 REMARK 465 GLN A 243 REMARK 465 PRO A 244 REMARK 465 SER A 245 REMARK 465 SER A 246 REMARK 465 GLN A 247 REMARK 465 LYS A 248 REMARK 465 ALA A 249 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 LEU A 254 CD1 REMARK 470 HIS A 255 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 258 CG CD OE1 OE2 REMARK 470 LYS A 259 CE NZ REMARK 470 LYS A 281 CB CG CD CE NZ REMARK 470 PHE A 289 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 291 CG CD CE NZ REMARK 470 GLN A 297 CG CD OE1 NE2 REMARK 470 LYS A 307 CD CE NZ REMARK 470 HIS A 321 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 323 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 385 CD OE1 OE2 REMARK 470 GLU A 390 CG CD OE1 OE2 REMARK 470 LYS A 401 CD CE NZ REMARK 470 LEU A 411 CG CD1 CD2 REMARK 470 ARG A 438 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 441 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 453 CG CD OE1 NE2 REMARK 470 GLU A 466 CG CD OE1 OE2 REMARK 470 GLN A 469 CG CD OE1 NE2 REMARK 470 LYS A 544 CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 710 O HOH A 911 1.80 REMARK 500 OD2 ASP A 382 O HOH A 701 2.06 REMARK 500 O HOH A 897 O HOH A 901 2.07 REMARK 500 O HOH A 725 O HOH A 936 2.09 REMARK 500 O HOH A 704 O HOH A 909 2.12 REMARK 500 OD2 ASP A 459 O HOH A 702 2.12 REMARK 500 O HOH A 827 O HOH A 907 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 741 O HOH T 121 4555 2.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DG D 1 P DG D 1 OP3 -0.126 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 DG T 2 O4' - C1' - N9 ANGL. DEV. = 2.7 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 415 -136.57 -115.71 REMARK 500 ARG A 438 -35.32 -141.58 REMARK 500 SER A 463 92.46 -170.43 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 603 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 339 O REMARK 620 2 ILE A 341 O 99.5 REMARK 620 3 ALA A 344 O 87.8 87.6 REMARK 620 4 DA P 5 OP1 160.6 99.9 91.9 REMARK 620 5 HOH P 104 O 72.4 166.9 82.0 88.3 REMARK 620 6 HOH P 127 O 90.4 97.1 175.2 88.3 93.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 602 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 427 OD1 REMARK 620 2 ASP A 429 OD2 87.8 REMARK 620 3 DUP A 601 O1A 97.7 91.1 REMARK 620 4 DUP A 601 O2B 170.7 94.3 91.3 REMARK 620 5 DUP A 601 O1G 90.6 175.1 93.6 86.6 REMARK 620 6 HOH A 763 O 80.2 86.5 176.9 90.9 88.7 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 DUP A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 603 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5III RELATED DB: PDB REMARK 900 RELATED ID: 5IIJ RELATED DB: PDB REMARK 900 RELATED ID: 5IIK RELATED DB: PDB REMARK 900 RELATED ID: 5IIL RELATED DB: PDB REMARK 900 RELATED ID: 5IIN RELATED DB: PDB REMARK 900 RELATED ID: 5IIO RELATED DB: PDB DBREF 5IIM A 242 575 UNP Q9UGP5 DPOLL_HUMAN 242 575 DBREF 5IIM D 1 4 PDB 5IIM 5IIM 1 4 DBREF 5IIM P 1 6 PDB 5IIM 5IIM 1 6 DBREF 5IIM T 1 11 PDB 5IIM 5IIM 1 11 SEQRES 1 A 334 ALA GLN PRO SER SER GLN LYS ALA THR ASN HIS ASN LEU SEQRES 2 A 334 HIS ILE THR GLU LYS LEU GLU VAL LEU ALA LYS ALA TYR SEQRES 3 A 334 SER VAL GLN GLY ASP LYS TRP ARG ALA LEU GLY TYR ALA SEQRES 4 A 334 LYS ALA ILE ASN ALA LEU LYS SER PHE HIS LYS PRO VAL SEQRES 5 A 334 THR SER TYR GLN GLU ALA CYS SER ILE PRO GLY ILE GLY SEQRES 6 A 334 LYS ARG MET ALA GLU LYS ILE ILE GLU ILE LEU GLU SER SEQRES 7 A 334 GLY HIS LEU ARG LYS LEU ASP HIS ILE SER GLU SER VAL SEQRES 8 A 334 PRO VAL LEU GLU LEU PHE SER ASN ILE TRP GLY ALA GLY SEQRES 9 A 334 THR LYS THR ALA GLN MET TRP TYR GLN GLN GLY PHE ARG SEQRES 10 A 334 SER LEU GLU ASP ILE ARG SER GLN ALA SER LEU THR THR SEQRES 11 A 334 GLN GLN ALA ILE GLY LEU LYS HIS TYR SER ASP PHE LEU SEQRES 12 A 334 GLU ARG MET PRO ARG GLU GLU ALA THR GLU ILE GLU GLN SEQRES 13 A 334 THR VAL GLN LYS ALA ALA GLN ALA PHE ASN SER GLY LEU SEQRES 14 A 334 LEU CYS VAL ALA CYS GLY SER TYR ARG ARG GLY LYS ALA SEQRES 15 A 334 THR CYS GLY ASP VAL ASP VAL LEU ILE THR HIS PRO ASP SEQRES 16 A 334 GLY ARG SER HIS ARG GLY ILE PHE SER ARG LEU LEU ASP SEQRES 17 A 334 SER LEU ARG GLN GLU GLY PHE LEU THR ASP ASP LEU VAL SEQRES 18 A 334 SER GLN GLU GLU ASN GLY GLN GLN GLN LYS TYR LEU GLY SEQRES 19 A 334 VAL CYS ARG LEU PRO GLY PRO GLY ARG ARG HIS ARG ARG SEQRES 20 A 334 LEU ASP ILE ILE VAL VAL PRO TYR SER GLU PHE ALA CYS SEQRES 21 A 334 ALA LEU LEU TYR PHE THR GLY SER ALA HIS PHE ASN ARG SEQRES 22 A 334 SER MET ARG ALA LEU ALA LYS THR LYS GLY MET SER LEU SEQRES 23 A 334 SER GLU HIS ALA LEU SER THR ALA VAL VAL ARG ASN THR SEQRES 24 A 334 HIS GLY CYS LYS VAL GLY PRO GLY ARG VAL LEU PRO THR SEQRES 25 A 334 PRO THR GLU LYS ASP VAL PHE ARG LEU LEU GLY LEU PRO SEQRES 26 A 334 TYR ARG GLU PRO ALA GLU ARG ASP TRP SEQRES 1 D 4 DG DC DC DG SEQRES 1 P 6 DC DA DG DT DA DA SEQRES 1 T 11 DC DG DG DC DA 8OG DT DA DC DT DG HET 8OG T 6 23 HET DUP A 601 28 HET NA A 602 1 HET NA A 603 1 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE HETNAM NA SODIUM ION HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE FORMUL 4 8OG C10 H14 N5 O8 P FORMUL 5 DUP C9 H16 N3 O13 P3 FORMUL 6 NA 2(NA 1+) FORMUL 8 HOH *349(H2 O) HELIX 1 AA1 ASN A 253 GLN A 270 1 18 HELIX 2 AA2 ASP A 272 SER A 288 1 17 HELIX 3 AA3 SER A 295 SER A 301 1 7 HELIX 4 AA4 GLY A 306 GLY A 320 1 15 HELIX 5 AA5 LEU A 322 ILE A 328 5 7 HELIX 6 AA6 SER A 331 ASN A 340 1 10 HELIX 7 AA7 GLY A 345 GLN A 355 1 11 HELIX 8 AA8 SER A 359 ALA A 367 1 9 HELIX 9 AA9 THR A 370 HIS A 379 1 10 HELIX 10 AB1 HIS A 379 GLU A 385 1 7 HELIX 11 AB2 ARG A 389 ASN A 407 1 19 HELIX 12 AB3 CYS A 415 ARG A 420 1 6 HELIX 13 AB4 GLY A 442 GLU A 454 1 13 HELIX 14 AB5 PRO A 495 SER A 497 5 3 HELIX 15 AB6 GLU A 498 GLY A 508 1 11 HELIX 16 AB7 SER A 509 LYS A 523 1 15 HELIX 17 AB8 THR A 555 LEU A 563 1 9 HELIX 18 AB9 GLU A 569 ARG A 573 5 5 SHEET 1 AA1 2 MET A 387 PRO A 388 0 SHEET 2 AA1 2 THR A 424 CYS A 425 -1 O CYS A 425 N MET A 387 SHEET 1 AA2 5 LEU A 411 ALA A 414 0 SHEET 2 AA2 5 VAL A 428 THR A 433 -1 O LEU A 431 N VAL A 413 SHEET 3 AA2 5 ARG A 487 VAL A 493 1 O ASP A 490 N VAL A 430 SHEET 4 AA2 5 LYS A 472 CYS A 477 -1 N CYS A 477 O ARG A 487 SHEET 5 AA2 5 LEU A 457 VAL A 462 -1 N THR A 458 O VAL A 476 SHEET 1 AA3 3 SER A 526 LEU A 527 0 SHEET 2 AA3 3 LEU A 532 THR A 534 -1 O SER A 533 N SER A 526 SHEET 3 AA3 3 ARG A 549 LEU A 551 -1 O LEU A 551 N LEU A 532 SHEET 1 AA4 2 VAL A 537 ARG A 538 0 SHEET 2 AA4 2 LYS A 544 GLY A 546 -1 O VAL A 545 N VAL A 537 LINK O3' DA T 5 P 8OG T 6 1555 1555 1.60 LINK O3' 8OG T 6 P DT T 7 1555 1555 1.61 LINK O SER A 339 NA NA A 603 1555 1555 2.37 LINK O ILE A 341 NA NA A 603 1555 1555 2.42 LINK O ALA A 344 NA NA A 603 1555 1555 2.38 LINK OD1 ASP A 427 NA NA A 602 1555 1555 2.07 LINK OD2 ASP A 429 NA NA A 602 1555 1555 2.12 LINK O1A DUP A 601 NA NA A 602 1555 1555 2.06 LINK O2B DUP A 601 NA NA A 602 1555 1555 2.03 LINK O1G DUP A 601 NA NA A 602 1555 1555 2.23 LINK NA NA A 602 O HOH A 763 1555 1555 2.20 LINK NA NA A 603 OP1 DA P 5 1555 1555 2.35 LINK NA NA A 603 O HOH P 104 1555 1555 2.60 LINK NA NA A 603 O HOH P 127 1555 1555 2.48 CISPEP 1 GLY A 508 SER A 509 0 -0.67 SITE 1 AC1 23 ARG A 386 GLY A 416 SER A 417 ARG A 420 SITE 2 AC1 23 GLY A 426 ASP A 427 ASP A 429 TYR A 505 SITE 3 AC1 23 PHE A 506 THR A 507 GLY A 508 ASN A 513 SITE 4 AC1 23 NA A 602 HOH A 763 HOH A 768 HOH A 770 SITE 5 AC1 23 HOH A 778 HOH A 786 HOH A 823 HOH A 824 SITE 6 AC1 23 DA P 6 HOH P 111 DA T 5 SITE 1 AC2 4 ASP A 427 ASP A 429 DUP A 601 HOH A 763 SITE 1 AC3 6 SER A 339 ILE A 341 ALA A 344 DA P 5 SITE 2 AC3 6 HOH P 104 HOH P 127 CRYST1 56.274 63.700 140.725 90.00 90.00 90.00 P 21 21 21 4 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 0.017770 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015699 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007106 0.00000