HEADER LIGASE 01-NOV-16 5TT5 TITLE ESCHERICHIA COLI LIGA (K115M) IN COMPLEX WITH NAD+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA LIGASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-586; COMPND 5 SYNONYM: POLYDEOXYRIBONUCLEOTIDE SYNTHASE [NAD(+)]; COMPND 6 EC: 6.5.1.2; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI (STRAIN K12); SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: LIGA, DNAL, LIG, LOP, PDEC, B2411, JW2403; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS METAL CATALYSIS, COVALENT NUCLEOTIDYLTRANSFERASE, LYSYL-AMP, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.GOLDGUR,M.-C.UNCIULEAC,S.H.SHUMAN REVDAT 5 04-OCT-23 5TT5 1 LINK REVDAT 4 04-DEC-19 5TT5 1 REMARK REVDAT 3 20-SEP-17 5TT5 1 REMARK REVDAT 2 22-MAR-17 5TT5 1 JRNL REVDAT 1 08-MAR-17 5TT5 0 JRNL AUTH M.C.UNCIULEAC,Y.GOLDGUR,S.SHUMAN JRNL TITL TWO-METAL VERSUS ONE-METAL MECHANISMS OF LYSINE JRNL TITL 2 ADENYLYLATION BY ATP-DEPENDENT AND NAD(+)-DEPENDENT JRNL TITL 3 POLYNUCLEOTIDE LIGASES. JRNL REF PROC. NATL. ACAD. SCI. V. 114 2592 2017 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 28223499 JRNL DOI 10.1073/PNAS.1619220114 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 83914 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 4151 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 39.4952 - 4.8182 0.96 2849 159 0.1724 0.1899 REMARK 3 2 4.8182 - 3.8254 0.98 2735 168 0.1489 0.1788 REMARK 3 3 3.8254 - 3.3421 0.99 2761 146 0.1634 0.2020 REMARK 3 4 3.3421 - 3.0367 0.99 2736 135 0.1766 0.2178 REMARK 3 5 3.0367 - 2.8191 0.99 2735 132 0.1831 0.2117 REMARK 3 6 2.8191 - 2.6529 0.99 2698 132 0.1761 0.1877 REMARK 3 7 2.6529 - 2.5201 0.99 2712 146 0.1808 0.2239 REMARK 3 8 2.5201 - 2.4104 1.00 2701 127 0.1730 0.2229 REMARK 3 9 2.4104 - 2.3176 1.00 2699 156 0.1770 0.2043 REMARK 3 10 2.3176 - 2.2376 0.99 2672 138 0.1659 0.1688 REMARK 3 11 2.2376 - 2.1677 0.99 2691 118 0.1643 0.1776 REMARK 3 12 2.1677 - 2.1057 0.99 2684 141 0.1617 0.1813 REMARK 3 13 2.1057 - 2.0503 0.99 2626 145 0.1734 0.1903 REMARK 3 14 2.0503 - 2.0003 0.99 2699 148 0.1769 0.2173 REMARK 3 15 2.0003 - 1.9548 0.99 2645 143 0.1767 0.2008 REMARK 3 16 1.9548 - 1.9132 0.99 2706 141 0.1808 0.2121 REMARK 3 17 1.9132 - 1.8749 0.99 2632 145 0.1896 0.2318 REMARK 3 18 1.8749 - 1.8396 0.99 2676 138 0.1869 0.2135 REMARK 3 19 1.8396 - 1.8067 0.98 2661 121 0.1858 0.2213 REMARK 3 20 1.8067 - 1.7761 0.99 2609 129 0.1890 0.1909 REMARK 3 21 1.7761 - 1.7474 0.99 2712 130 0.1832 0.2245 REMARK 3 22 1.7474 - 1.7205 0.99 2651 135 0.1950 0.2262 REMARK 3 23 1.7205 - 1.6952 0.99 2650 134 0.1953 0.2398 REMARK 3 24 1.6952 - 1.6714 0.99 2676 144 0.1992 0.2527 REMARK 3 25 1.6714 - 1.6488 0.99 2624 148 0.2079 0.2652 REMARK 3 26 1.6488 - 1.6274 0.99 2660 129 0.2152 0.2570 REMARK 3 27 1.6274 - 1.6070 0.98 2631 139 0.2335 0.2405 REMARK 3 28 1.6070 - 1.5877 0.97 2568 142 0.2374 0.2646 REMARK 3 29 1.5877 - 1.5692 0.94 2509 132 0.2576 0.2766 REMARK 3 30 1.5692 - 1.5516 0.80 2155 110 0.2896 0.3134 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.750 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 : 0.007 4659 REMARK 3 ANGLE : 0.924 6319 REMARK 3 CHIRALITY : 0.055 720 REMARK 3 PLANARITY : 0.005 829 REMARK 3 DIHEDRAL : 16.605 2814 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5TT5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-NOV-16. REMARK 100 THE DEPOSITION ID IS D_1000224768. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-OCT-16 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 : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97920 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 83987 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.47600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2OWO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M NA ACETATE, 20% PEG3350, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 295K 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 20.45350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 75.46350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.15600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 75.46350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.45350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.15600 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 MET A -19 REMARK 465 GLY A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 SER A -7 REMARK 465 SER A -6 REMARK 465 HIS A -5 REMARK 465 ILE A -4 REMARK 465 GLU A -3 REMARK 465 GLY A -2 REMARK 465 ARG A -1 REMARK 465 HIS A 0 REMARK 465 LYS A 103 REMARK 465 ASN A 104 REMARK 465 ASN A 105 REMARK 465 GLU A 106 REMARK 465 LYS A 107 REMARK 465 ILE A 587 REMARK 465 VAL A 588 REMARK 465 ILE A 589 REMARK 465 ASN A 590 REMARK 465 ALA A 591 REMARK 465 GLU A 592 REMARK 465 GLU A 593 REMARK 465 ILE A 594 REMARK 465 ASP A 595 REMARK 465 SER A 596 REMARK 465 PRO A 597 REMARK 465 PHE A 598 REMARK 465 ALA A 599 REMARK 465 GLY A 600 REMARK 465 LYS A 601 REMARK 465 THR A 602 REMARK 465 VAL A 603 REMARK 465 VAL A 604 REMARK 465 LEU A 605 REMARK 465 THR A 606 REMARK 465 GLY A 607 REMARK 465 SER A 608 REMARK 465 LEU A 609 REMARK 465 SER A 610 REMARK 465 GLN A 611 REMARK 465 MET A 612 REMARK 465 SER A 613 REMARK 465 ARG A 614 REMARK 465 ASP A 615 REMARK 465 ASP A 616 REMARK 465 ALA A 617 REMARK 465 LYS A 618 REMARK 465 ALA A 619 REMARK 465 ARG A 620 REMARK 465 LEU A 621 REMARK 465 VAL A 622 REMARK 465 GLU A 623 REMARK 465 LEU A 624 REMARK 465 GLY A 625 REMARK 465 ALA A 626 REMARK 465 LYS A 627 REMARK 465 VAL A 628 REMARK 465 ALA A 629 REMARK 465 GLY A 630 REMARK 465 SER A 631 REMARK 465 VAL A 632 REMARK 465 SER A 633 REMARK 465 LYS A 634 REMARK 465 LYS A 635 REMARK 465 THR A 636 REMARK 465 ASP A 637 REMARK 465 LEU A 638 REMARK 465 VAL A 639 REMARK 465 ILE A 640 REMARK 465 ALA A 641 REMARK 465 GLY A 642 REMARK 465 GLU A 643 REMARK 465 ALA A 644 REMARK 465 ALA A 645 REMARK 465 GLY A 646 REMARK 465 SER A 647 REMARK 465 LYS A 648 REMARK 465 LEU A 649 REMARK 465 ALA A 650 REMARK 465 LYS A 651 REMARK 465 ALA A 652 REMARK 465 GLN A 653 REMARK 465 GLU A 654 REMARK 465 LEU A 655 REMARK 465 GLY A 656 REMARK 465 ILE A 657 REMARK 465 GLU A 658 REMARK 465 VAL A 659 REMARK 465 ILE A 660 REMARK 465 ASP A 661 REMARK 465 GLU A 662 REMARK 465 ALA A 663 REMARK 465 GLU A 664 REMARK 465 MET A 665 REMARK 465 LEU A 666 REMARK 465 ARG A 667 REMARK 465 LEU A 668 REMARK 465 LEU A 669 REMARK 465 GLY A 670 REMARK 465 SER A 671 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 NE ARG A 425 O HOH A 801 1.91 REMARK 500 O HOH A 1208 O HOH A 1351 1.92 REMARK 500 OD1 ASP A 187 O HOH A 802 1.95 REMARK 500 OE2 GLU A 397 O HOH A 803 1.98 REMARK 500 OE2 GLU A 544 O HOH A 804 1.99 REMARK 500 O HOH A 1225 O HOH A 1412 1.99 REMARK 500 NH1 ARG A 242 O HOH A 805 1.99 REMARK 500 O HOH A 1449 O HOH A 1510 2.00 REMARK 500 O HOH A 1379 O HOH A 1467 2.02 REMARK 500 O HOH A 977 O HOH A 981 2.02 REMARK 500 O HOH A 1114 O HOH A 1367 2.03 REMARK 500 O HOH A 1291 O HOH A 1405 2.04 REMARK 500 OE2 GLU A 10 O HOH A 806 2.05 REMARK 500 O HOH A 1022 O HOH A 1464 2.05 REMARK 500 O HOH A 848 O HOH A 1361 2.06 REMARK 500 O HOH A 1006 O HOH A 1178 2.08 REMARK 500 O HOH A 961 O HOH A 1601 2.09 REMARK 500 NH1 ARG A 40 O HOH A 807 2.10 REMARK 500 O HOH A 1161 O HOH A 1478 2.10 REMARK 500 O MET A 488 O HOH A 808 2.13 REMARK 500 O HOH A 1102 O HOH A 1247 2.13 REMARK 500 O HOH A 969 O HOH A 1220 2.14 REMARK 500 O HOH A 1111 O HOH A 1480 2.14 REMARK 500 O HIS A 469 O HOH A 809 2.16 REMARK 500 O HOH A 948 O HOH A 1115 2.16 REMARK 500 O HOH A 1396 O HOH A 1430 2.16 REMARK 500 NH2 ARG A 43 O HOH A 810 2.16 REMARK 500 O HOH A 1134 O HOH A 1434 2.16 REMARK 500 O HOH A 1151 O HOH A 1483 2.17 REMARK 500 O HOH A 1008 O HOH A 1440 2.17 REMARK 500 NH2 ARG A 305 O HOH A 811 2.18 REMARK 500 OD2 ASP A 100 O HOH A 812 2.18 REMARK 500 O HOH A 854 O HOH A 1002 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 1133 O HOH A 1501 3554 1.97 REMARK 500 O HOH A 1181 O HOH A 1228 3444 2.01 REMARK 500 O HOH A 1529 O HOH A 1605 1455 2.03 REMARK 500 O HOH A 1351 O HOH A 1411 3554 2.08 REMARK 500 O HOH A 1521 O HOH A 1579 1655 2.16 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 ALA A 27 59.77 -149.20 REMARK 500 LEU A 80 -167.04 -125.57 REMARK 500 SER A 81 -160.74 -109.57 REMARK 500 TYR A 225 -7.31 -142.39 REMARK 500 SER A 354 16.76 -140.96 REMARK 500 HIS A 359 -69.94 69.75 REMARK 500 ALA A 448 -118.49 -106.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1638 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH A1639 DISTANCE = 6.49 ANGSTROMS REMARK 525 HOH A1640 DISTANCE = 7.57 ANGSTROMS 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 ZN A 702 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 408 SG REMARK 620 2 CYS A 411 SG 109.6 REMARK 620 3 CYS A 426 SG 107.1 95.8 REMARK 620 4 CYS A 432 SG 117.3 109.9 114.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 703 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 NAD A 701 O1A REMARK 620 2 HOH A 905 O 92.7 REMARK 620 3 HOH A 949 O 93.3 173.9 REMARK 620 4 HOH A 958 O 86.3 91.6 89.8 REMARK 620 5 HOH A 962 O 173.9 87.4 86.8 87.7 REMARK 620 6 HOH A1182 O 96.7 88.9 89.5 177.0 89.4 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 NAD A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 703 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5TT6 RELATED DB: PDB DBREF 5TT5 A 1 671 UNP P15042 DNLJ_ECOLI 1 671 SEQADV 5TT5 MET A -19 UNP P15042 INITIATING METHIONINE SEQADV 5TT5 GLY A -18 UNP P15042 EXPRESSION TAG SEQADV 5TT5 HIS A -17 UNP P15042 EXPRESSION TAG SEQADV 5TT5 HIS A -16 UNP P15042 EXPRESSION TAG SEQADV 5TT5 HIS A -15 UNP P15042 EXPRESSION TAG SEQADV 5TT5 HIS A -14 UNP P15042 EXPRESSION TAG SEQADV 5TT5 HIS A -13 UNP P15042 EXPRESSION TAG SEQADV 5TT5 HIS A -12 UNP P15042 EXPRESSION TAG SEQADV 5TT5 HIS A -11 UNP P15042 EXPRESSION TAG SEQADV 5TT5 HIS A -10 UNP P15042 EXPRESSION TAG SEQADV 5TT5 HIS A -9 UNP P15042 EXPRESSION TAG SEQADV 5TT5 HIS A -8 UNP P15042 EXPRESSION TAG SEQADV 5TT5 SER A -7 UNP P15042 EXPRESSION TAG SEQADV 5TT5 SER A -6 UNP P15042 EXPRESSION TAG SEQADV 5TT5 HIS A -5 UNP P15042 EXPRESSION TAG SEQADV 5TT5 ILE A -4 UNP P15042 EXPRESSION TAG SEQADV 5TT5 GLU A -3 UNP P15042 EXPRESSION TAG SEQADV 5TT5 GLY A -2 UNP P15042 EXPRESSION TAG SEQADV 5TT5 ARG A -1 UNP P15042 EXPRESSION TAG SEQADV 5TT5 HIS A 0 UNP P15042 EXPRESSION TAG SEQADV 5TT5 MET A 115 UNP P15042 LYS 115 ENGINEERED MUTATION SEQRES 1 A 691 MET GLY HIS HIS HIS HIS HIS HIS HIS HIS HIS HIS SER SEQRES 2 A 691 SER HIS ILE GLU GLY ARG HIS MET GLU SER ILE GLU GLN SEQRES 3 A 691 GLN LEU THR GLU LEU ARG THR THR LEU ARG HIS HIS GLU SEQRES 4 A 691 TYR LEU TYR HIS VAL MET ASP ALA PRO GLU ILE PRO ASP SEQRES 5 A 691 ALA GLU TYR ASP ARG LEU MET ARG GLU LEU ARG GLU LEU SEQRES 6 A 691 GLU THR LYS HIS PRO GLU LEU ILE THR PRO ASP SER PRO SEQRES 7 A 691 THR GLN ARG VAL GLY ALA ALA PRO LEU ALA ALA PHE SER SEQRES 8 A 691 GLN ILE ARG HIS GLU VAL PRO MET LEU SER LEU ASP ASN SEQRES 9 A 691 VAL PHE ASP GLU GLU SER PHE LEU ALA PHE ASN LYS ARG SEQRES 10 A 691 VAL GLN ASP ARG LEU LYS ASN ASN GLU LYS VAL THR TRP SEQRES 11 A 691 CYS CYS GLU LEU MET LEU ASP GLY LEU ALA VAL SER ILE SEQRES 12 A 691 LEU TYR GLU ASN GLY VAL LEU VAL SER ALA ALA THR ARG SEQRES 13 A 691 GLY ASP GLY THR THR GLY GLU ASP ILE THR SER ASN VAL SEQRES 14 A 691 ARG THR ILE ARG ALA ILE PRO LEU LYS LEU HIS GLY GLU SEQRES 15 A 691 ASN ILE PRO ALA ARG LEU GLU VAL ARG GLY GLU VAL PHE SEQRES 16 A 691 LEU PRO GLN ALA GLY PHE GLU LYS ILE ASN GLU ASP ALA SEQRES 17 A 691 ARG ARG THR GLY GLY LYS VAL PHE ALA ASN PRO ARG ASN SEQRES 18 A 691 ALA ALA ALA GLY SER LEU ARG GLN LEU ASP PRO ARG ILE SEQRES 19 A 691 THR ALA LYS ARG PRO LEU THR PHE PHE CYS TYR GLY VAL SEQRES 20 A 691 GLY VAL LEU GLU GLY GLY GLU LEU PRO ASP THR HIS LEU SEQRES 21 A 691 GLY ARG LEU LEU GLN PHE LYS LYS TRP GLY LEU PRO VAL SEQRES 22 A 691 SER ASP ARG VAL THR LEU CYS GLU SER ALA GLU GLU VAL SEQRES 23 A 691 LEU ALA PHE TYR HIS LYS VAL GLU GLU ASP ARG PRO THR SEQRES 24 A 691 LEU GLY PHE ASP ILE ASP GLY VAL VAL ILE LYS VAL ASN SEQRES 25 A 691 SER LEU ALA GLN GLN GLU GLN LEU GLY PHE VAL ALA ARG SEQRES 26 A 691 ALA PRO ARG TRP ALA VAL ALA PHE LYS PHE PRO ALA GLN SEQRES 27 A 691 GLU GLN MET THR PHE VAL ARG ASP VAL GLU PHE GLN VAL SEQRES 28 A 691 GLY ARG THR GLY ALA ILE THR PRO VAL ALA ARG LEU GLU SEQRES 29 A 691 PRO VAL HIS VAL ALA GLY VAL LEU VAL SER ASN ALA THR SEQRES 30 A 691 LEU HIS ASN ALA ASP GLU ILE GLU ARG LEU GLY LEU ARG SEQRES 31 A 691 ILE GLY ASP LYS VAL VAL ILE ARG ARG ALA GLY ASP VAL SEQRES 32 A 691 ILE PRO GLN VAL VAL ASN VAL VAL LEU SER GLU ARG PRO SEQRES 33 A 691 GLU ASP THR ARG GLU VAL VAL PHE PRO THR HIS CYS PRO SEQRES 34 A 691 VAL CYS GLY SER ASP VAL GLU ARG VAL GLU GLY GLU ALA SEQRES 35 A 691 VAL ALA ARG CYS THR GLY GLY LEU ILE CYS GLY ALA GLN SEQRES 36 A 691 ARG LYS GLU SER LEU LYS HIS PHE VAL SER ARG ARG ALA SEQRES 37 A 691 MET ASP VAL ASP GLY MET GLY ASP LYS ILE ILE ASP GLN SEQRES 38 A 691 LEU VAL GLU LYS GLU TYR VAL HIS THR PRO ALA ASP LEU SEQRES 39 A 691 PHE LYS LEU THR ALA GLY LYS LEU THR GLY LEU GLU ARG SEQRES 40 A 691 MET GLY PRO LYS SER ALA GLN ASN VAL VAL ASN ALA LEU SEQRES 41 A 691 GLU LYS ALA LYS GLU THR THR PHE ALA ARG PHE LEU TYR SEQRES 42 A 691 ALA LEU GLY ILE ARG GLU VAL GLY GLU ALA THR ALA ALA SEQRES 43 A 691 GLY LEU ALA ALA TYR PHE GLY THR LEU GLU ALA LEU GLU SEQRES 44 A 691 ALA ALA SER ILE GLU GLU LEU GLN LYS VAL PRO ASP VAL SEQRES 45 A 691 GLY ILE VAL VAL ALA SER HIS VAL HIS ASN PHE PHE ALA SEQRES 46 A 691 GLU GLU SER ASN ARG ASN VAL ILE SER GLU LEU LEU ALA SEQRES 47 A 691 GLU GLY VAL HIS TRP PRO ALA PRO ILE VAL ILE ASN ALA SEQRES 48 A 691 GLU GLU ILE ASP SER PRO PHE ALA GLY LYS THR VAL VAL SEQRES 49 A 691 LEU THR GLY SER LEU SER GLN MET SER ARG ASP ASP ALA SEQRES 50 A 691 LYS ALA ARG LEU VAL GLU LEU GLY ALA LYS VAL ALA GLY SEQRES 51 A 691 SER VAL SER LYS LYS THR ASP LEU VAL ILE ALA GLY GLU SEQRES 52 A 691 ALA ALA GLY SER LYS LEU ALA LYS ALA GLN GLU LEU GLY SEQRES 53 A 691 ILE GLU VAL ILE ASP GLU ALA GLU MET LEU ARG LEU LEU SEQRES 54 A 691 GLY SER HET NAD A 701 44 HET ZN A 702 1 HET MG A 703 1 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION FORMUL 2 NAD C21 H27 N7 O14 P2 FORMUL 3 ZN ZN 2+ FORMUL 4 MG MG 2+ FORMUL 5 HOH *840(H2 O) HELIX 1 AA1 SER A 3 VAL A 24 1 22 HELIX 2 AA2 PRO A 31 HIS A 49 1 19 HELIX 3 AA3 PRO A 50 ILE A 53 5 4 HELIX 4 AA4 SER A 57 ARG A 61 5 5 HELIX 5 AA5 ASP A 87 LEU A 102 1 16 HELIX 6 AA6 ILE A 145 ARG A 150 1 6 HELIX 7 AA7 PRO A 177 GLY A 192 1 16 HELIX 8 AA8 ASN A 198 ARG A 208 1 11 HELIX 9 AA9 ASP A 211 LYS A 217 1 7 HELIX 10 AB1 THR A 238 GLY A 250 1 13 HELIX 11 AB2 SER A 262 ARG A 277 1 16 HELIX 12 AB3 PRO A 278 LEU A 280 5 3 HELIX 13 AB4 SER A 293 GLY A 301 1 9 HELIX 14 AB5 ASN A 360 GLY A 368 1 9 HELIX 15 AB6 LEU A 392 ARG A 395 5 4 HELIX 16 AB7 CYS A 432 ALA A 434 5 3 HELIX 17 AB8 GLN A 435 VAL A 444 1 10 HELIX 18 AB9 GLY A 455 LYS A 465 1 11 HELIX 19 AC1 THR A 470 LYS A 476 1 7 HELIX 20 AC2 THR A 478 GLY A 484 1 7 HELIX 21 AC3 GLY A 489 LYS A 504 1 16 HELIX 22 AC4 THR A 507 LEU A 515 1 9 HELIX 23 AC5 GLY A 521 GLY A 533 1 13 HELIX 24 AC6 THR A 534 ALA A 541 1 8 HELIX 25 AC7 SER A 542 LYS A 548 1 7 HELIX 26 AC8 GLY A 553 GLU A 566 1 14 HELIX 27 AC9 GLU A 566 GLU A 579 1 14 SHEET 1 AA1 2 GLN A 72 ARG A 74 0 SHEET 2 AA1 2 THR A 141 GLU A 143 -1 O GLY A 142 N ILE A 73 SHEET 1 AA2 5 ASN A 84 VAL A 85 0 SHEET 2 AA2 5 ALA A 310 LYS A 314 1 O LYS A 314 N VAL A 85 SHEET 3 AA2 5 ILE A 284 VAL A 291 -1 N VAL A 287 O PHE A 313 SHEET 4 AA2 5 TRP A 110 LEU A 116 -1 N CYS A 111 O LYS A 290 SHEET 5 AA2 5 THR A 258 CYS A 260 -1 O THR A 258 N CYS A 112 SHEET 1 AA3 4 VAL A 129 THR A 135 0 SHEET 2 AA3 4 LEU A 119 GLU A 126 -1 N LEU A 124 O VAL A 131 SHEET 3 AA3 4 ARG A 167 PHE A 175 -1 O LEU A 168 N TYR A 125 SHEET 4 AA3 4 THR A 221 GLU A 231 -1 O TYR A 225 N ARG A 171 SHEET 1 AA4 8 VAL A 415 GLU A 416 0 SHEET 2 AA4 8 ALA A 424 CYS A 426 -1 O ARG A 425 N GLU A 416 SHEET 3 AA4 8 ALA A 336 VAL A 348 -1 N ILE A 337 O ALA A 424 SHEET 4 AA4 8 VAL A 351 THR A 357 -1 O VAL A 351 N VAL A 348 SHEET 5 AA4 8 GLN A 386 VAL A 390 1 O VAL A 387 N THR A 357 SHEET 6 AA4 8 LYS A 374 ARG A 378 -1 N VAL A 376 O VAL A 388 SHEET 7 AA4 8 GLU A 319 VAL A 331 -1 N THR A 322 O VAL A 375 SHEET 8 AA4 8 ALA A 336 VAL A 348 -1 O VAL A 340 N GLU A 328 LINK SG CYS A 408 ZN ZN A 702 1555 1555 2.30 LINK SG CYS A 411 ZN ZN A 702 1555 1555 2.31 LINK SG CYS A 426 ZN ZN A 702 1555 1555 2.32 LINK SG CYS A 432 ZN ZN A 702 1555 1555 2.33 LINK O1A NAD A 701 MG MG A 703 1555 1555 2.03 LINK MG MG A 703 O HOH A 905 1555 1555 2.08 LINK MG MG A 703 O HOH A 949 1555 1555 2.09 LINK MG MG A 703 O HOH A 958 1555 1555 2.14 LINK MG MG A 703 O HOH A 962 1555 1555 2.11 LINK MG MG A 703 O HOH A1182 1555 1555 2.12 SITE 1 AC1 34 HIS A 18 TYR A 22 HIS A 23 PRO A 28 SITE 2 AC1 34 ILE A 30 ASP A 32 TYR A 35 ASP A 36 SITE 3 AC1 34 LEU A 80 SER A 81 LEU A 82 GLU A 113 SITE 4 AC1 34 LEU A 114 MET A 115 LEU A 116 ALA A 120 SITE 5 AC1 34 ARG A 136 GLU A 173 TYR A 225 VAL A 288 SITE 6 AC1 34 LYS A 290 LYS A 314 MG A 703 HOH A 900 SITE 7 AC1 34 HOH A 905 HOH A 949 HOH A 958 HOH A 968 SITE 8 AC1 34 HOH A 969 HOH A1031 HOH A1041 HOH A1083 SITE 9 AC1 34 HOH A1182 HOH A1275 SITE 1 AC2 4 CYS A 408 CYS A 411 CYS A 426 CYS A 432 SITE 1 AC3 6 NAD A 701 HOH A 905 HOH A 949 HOH A 958 SITE 2 AC3 6 HOH A 962 HOH A1182 CRYST1 40.907 94.312 150.927 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 0.024446 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010603 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006626 0.00000