PDB Short entry for 4X5V HEADER TRANSFERASE/DNA 05-DEC-14 4X5V TITLE CRYSTAL STRUCTURE OF THE POST-CATALYTIC NICK COMPLEX OF DNA POLYMERASE TITLE 2 LAMBDA WITH A TEMPLATING A AND INCORPORATED 8-OXO-DGMP 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 OTHER_DETAILS: DOWNSTREAM PRIMER DNA; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*CP*AP*GP*TP*AP*CP*(8OG))-3'); COMPND 15 CHAIN: P; COMPND 16 ENGINEERED: YES; COMPND 17 OTHER_DETAILS: PRIMER DNA; COMPND 18 MOL_ID: 4; COMPND 19 MOLECULE: DNA (5'-D(*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3'); COMPND 20 CHAIN: T; COMPND 21 ENGINEERED: YES; COMPND 22 OTHER_DETAILS: TEMPLATE DNA 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630; SOURCE 16 MOL_ID: 4; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 19 ORGANISM_TAXID: 32630 KEYWDS DNA POLYMERASE LAMBDA, PROTEIN-DNA COMPLEX, HELIX-HAIRPIN-HELIX, KEYWDS 2 TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.J.BURAK,K.E.GUJA,M.GARCIA-DIAZ REVDAT 2 28-FEB-24 4X5V 1 JRNL REMARK LINK REVDAT 1 28-OCT-15 4X5V 0 JRNL AUTH M.J.BURAK,K.E.GUJA,M.GARCIA-DIAZ JRNL TITL NUCLEOTIDE BINDING INTERACTIONS MODULATE DNTP SELECTIVITY JRNL TITL 2 AND FACILITATE 8-OXO-DGTP INCORPORATION BY DNA POLYMERASE JRNL TITL 3 LAMBDA. JRNL REF NUCLEIC ACIDS RES. V. 43 8089 2015 JRNL REFN ESSN 1362-4962 JRNL PMID 26220180 JRNL DOI 10.1093/NAR/GKV760 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.910 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 27911 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.170 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 46.9964 - 5.1797 1.00 2000 156 0.2108 0.2642 REMARK 3 2 5.1797 - 4.1120 1.00 1906 147 0.1843 0.1926 REMARK 3 3 4.1120 - 3.5925 1.00 1878 144 0.1860 0.2098 REMARK 3 4 3.5925 - 3.2641 1.00 1847 143 0.1975 0.2310 REMARK 3 5 3.2641 - 3.0302 1.00 1863 144 0.2166 0.2467 REMARK 3 6 3.0302 - 2.8516 1.00 1826 140 0.2266 0.2685 REMARK 3 7 2.8516 - 2.7088 1.00 1846 143 0.2336 0.2521 REMARK 3 8 2.7088 - 2.5909 1.00 1837 141 0.2444 0.2731 REMARK 3 9 2.5909 - 2.4911 1.00 1829 141 0.2458 0.2760 REMARK 3 10 2.4911 - 2.4052 1.00 1818 141 0.2401 0.2914 REMARK 3 11 2.4052 - 2.3300 1.00 1804 140 0.2466 0.2804 REMARK 3 12 2.3300 - 2.2634 1.00 1853 142 0.2529 0.2860 REMARK 3 13 2.2634 - 2.2038 1.00 1824 141 0.2678 0.2941 REMARK 3 14 2.2038 - 2.1500 0.99 1780 137 0.2910 0.3420 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.770 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 : 0.005 2933 REMARK 3 ANGLE : 0.958 4061 REMARK 3 CHIRALITY : 0.042 450 REMARK 3 PLANARITY : 0.004 452 REMARK 3 DIHEDRAL : 18.691 1093 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 251 THROUGH 326 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.6060 30.1286 -23.3195 REMARK 3 T TENSOR REMARK 3 T11: 0.8128 T22: 0.7175 REMARK 3 T33: 0.5634 T12: -0.1582 REMARK 3 T13: 0.0892 T23: 0.0669 REMARK 3 L TENSOR REMARK 3 L11: 0.4900 L22: 0.5036 REMARK 3 L33: 0.4852 L12: -0.1318 REMARK 3 L13: 0.2489 L23: 0.0537 REMARK 3 S TENSOR REMARK 3 S11: -0.1898 S12: 0.5933 S13: 0.2532 REMARK 3 S21: -0.8107 S22: 0.2724 S23: -0.6675 REMARK 3 S31: -0.5256 S32: 0.7181 S33: 0.0002 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 327 THROUGH 427 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.0721 11.2958 -4.9429 REMARK 3 T TENSOR REMARK 3 T11: 0.2205 T22: 0.1941 REMARK 3 T33: 0.2571 T12: -0.0226 REMARK 3 T13: 0.0051 T23: 0.0112 REMARK 3 L TENSOR REMARK 3 L11: 3.2166 L22: 1.2380 REMARK 3 L33: 1.7322 L12: 0.0424 REMARK 3 L13: 1.2945 L23: -0.0462 REMARK 3 S TENSOR REMARK 3 S11: 0.0662 S12: -0.0839 S13: -0.3313 REMARK 3 S21: 0.0661 S22: 0.1960 S23: -0.0822 REMARK 3 S31: 0.0954 S32: -0.0197 S33: 0.0148 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 428 THROUGH 486 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.5225 -4.1349 -4.9723 REMARK 3 T TENSOR REMARK 3 T11: 0.3794 T22: 0.3148 REMARK 3 T33: 0.7413 T12: -0.0443 REMARK 3 T13: -0.0756 T23: 0.0742 REMARK 3 L TENSOR REMARK 3 L11: 0.5811 L22: 0.8346 REMARK 3 L33: 1.5104 L12: -0.4008 REMARK 3 L13: -0.8149 L23: -0.1162 REMARK 3 S TENSOR REMARK 3 S11: 0.2944 S12: -0.2010 S13: -1.2723 REMARK 3 S21: 0.0112 S22: 0.1071 S23: 0.2125 REMARK 3 S31: 0.4347 S32: -0.4594 S33: 0.0055 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 487 THROUGH 543 ) REMARK 3 ORIGIN FOR THE GROUP (A): -22.0609 5.3645 -23.9032 REMARK 3 T TENSOR REMARK 3 T11: 0.4175 T22: 0.4010 REMARK 3 T33: 0.4421 T12: -0.0144 REMARK 3 T13: -0.0690 T23: -0.0594 REMARK 3 L TENSOR REMARK 3 L11: 0.7405 L22: 0.8438 REMARK 3 L33: 0.7601 L12: 0.6290 REMARK 3 L13: -0.0508 L23: 0.1385 REMARK 3 S TENSOR REMARK 3 S11: 0.1269 S12: 0.2304 S13: -0.3115 REMARK 3 S21: -0.2761 S22: 0.2397 S23: 0.2761 REMARK 3 S31: 0.0224 S32: -0.2215 S33: -0.0000 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 544 THROUGH 575 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.7008 2.7396 -31.4053 REMARK 3 T TENSOR REMARK 3 T11: 0.5379 T22: 0.5527 REMARK 3 T33: 0.4592 T12: -0.0255 REMARK 3 T13: -0.0585 T23: -0.2083 REMARK 3 L TENSOR REMARK 3 L11: 0.1217 L22: 0.4122 REMARK 3 L33: 0.7631 L12: 0.1289 REMARK 3 L13: 0.1178 L23: -0.4373 REMARK 3 S TENSOR REMARK 3 S11: 0.1162 S12: 0.3586 S13: 0.2152 REMARK 3 S21: -0.3302 S22: 0.0258 S23: 0.2587 REMARK 3 S31: 0.0541 S32: 0.0727 S33: -0.0000 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 1 THROUGH 4 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.4780 28.2017 -30.0528 REMARK 3 T TENSOR REMARK 3 T11: 0.6799 T22: 0.7766 REMARK 3 T33: -0.8103 T12: 0.2762 REMARK 3 T13: -0.4205 T23: 0.3007 REMARK 3 L TENSOR REMARK 3 L11: 0.1106 L22: 0.1673 REMARK 3 L33: 0.3535 L12: 0.0130 REMARK 3 L13: -0.1045 L23: 0.1342 REMARK 3 S TENSOR REMARK 3 S11: 0.6912 S12: 0.2782 S13: 0.0688 REMARK 3 S21: -0.3709 S22: 0.2534 S23: 0.0449 REMARK 3 S31: -0.4875 S32: 0.1023 S33: 1.0064 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'P' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): -25.4339 14.9661 -8.5000 REMARK 3 T TENSOR REMARK 3 T11: 0.2263 T22: 0.3203 REMARK 3 T33: 0.2045 T12: -0.0300 REMARK 3 T13: 0.0439 T23: 0.0040 REMARK 3 L TENSOR REMARK 3 L11: 0.0506 L22: 0.1841 REMARK 3 L33: 0.1637 L12: 0.0730 REMARK 3 L13: -0.0357 L23: -0.1291 REMARK 3 S TENSOR REMARK 3 S11: -0.2553 S12: 0.2284 S13: 0.1693 REMARK 3 S21: -0.2554 S22: 0.2225 S23: -0.2006 REMARK 3 S31: 0.1397 S32: -0.1353 S33: -0.0000 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'T' AND (RESID 1 THROUGH 11 ) REMARK 3 ORIGIN FOR THE GROUP (A): -27.1779 15.0678 -17.3862 REMARK 3 T TENSOR REMARK 3 T11: 0.4585 T22: 0.4834 REMARK 3 T33: 0.3074 T12: 0.0066 REMARK 3 T13: -0.0645 T23: 0.0465 REMARK 3 L TENSOR REMARK 3 L11: 0.3882 L22: 0.0299 REMARK 3 L33: 0.3319 L12: -0.1779 REMARK 3 L13: -0.0565 L23: 0.2150 REMARK 3 S TENSOR REMARK 3 S11: 0.1162 S12: 0.3211 S13: 0.1083 REMARK 3 S21: -0.4407 S22: 0.2724 S23: 0.6667 REMARK 3 S31: 0.4311 S32: -0.7515 S33: 0.0008 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 4X5V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-DEC-14. REMARK 100 THE DEPOSITION ID IS D_1000205108. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUL-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27980 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 46.985 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 8.700 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.70 REMARK 200 R MERGE FOR SHELL (I) : 0.80000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL 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 (%): 57.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE PH 5.6 AND 1 M REMARK 280 AMMONIUM PHOSPHATE MONOBASIC, 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 28.00500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.75350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.42100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.75350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.00500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.42100 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: 5820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 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 SER A 288 REMARK 465 PHE A 289 REMARK 465 HIS A 290 REMARK 465 LYS A 291 REMARK 465 PRO A 292 REMARK 465 VAL A 293 REMARK 465 THR A 294 REMARK 465 SER A 295 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 HIS A 252 CG ND1 CD2 CE1 NE2 REMARK 470 LEU A 254 CG CD1 CD2 REMARK 470 HIS A 255 CG ND1 CD2 CE1 NE2 REMARK 470 ILE A 256 CG1 CG2 CD1 REMARK 470 LYS A 287 CG CD CE NZ REMARK 470 GLN A 297 CG CD OE1 NE2 REMARK 470 SER A 301 OG REMARK 470 ILE A 313 CG1 CG2 CD1 REMARK 470 ILE A 314 CG1 CG2 CD1 REMARK 470 ILE A 316 CG1 CG2 CD1 REMARK 470 LEU A 317 CG CD1 CD2 REMARK 470 GLU A 318 CG CD OE1 OE2 REMARK 470 SER A 319 OG 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 330 CG CD OE1 OE2 REMARK 470 LYS A 378 CD CE NZ REMARK 470 PHE A 406 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASP A 436 CG OD1 OD2 REMARK 470 ARG A 438 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 440 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 441 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 443 CG1 CG2 CD1 REMARK 470 ARG A 446 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 449 CG OD1 OD2 REMARK 470 GLN A 453 CG CD OE1 NE2 REMARK 470 GLU A 466 CG CD OE1 OE2 REMARK 470 ASN A 467 CG OD1 ND2 REMARK 470 GLN A 469 CG CD OE1 NE2 REMARK 470 THR A 540 OG1 CG2 REMARK 470 CYS A 543 SG REMARK 470 VAL A 545 CG1 CG2 REMARK 470 GLU A 572 CG CD OE1 OE2 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 T 110 O HOH T 124 1.96 REMARK 500 OE1 GLU A 394 O HOH A 701 1.99 REMARK 500 O HOH P 101 O HOH P 120 2.02 REMARK 500 OD1 ASP A 558 O HOH A 702 2.05 REMARK 500 O HOH P 114 O HOH P 118 2.05 REMARK 500 OD2 ASP A 574 O HOH A 703 2.07 REMARK 500 O HOH A 715 O HOH A 788 2.08 REMARK 500 O GLY A 442 OG SER A 445 2.14 REMARK 500 OP2 DA T 8 O HOH T 101 2.16 REMARK 500 OE2 GLU A 454 O HOH A 704 2.17 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 -0.127 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. = 2.6 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 ASN A 253 32.39 -143.81 REMARK 500 CYS A 415 -140.79 -111.65 REMARK 500 SER A 463 84.77 -161.57 REMARK 500 ASN A 467 -63.29 -91.63 REMARK 500 GLN A 469 37.24 -83.25 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 MG A 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 339 O REMARK 620 2 ILE A 341 O 91.4 REMARK 620 3 ALA A 344 O 87.5 89.4 REMARK 620 4 HOH A 816 O 89.5 92.4 176.5 REMARK 620 5 DA P 5 OP1 167.5 101.0 90.9 91.7 REMARK 620 6 HOH P 103 O 78.9 169.9 87.7 89.9 88.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 601 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 427 OD1 REMARK 620 2 ASP A 429 OD2 91.8 REMARK 620 3 CIT A 603 O7 89.7 153.6 REMARK 620 4 CIT A 603 O4 157.3 110.2 73.2 REMARK 620 5 HOH A 741 O 93.9 87.7 118.6 81.8 REMARK 620 6 8OG P 7 OP1 72.0 78.6 76.8 116.8 159.7 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 NA A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CIT A 603 DBREF 4X5V A 251 575 UNP Q9UGP5 DPOLL_HUMAN 251 575 DBREF 4X5V D 1 4 PDB 4X5V 4X5V 1 4 DBREF 4X5V P 1 7 PDB 4X5V 4X5V 1 7 DBREF 4X5V T 1 11 PDB 4X5V 4X5V 1 11 SEQRES 1 A 325 ASN HIS ASN LEU HIS ILE THR GLU LYS LEU GLU VAL LEU SEQRES 2 A 325 ALA LYS ALA TYR SER VAL GLN GLY ASP LYS TRP ARG ALA SEQRES 3 A 325 LEU GLY TYR ALA LYS ALA ILE ASN ALA LEU LYS SER PHE SEQRES 4 A 325 HIS LYS PRO VAL THR SER TYR GLN GLU ALA CYS SER ILE SEQRES 5 A 325 PRO GLY ILE GLY LYS ARG MET ALA GLU LYS ILE ILE GLU SEQRES 6 A 325 ILE LEU GLU SER GLY HIS LEU ARG LYS LEU ASP HIS ILE SEQRES 7 A 325 SER GLU SER VAL PRO VAL LEU GLU LEU PHE SER ASN ILE SEQRES 8 A 325 TRP GLY ALA GLY THR LYS THR ALA GLN MET TRP TYR GLN SEQRES 9 A 325 GLN GLY PHE ARG SER LEU GLU ASP ILE ARG SER GLN ALA SEQRES 10 A 325 SER LEU THR THR GLN GLN ALA ILE GLY LEU LYS HIS TYR SEQRES 11 A 325 SER ASP PHE LEU GLU ARG MET PRO ARG GLU GLU ALA THR SEQRES 12 A 325 GLU ILE GLU GLN THR VAL GLN LYS ALA ALA GLN ALA PHE SEQRES 13 A 325 ASN SER GLY LEU LEU CYS VAL ALA CYS GLY SER TYR ARG SEQRES 14 A 325 ARG GLY LYS ALA THR CYS GLY ASP VAL ASP VAL LEU ILE SEQRES 15 A 325 THR HIS PRO ASP GLY ARG SER HIS ARG GLY ILE PHE SER SEQRES 16 A 325 ARG LEU LEU ASP SER LEU ARG GLN GLU GLY PHE LEU THR SEQRES 17 A 325 ASP ASP LEU VAL SER GLN GLU GLU ASN GLY GLN GLN GLN SEQRES 18 A 325 LYS TYR LEU GLY VAL CYS ARG LEU PRO GLY PRO GLY ARG SEQRES 19 A 325 ARG HIS ARG ARG LEU ASP ILE ILE VAL VAL PRO TYR SER SEQRES 20 A 325 GLU PHE ALA CYS ALA LEU LEU TYR PHE THR GLY SER ALA SEQRES 21 A 325 HIS PHE ASN ARG SER MET ARG ALA LEU ALA LYS THR LYS SEQRES 22 A 325 GLY MET SER LEU SER GLU HIS ALA LEU SER THR ALA VAL SEQRES 23 A 325 VAL ARG ASN THR HIS GLY CYS LYS VAL GLY PRO GLY ARG SEQRES 24 A 325 VAL LEU PRO THR PRO THR GLU LYS ASP VAL PHE ARG LEU SEQRES 25 A 325 LEU GLY LEU PRO TYR ARG GLU PRO ALA GLU ARG ASP TRP SEQRES 1 D 4 DG DC DC DG SEQRES 1 P 7 DC DA DG DT DA DC 8OG SEQRES 1 T 11 DC DG DG DC DA DG DT DA DC DT DG HET 8OG P 7 23 HET NA A 601 1 HET MG A 602 1 HET CIT A 603 13 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM NA SODIUM ION HETNAM MG MAGNESIUM ION HETNAM CIT CITRIC ACID HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE FORMUL 3 8OG C10 H14 N5 O8 P FORMUL 5 NA NA 1+ FORMUL 6 MG MG 2+ FORMUL 7 CIT C6 H8 O7 FORMUL 8 HOH *180(H2 O) HELIX 1 AA1 ASN A 253 GLN A 270 1 18 HELIX 2 AA2 ASP A 272 LYS A 287 1 16 HELIX 3 AA3 GLN A 297 ILE A 302 1 6 HELIX 4 AA4 GLY A 306 SER A 319 1 14 HELIX 5 AA5 LEU A 322 HIS A 327 1 6 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 ASP A 574 5 6 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 THR A 433 N LEU A 411 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 VAL A 550 -1 O ARG A 549 N THR A 534 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' DC P 6 P 8OG P 7 1555 1555 1.61 LINK O SER A 339 MG MG A 602 1555 1555 2.31 LINK O ILE A 341 MG MG A 602 1555 1555 2.43 LINK O ALA A 344 MG MG A 602 1555 1555 2.17 LINK OD1 ASP A 427 NA NA A 601 1555 1555 2.25 LINK OD2 ASP A 429 NA NA A 601 1555 1555 2.33 LINK NA NA A 601 O7 CIT A 603 1555 1555 2.49 LINK NA NA A 601 O4 CIT A 603 1555 1555 2.22 LINK NA NA A 601 O HOH A 741 1555 1555 2.82 LINK NA NA A 601 OP1 8OG P 7 1555 1555 2.77 LINK MG MG A 602 O HOH A 816 1555 1555 2.64 LINK MG MG A 602 OP1 DA P 5 1555 1555 2.26 LINK MG MG A 602 O HOH P 103 1555 1555 2.73 CISPEP 1 GLY A 508 SER A 509 0 2.66 SITE 1 AC1 5 ASP A 427 ASP A 429 CIT A 603 HOH A 741 SITE 2 AC1 5 8OG P 7 SITE 1 AC2 6 SER A 339 ILE A 341 ALA A 344 HOH A 816 SITE 2 AC2 6 DA P 5 HOH P 103 SITE 1 AC3 13 ARG A 386 GLY A 416 SER A 417 ARG A 420 SITE 2 AC3 13 GLY A 426 ASP A 427 ARG A 488 NA A 601 SITE 3 AC3 13 HOH A 726 HOH A 790 HOH A 792 8OG P 7 SITE 4 AC3 13 HOH P 102 CRYST1 56.010 62.842 141.507 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 0.017854 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015913 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007067 0.00000