HEADER TRANSFERASE/DNA 12-MAR-14 4P4M TITLE CRYSTAL STRUCTURE OF LEISHMANIA INFANTUM POLYMERASE BETA: TERNARY P/T TITLE 2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE BETA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*CP*AP*GP*TP*A)-3'); COMPND 7 CHAIN: D; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (5'-D(P*AP*TP*AP*CP*TP*G)-3'); COMPND 11 CHAIN: E; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEISHMANIA INFANTUM; SOURCE 3 ORGANISM_TAXID: 5671; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 9 ORGANISM_TAXID: 32630; SOURCE 10 MOL_ID: 3; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS DNA POLYMERASE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.MEJIA,M.BURAK,A.ALONSO,V.LARRAGA,T.A.KUNKEL,K.BEBENEK,M.GARCIA-DIAZ REVDAT 5 27-SEP-23 4P4M 1 REMARK LINK REVDAT 4 25-DEC-19 4P4M 1 REMARK REVDAT 3 22-NOV-17 4P4M 1 REMARK REVDAT 2 06-SEP-17 4P4M 1 SOURCE REMARK REVDAT 1 06-AUG-14 4P4M 0 JRNL AUTH E.MEJIA,M.BURAK,A.ALONSO,V.LARRAGA,T.A.KUNKEL,K.BEBENEK, JRNL AUTH 2 M.GARCIA-DIAZ JRNL TITL STRUCTURES OF THE LEISHMANIA INFANTUM POLYMERASE BETA. JRNL REF DNA REPAIR (AMST.) V. 18 1 2014 JRNL REFN ISSN 1568-7856 JRNL PMID 24666693 JRNL DOI 10.1016/J.DNAREP.2014.03.001 REMARK 2 REMARK 2 RESOLUTION. 1.92 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) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 41054 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.550 REMARK 3 FREE R VALUE TEST SET COUNT : 3100 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 44.9576 - 5.3728 1.00 1927 157 0.2027 0.2247 REMARK 3 2 5.3728 - 4.2656 1.00 1801 147 0.1529 0.1661 REMARK 3 3 4.2656 - 3.7267 1.00 1768 145 0.1323 0.1260 REMARK 3 4 3.7267 - 3.3861 1.00 1751 142 0.1450 0.1447 REMARK 3 5 3.3861 - 3.1435 1.00 1755 143 0.1575 0.1746 REMARK 3 6 3.1435 - 2.9582 1.00 1725 142 0.1661 0.2081 REMARK 3 7 2.9582 - 2.8100 1.00 1728 141 0.1678 0.1702 REMARK 3 8 2.8100 - 2.6877 1.00 1719 140 0.1681 0.1920 REMARK 3 9 2.6877 - 2.5843 1.00 1715 141 0.1739 0.1862 REMARK 3 10 2.5843 - 2.4951 1.00 1719 140 0.1656 0.1952 REMARK 3 11 2.4951 - 2.4171 1.00 1695 139 0.1663 0.1950 REMARK 3 12 2.4171 - 2.3480 1.00 1718 140 0.1724 0.2145 REMARK 3 13 2.3480 - 2.2862 1.00 1714 140 0.1716 0.1852 REMARK 3 14 2.2862 - 2.2304 1.00 1700 139 0.1697 0.2533 REMARK 3 15 2.2304 - 2.1797 1.00 1692 138 0.1685 0.1880 REMARK 3 16 2.1797 - 2.1333 1.00 1697 139 0.1636 0.1789 REMARK 3 17 2.1333 - 2.0907 1.00 1687 138 0.1570 0.1827 REMARK 3 18 2.0907 - 2.0512 1.00 1689 138 0.1614 0.1803 REMARK 3 19 2.0512 - 2.0146 1.00 1704 139 0.1703 0.1697 REMARK 3 20 2.0146 - 1.9804 1.00 1698 139 0.1681 0.1767 REMARK 3 21 1.9804 - 1.9485 1.00 1689 137 0.1738 0.1963 REMARK 3 22 1.9485 - 1.9185 0.99 1663 136 0.1866 0.2329 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 1.00 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.680 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 : 0.014 2502 REMARK 3 ANGLE : 1.292 3443 REMARK 3 CHIRALITY : 0.071 377 REMARK 3 PLANARITY : 0.004 410 REMARK 3 DIHEDRAL : 15.647 984 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 90 THROUGH 117 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.9517 -19.6825 11.4984 REMARK 3 T TENSOR REMARK 3 T11: 0.3564 T22: 0.7602 REMARK 3 T33: 0.3717 T12: -0.0377 REMARK 3 T13: 0.0169 T23: -0.1875 REMARK 3 L TENSOR REMARK 3 L11: 3.3784 L22: 6.3754 REMARK 3 L33: 3.3111 L12: 1.1769 REMARK 3 L13: 0.5137 L23: 1.7171 REMARK 3 S TENSOR REMARK 3 S11: 0.0328 S12: -1.1352 S13: 0.4223 REMARK 3 S21: 0.7095 S22: 0.2619 S23: -0.1683 REMARK 3 S31: -0.2612 S32: 0.5529 S33: -0.2847 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 118 THROUGH 304 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.4970 -34.1001 -9.3048 REMARK 3 T TENSOR REMARK 3 T11: 0.1867 T22: 0.1190 REMARK 3 T33: 0.1554 T12: 0.0050 REMARK 3 T13: 0.0415 T23: -0.0071 REMARK 3 L TENSOR REMARK 3 L11: 2.0873 L22: 0.8891 REMARK 3 L33: 1.3152 L12: -0.7152 REMARK 3 L13: -0.5981 L23: 0.2658 REMARK 3 S TENSOR REMARK 3 S11: 0.0541 S12: -0.0730 S13: 0.0115 REMARK 3 S21: 0.0529 S22: -0.0404 S23: 0.0920 REMARK 3 S31: -0.1111 S32: -0.0659 S33: -0.0178 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 305 THROUGH 376 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.0457 -46.3236 -9.5346 REMARK 3 T TENSOR REMARK 3 T11: 0.1669 T22: 0.1589 REMARK 3 T33: 0.1503 T12: 0.0318 REMARK 3 T13: -0.0237 T23: -0.0040 REMARK 3 L TENSOR REMARK 3 L11: 2.5706 L22: 4.1480 REMARK 3 L33: 3.0684 L12: -0.0381 REMARK 3 L13: -1.2956 L23: -1.2630 REMARK 3 S TENSOR REMARK 3 S11: -0.0007 S12: -0.1543 S13: -0.0606 REMARK 3 S21: 0.2341 S22: -0.0281 S23: -0.2847 REMARK 3 S31: 0.0550 S32: 0.2755 S33: 0.0101 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 1 THROUGH 5 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.0100 -26.6803 0.4207 REMARK 3 T TENSOR REMARK 3 T11: 0.2410 T22: 0.4194 REMARK 3 T33: 0.2638 T12: -0.0736 REMARK 3 T13: -0.0398 T23: 0.0207 REMARK 3 L TENSOR REMARK 3 L11: 5.8851 L22: 6.1217 REMARK 3 L33: 7.1247 L12: -3.6715 REMARK 3 L13: -4.1880 L23: -1.3724 REMARK 3 S TENSOR REMARK 3 S11: 0.2817 S12: -1.0369 S13: 0.1344 REMARK 3 S21: 0.0312 S22: -0.1897 S23: 0.0503 REMARK 3 S31: -0.1889 S32: 0.2821 S33: -0.0895 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'E' AND (RESID 6 THROUGH 11 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.7601 -31.4810 -5.0266 REMARK 3 T TENSOR REMARK 3 T11: 0.2197 T22: 0.2032 REMARK 3 T33: 0.2195 T12: -0.0436 REMARK 3 T13: 0.0402 T23: -0.0222 REMARK 3 L TENSOR REMARK 3 L11: 2.8841 L22: 4.3128 REMARK 3 L33: 2.4292 L12: -1.1087 REMARK 3 L13: 0.1605 L23: -0.5159 REMARK 3 S TENSOR REMARK 3 S11: 0.0794 S12: -0.2318 S13: 0.3967 REMARK 3 S21: 0.3135 S22: -0.0138 S23: -0.2167 REMARK 3 S31: -0.2751 S32: 0.1655 S33: -0.0750 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 4P4M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAR-14. REMARK 100 THE DEPOSITION ID IS D_1000200690. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-11 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 : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.075 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 : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41119 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.918 REMARK 200 RESOLUTION RANGE LOW (A) : 94.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 18.70 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 38.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.61300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 1BPY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 120 MM MAGNESIUM CHLORIDE, 0.4 M TRIS REMARK 280 -HCL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 101.09400 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 50.54700 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 75.82050 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 25.27350 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 126.36750 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 101.09400 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 50.54700 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 25.27350 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 75.82050 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 126.36750 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: 3830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, E 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 531 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 555 LIES ON A SPECIAL POSITION. 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 GLY A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 LEU A 2 REMARK 465 ARG A 3 REMARK 465 ARG A 4 REMARK 465 LYS A 5 REMARK 465 PHE A 6 REMARK 465 LEU A 7 REMARK 465 ARG A 8 REMARK 465 ARG A 9 REMARK 465 ASP A 10 REMARK 465 HIS A 11 REMARK 465 ARG A 12 REMARK 465 GLU A 13 REMARK 465 ASN A 14 REMARK 465 ILE A 15 REMARK 465 ILE A 16 REMARK 465 ARG A 17 REMARK 465 ILE A 18 REMARK 465 PHE A 19 REMARK 465 GLN A 20 REMARK 465 GLU A 21 REMARK 465 MET A 22 REMARK 465 ALA A 23 REMARK 465 ASP A 24 REMARK 465 LEU A 25 REMARK 465 ASN A 26 REMARK 465 ASN A 27 REMARK 465 ALA A 28 REMARK 465 LEU A 29 REMARK 465 GLY A 30 REMARK 465 GLU A 31 REMARK 465 LYS A 32 REMARK 465 TYR A 33 REMARK 465 LYS A 34 REMARK 465 VAL A 35 REMARK 465 SER A 36 REMARK 465 SER A 37 REMARK 465 TYR A 38 REMARK 465 HIS A 39 REMARK 465 ARG A 40 REMARK 465 SER A 41 REMARK 465 ILE A 42 REMARK 465 GLU A 43 REMARK 465 SER A 44 REMARK 465 LEU A 45 REMARK 465 LYS A 46 REMARK 465 THR A 47 REMARK 465 ASN A 48 REMARK 465 LEU A 49 REMARK 465 ASP A 50 REMARK 465 LYS A 51 REMARK 465 PRO A 52 REMARK 465 LEU A 53 REMARK 465 ASN A 54 REMARK 465 THR A 55 REMARK 465 PRO A 56 REMARK 465 GLN A 57 REMARK 465 ASP A 58 REMARK 465 LEU A 59 REMARK 465 LYS A 60 REMARK 465 ALA A 61 REMARK 465 PHE A 62 REMARK 465 SER A 63 REMARK 465 GLY A 64 REMARK 465 PHE A 65 REMARK 465 GLY A 66 REMARK 465 ALA A 67 REMARK 465 LYS A 68 REMARK 465 LEU A 69 REMARK 465 LEU A 70 REMARK 465 LYS A 71 REMARK 465 LYS A 72 REMARK 465 ALA A 73 REMARK 465 GLU A 74 REMARK 465 GLU A 75 REMARK 465 ILE A 76 REMARK 465 MET A 77 REMARK 465 ALA A 78 REMARK 465 THR A 79 REMARK 465 GLY A 80 REMARK 465 LYS A 81 REMARK 465 LEU A 82 REMARK 465 GLU A 83 REMARK 465 GLU A 84 REMARK 465 LEU A 85 REMARK 465 GLU A 86 REMARK 465 SER A 87 REMARK 465 LYS A 88 REMARK 465 THR A 89 REMARK 465 VAL A 253 REMARK 465 ARG A 254 REMARK 465 ASP A 255 REMARK 465 LYS A 256 REMARK 465 ALA A 257 REMARK 465 GLY A 258 REMARK 465 ARG A 259 REMARK 465 GLU A 260 REMARK 465 ALA A 324 REMARK 465 LEU A 325 REMARK 465 TYR A 326 REMARK 465 GLU A 327 REMARK 465 ARG A 328 REMARK 465 ILE A 329 REMARK 465 GLY A 330 REMARK 465 ILE A 331 REMARK 465 ARG A 332 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 LYS A 94 CG CD CE NZ REMARK 470 GLN A 97 CG CD OE1 NE2 REMARK 470 ARG A 116 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 251 CD NE CZ NH1 NH2 REMARK 470 ILE A 252 CG1 CG2 CD1 REMARK 470 ASN A 261 CG OD1 ND2 REMARK 470 ARG A 323 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 334 CG 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 NE2 GLN A 127 O HOH A 501 2.19 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 DA E 6 P DA E 6 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 D 3 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DT D 4 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT E 7 O4' - C1' - N1 ANGL. DEV. = 3.4 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 182 -129.43 -110.75 REMARK 500 ARG A 374 51.23 -108.53 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 403 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 100 O REMARK 620 2 VAL A 102 O 95.6 REMARK 620 3 PHE A 105 O 94.8 87.3 REMARK 620 4 DT D 4 OP1 168.8 89.7 95.3 REMARK 620 5 HOH D 104 O 85.7 89.9 177.2 84.4 REMARK 620 6 HOH D 110 O 80.3 175.4 95.1 94.0 87.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 194 OD1 REMARK 620 2 ASP A 196 OD2 89.1 REMARK 620 3 D3T A 401 O1A 94.7 95.8 REMARK 620 4 D3T A 401 O1B 177.6 91.6 87.5 REMARK 620 5 D3T A 401 O1G 87.7 170.8 93.1 91.2 REMARK 620 6 HOH A 596 O 84.4 82.7 178.3 93.5 88.4 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 D3T A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 403 DBREF 4P4M A 1 376 UNP Q9U6N3 Q9U6N3_LEIIN 1 376 DBREF 4P4M D 1 5 PDB 4P4M 4P4M 1 5 DBREF 4P4M E 6 11 PDB 4P4M 4P4M 6 11 SEQADV 4P4M GLY A -1 UNP Q9U6N3 EXPRESSION TAG SEQADV 4P4M HIS A 0 UNP Q9U6N3 EXPRESSION TAG SEQRES 1 A 378 GLY HIS MET LEU ARG ARG LYS PHE LEU ARG ARG ASP HIS SEQRES 2 A 378 ARG GLU ASN ILE ILE ARG ILE PHE GLN GLU MET ALA ASP SEQRES 3 A 378 LEU ASN ASN ALA LEU GLY GLU LYS TYR LYS VAL SER SER SEQRES 4 A 378 TYR HIS ARG SER ILE GLU SER LEU LYS THR ASN LEU ASP SEQRES 5 A 378 LYS PRO LEU ASN THR PRO GLN ASP LEU LYS ALA PHE SER SEQRES 6 A 378 GLY PHE GLY ALA LYS LEU LEU LYS LYS ALA GLU GLU ILE SEQRES 7 A 378 MET ALA THR GLY LYS LEU GLU GLU LEU GLU SER LYS THR SEQRES 8 A 378 LYS PRO LYS LEU LYS ALA ILE GLN GLU LEU THR GLN VAL SEQRES 9 A 378 HIS GLY PHE GLY PRO ARG ALA ALA ALA ALA LEU PHE ASP SEQRES 10 A 378 ARG GLU GLY ILE PHE THR VAL ASP GLU LEU LEU GLN LYS SEQRES 11 A 378 ALA ASP SER ILE PRO SER LEU THR ASP GLN GLN ARG VAL SEQRES 12 A 378 GLY ILE LYS TYR PHE TYR ASP ILE ASN GLU LYS ILE PRO SEQRES 13 A 378 MET GLN GLU SER VAL LEU HIS GLU ASN TYR LEU ARG GLU SEQRES 14 A 378 LYS CYS MET GLU VAL LEU GLY LYS ASP PHE SER ILE LEU SEQRES 15 A 378 ILE CYS GLY SER TYR ARG ARG ARG HIS PRO PHE SER GLY SEQRES 16 A 378 ASP VAL ASP ALA ILE LEU SER ARG THR LEU ASP ALA PRO SEQRES 17 A 378 PRO LEU SER GLU PRO VAL ALA ALA THR GLY VAL LEU GLY SEQRES 18 A 378 HIS PHE VAL GLU PHE LEU GLU SER LEU LYS TYR LEU GLU SEQRES 19 A 378 ALA THR MET ALA GLN GLY PRO LEU LYS TYR MET GLY MET SEQRES 20 A 378 GLY ARG LEU PRO PRO ARG ILE VAL ARG ASP LYS ALA GLY SEQRES 21 A 378 ARG GLU ASN THR LYS VAL TYR LYS ALA ARG ARG VAL ASP SEQRES 22 A 378 ILE ARG LEU ILE GLU THR LYS SER VAL PRO THR ALA MET SEQRES 23 A 378 LEU THR PHE THR GLY SER LYS ASN PHE ASN VAL ILE MET SEQRES 24 A 378 ARG GLN ALA ALA ILE SER LYS GLY TYR LEU LEU ASN GLU SEQRES 25 A 378 TYR GLY LEU PHE LYS LEU GLY THR PRO GLU GLU ALA ARG SEQRES 26 A 378 ALA LEU TYR GLU ARG ILE GLY ILE ARG GLY LYS ASN ALA SEQRES 27 A 378 GLY GLU GLU LEU GLY VAL PRO LYS ASP GLU LEU GLU ASP SEQRES 28 A 378 LYS ARG VAL GLU VAL ARG SER GLU GLN ASP VAL PHE ASP SEQRES 29 A 378 VAL LEU GLY MET PRO TYR ALA LYS PRO GLU ASN ARG ASP SEQRES 30 A 378 PRO SEQRES 1 D 5 DC DA DG DT DA SEQRES 1 E 6 DA DT DA DC DT DG HET D3T A 401 28 HET MG A 402 1 HET NA A 403 1 HETNAM D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION FORMUL 4 D3T C10 H17 N2 O13 P3 FORMUL 5 MG MG 2+ FORMUL 6 NA NA 1+ FORMUL 7 HOH *326(H2 O) HELIX 1 AA1 LYS A 90 THR A 100 1 11 HELIX 2 AA2 GLY A 106 GLY A 118 1 13 HELIX 3 AA3 THR A 121 ALA A 129 1 9 HELIX 4 AA4 ASP A 130 ILE A 132 5 3 HELIX 5 AA5 THR A 136 TYR A 145 1 10 HELIX 6 AA6 TYR A 145 ASN A 150 1 6 HELIX 7 AA7 MET A 155 GLY A 174 1 20 HELIX 8 AA8 CYS A 182 ARG A 187 1 6 HELIX 9 AA9 PRO A 211 THR A 215 5 5 HELIX 10 AB1 GLY A 216 LEU A 228 1 13 HELIX 11 AB2 GLU A 276 LYS A 278 5 3 HELIX 12 AB3 SER A 279 GLY A 289 1 11 HELIX 13 AB4 SER A 290 LYS A 304 1 15 HELIX 14 AB5 THR A 318 ARG A 323 1 6 HELIX 15 AB6 LYS A 344 ASP A 349 1 6 HELIX 16 AB7 SER A 356 LEU A 364 1 9 HELIX 17 AB8 LYS A 370 ARG A 374 5 5 SHEET 1 AA1 2 ILE A 153 PRO A 154 0 SHEET 2 AA1 2 PHE A 191 SER A 192 -1 O SER A 192 N ILE A 153 SHEET 1 AA2 5 PHE A 177 ILE A 181 0 SHEET 2 AA2 5 VAL A 195 ARG A 201 -1 O ILE A 198 N LEU A 180 SHEET 3 AA2 5 ARG A 268 ILE A 275 1 O ASP A 271 N VAL A 195 SHEET 4 AA2 5 LYS A 241 GLY A 246 -1 N GLY A 246 O ARG A 268 SHEET 5 AA2 5 LEU A 231 GLN A 237 -1 N ALA A 236 O MET A 243 SHEET 1 AA3 2 TYR A 306 LEU A 308 0 SHEET 2 AA3 2 LEU A 313 LYS A 315 -1 O PHE A 314 N LEU A 307 SHEET 1 AA4 2 GLU A 338 GLU A 339 0 SHEET 2 AA4 2 VAL A 342 PRO A 343 -1 O VAL A 342 N GLU A 339 LINK O THR A 100 NA NA A 403 1555 1555 2.64 LINK O VAL A 102 NA NA A 403 1555 1555 2.70 LINK O PHE A 105 NA NA A 403 1555 1555 2.64 LINK OD1 ASP A 194 MG MG A 402 1555 1555 2.16 LINK OD2 ASP A 196 MG MG A 402 1555 1555 2.17 LINK O1A D3T A 401 MG MG A 402 1555 1555 2.18 LINK O1B D3T A 401 MG MG A 402 1555 1555 2.13 LINK O1G D3T A 401 MG MG A 402 1555 1555 2.16 LINK MG MG A 402 O HOH A 596 1555 1555 2.28 LINK NA NA A 403 OP1 DT D 4 1555 1555 2.61 LINK NA NA A 403 O HOH D 104 1555 1555 2.42 LINK NA NA A 403 O HOH D 110 1555 1555 2.43 CISPEP 1 GLY A 289 SER A 290 0 2.46 SITE 1 AC1 23 GLY A 183 SER A 184 ARG A 187 SER A 192 SITE 2 AC1 23 GLY A 193 ASP A 194 ASP A 196 THR A 286 SITE 3 AC1 23 PHE A 287 GLY A 289 LYS A 291 ASN A 294 SITE 4 AC1 23 MG A 402 HOH A 596 HOH A 599 HOH A 672 SITE 5 AC1 23 HOH A 675 HOH A 681 HOH A 682 HOH A 688 SITE 6 AC1 23 HOH A 728 DA D 5 DA E 6 SITE 1 AC2 4 ASP A 194 ASP A 196 D3T A 401 HOH A 596 SITE 1 AC3 6 THR A 100 VAL A 102 PHE A 105 DT D 4 SITE 2 AC3 6 HOH D 104 HOH D 110 CRYST1 108.680 108.680 151.641 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 0.009201 0.005312 0.000000 0.00000 SCALE2 0.000000 0.010625 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006595 0.00000