HEADER TRANSFERASE 08-JAN-15 4XJ4 TITLE CRYSTAL STRUCTURE OF VIBRIO CHOLERAE DNCV 3'-DEOXY ATP BOUND FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLIC AMP-GMP SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-215,242-412; COMPND 5 SYNONYM: C-AMP-GMP SYNTHASE,DINUCLEOTIDE CYCLASE DNCV; COMPND 6 EC: 2.7.7.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO CHOLERAE O1 BIOVAR EL TOR STR. N16961; SOURCE 3 ORGANISM_TAXID: 243277; SOURCE 4 STRAIN: N16961; SOURCE 5 GENE: DNCV, VC_0179; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CYCLIC GMP-AMP SYNTHASE, BACTERIAL VIRULENCE, NUCLEOTIDYLTRANSFERASE, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR K.KATO,R.ISHII,R.ISHITANI,O.NUREKI REVDAT 4 08-NOV-23 4XJ4 1 REMARK REVDAT 3 05-FEB-20 4XJ4 1 SOURCE JRNL REMARK REVDAT 2 20-MAY-15 4XJ4 1 JRNL REVDAT 1 29-APR-15 4XJ4 0 JRNL AUTH K.KATO,R.ISHII,S.HIRANO,R.ISHITANI,O.NUREKI JRNL TITL STRUCTURAL BASIS FOR THE CATALYTIC MECHANISM OF DNCV, JRNL TITL 2 BACTERIAL HOMOLOG OF CYCLIC GMP-AMP SYNTHASE JRNL REF STRUCTURE V. 23 843 2015 JRNL REFN ISSN 0969-2126 JRNL PMID 25865248 JRNL DOI 10.1016/J.STR.2015.01.023 REMARK 2 REMARK 2 RESOLUTION. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 55525 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 2773 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 47.0555 - 4.3316 0.98 2775 142 0.1518 0.1713 REMARK 3 2 4.3316 - 3.4385 0.99 2707 144 0.1502 0.1928 REMARK 3 3 3.4385 - 3.0039 0.99 2688 136 0.1777 0.1815 REMARK 3 4 3.0039 - 2.7293 0.95 2602 144 0.1810 0.2103 REMARK 3 5 2.7293 - 2.5337 0.99 2686 137 0.1786 0.2007 REMARK 3 6 2.5337 - 2.3843 0.99 2663 146 0.1770 0.2086 REMARK 3 7 2.3843 - 2.2649 0.99 2706 137 0.1710 0.2057 REMARK 3 8 2.2649 - 2.1663 0.99 2663 149 0.1677 0.1978 REMARK 3 9 2.1663 - 2.0829 0.97 2602 137 0.1794 0.2239 REMARK 3 10 2.0829 - 2.0110 0.96 2606 136 0.1881 0.2261 REMARK 3 11 2.0110 - 1.9482 0.98 2622 137 0.1831 0.2165 REMARK 3 12 1.9482 - 1.8925 0.99 2683 138 0.1794 0.1939 REMARK 3 13 1.8925 - 1.8427 0.99 2662 144 0.1778 0.2237 REMARK 3 14 1.8427 - 1.7977 0.99 2691 128 0.1743 0.1929 REMARK 3 15 1.7977 - 1.7568 1.00 2669 156 0.1855 0.2284 REMARK 3 16 1.7568 - 1.7194 0.99 2718 133 0.1940 0.2299 REMARK 3 17 1.7194 - 1.6850 1.00 2647 131 0.1933 0.2553 REMARK 3 18 1.6850 - 1.6532 0.94 2496 140 0.2035 0.2410 REMARK 3 19 1.6532 - 1.6237 0.96 2640 136 0.2251 0.2665 REMARK 3 20 1.6237 - 1.5962 0.84 2226 122 0.2501 0.2594 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) : 19.970 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 : 0.011 3133 REMARK 3 ANGLE : 1.355 4246 REMARK 3 CHIRALITY : 0.057 462 REMARK 3 PLANARITY : 0.006 541 REMARK 3 DIHEDRAL : 15.605 1188 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 10 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 25 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.6065 -11.1688 -5.2320 REMARK 3 T TENSOR REMARK 3 T11: 0.1003 T22: 0.1130 REMARK 3 T33: 0.1428 T12: 0.0055 REMARK 3 T13: -0.0064 T23: 0.0134 REMARK 3 L TENSOR REMARK 3 L11: 3.7242 L22: 4.4650 REMARK 3 L33: 2.8870 L12: -1.1573 REMARK 3 L13: -2.1172 L23: 2.9294 REMARK 3 S TENSOR REMARK 3 S11: 0.1556 S12: 0.0899 S13: 0.0053 REMARK 3 S21: -0.2121 S22: -0.1752 S23: 0.1603 REMARK 3 S31: -0.0231 S32: -0.0772 S33: 0.0536 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 26 THROUGH 93 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.5858 -32.8991 -45.6893 REMARK 3 T TENSOR REMARK 3 T11: 0.2961 T22: 0.3321 REMARK 3 T33: 0.1800 T12: 0.0308 REMARK 3 T13: -0.0316 T23: -0.0529 REMARK 3 L TENSOR REMARK 3 L11: 2.2141 L22: 3.2697 REMARK 3 L33: 6.4957 L12: -1.9193 REMARK 3 L13: -2.9787 L23: 4.3087 REMARK 3 S TENSOR REMARK 3 S11: 0.1516 S12: 0.1089 S13: -0.0820 REMARK 3 S21: -0.3784 S22: -0.1777 S23: -0.0235 REMARK 3 S31: -0.7802 S32: -0.2535 S33: -0.0066 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 94 THROUGH 117 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.5418 -39.9730 -35.5735 REMARK 3 T TENSOR REMARK 3 T11: 0.3904 T22: 0.2889 REMARK 3 T33: 0.2856 T12: -0.0187 REMARK 3 T13: 0.0483 T23: -0.0934 REMARK 3 L TENSOR REMARK 3 L11: 4.3184 L22: 2.1701 REMARK 3 L33: 2.4446 L12: -3.0322 REMARK 3 L13: -3.2562 L23: 2.2754 REMARK 3 S TENSOR REMARK 3 S11: -0.3698 S12: 0.3341 S13: -0.6717 REMARK 3 S21: 0.6244 S22: -0.3034 S23: 0.5426 REMARK 3 S31: 0.8958 S32: -0.4704 S33: 0.7081 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 118 THROUGH 150 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.4843 -30.6251 -26.5476 REMARK 3 T TENSOR REMARK 3 T11: 0.2441 T22: 0.2676 REMARK 3 T33: 0.2152 T12: 0.0552 REMARK 3 T13: -0.0307 T23: -0.0510 REMARK 3 L TENSOR REMARK 3 L11: 1.3850 L22: 2.0774 REMARK 3 L33: 3.3424 L12: 0.8703 REMARK 3 L13: -0.2877 L23: 1.4053 REMARK 3 S TENSOR REMARK 3 S11: 0.0389 S12: 0.2821 S13: -0.2939 REMARK 3 S21: -0.0313 S22: -0.0057 S23: -0.2192 REMARK 3 S31: 0.2380 S32: -0.0047 S33: 0.0043 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 151 THROUGH 245 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.3369 -28.4212 -33.4169 REMARK 3 T TENSOR REMARK 3 T11: 0.1952 T22: 0.2937 REMARK 3 T33: 0.1802 T12: 0.0090 REMARK 3 T13: -0.0025 T23: -0.0914 REMARK 3 L TENSOR REMARK 3 L11: 1.9405 L22: 7.0102 REMARK 3 L33: 4.6418 L12: -1.8748 REMARK 3 L13: -0.7876 L23: 0.9219 REMARK 3 S TENSOR REMARK 3 S11: 0.0480 S12: 0.0620 S13: 0.0999 REMARK 3 S21: -0.2158 S22: 0.0841 S23: -0.2359 REMARK 3 S31: -0.4267 S32: 0.1061 S33: -0.1120 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 246 THROUGH 277 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.2595 -36.8102 -18.3968 REMARK 3 T TENSOR REMARK 3 T11: 0.2230 T22: 0.2149 REMARK 3 T33: 0.2716 T12: 0.0324 REMARK 3 T13: -0.0495 T23: -0.0100 REMARK 3 L TENSOR REMARK 3 L11: 4.8171 L22: 3.1586 REMARK 3 L33: 8.7165 L12: -1.7065 REMARK 3 L13: -5.2108 L23: 2.7398 REMARK 3 S TENSOR REMARK 3 S11: -0.1502 S12: 0.1980 S13: -0.3613 REMARK 3 S21: -0.0300 S22: -0.1351 S23: 0.1367 REMARK 3 S31: 0.5474 S32: 0.2104 S33: 0.3060 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 278 THROUGH 338 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.9758 -22.9150 -4.0770 REMARK 3 T TENSOR REMARK 3 T11: 0.1164 T22: 0.1014 REMARK 3 T33: 0.1467 T12: -0.0044 REMARK 3 T13: -0.0207 T23: 0.0140 REMARK 3 L TENSOR REMARK 3 L11: 3.6553 L22: 1.7522 REMARK 3 L33: 1.7550 L12: -0.6514 REMARK 3 L13: -0.4563 L23: 0.1104 REMARK 3 S TENSOR REMARK 3 S11: 0.0131 S12: -0.1201 S13: -0.2878 REMARK 3 S21: -0.0048 S22: -0.0215 S23: 0.1513 REMARK 3 S31: 0.0732 S32: 0.0268 S33: 0.0064 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 339 THROUGH 360 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.9481 -34.6743 -8.0342 REMARK 3 T TENSOR REMARK 3 T11: 0.2149 T22: 0.1533 REMARK 3 T33: 0.2749 T12: 0.0519 REMARK 3 T13: -0.0188 T23: -0.0183 REMARK 3 L TENSOR REMARK 3 L11: 5.8643 L22: 5.9364 REMARK 3 L33: 4.7908 L12: 4.1268 REMARK 3 L13: 3.5055 L23: 1.9024 REMARK 3 S TENSOR REMARK 3 S11: 0.2678 S12: 0.3521 S13: -0.6693 REMARK 3 S21: 0.0118 S22: -0.0266 S23: -0.2695 REMARK 3 S31: 0.6348 S32: 0.2024 S33: -0.2053 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 361 THROUGH 382 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.7475 -16.4942 -0.3579 REMARK 3 T TENSOR REMARK 3 T11: 0.1126 T22: 0.1119 REMARK 3 T33: 0.0760 T12: -0.0076 REMARK 3 T13: -0.0238 T23: 0.1138 REMARK 3 L TENSOR REMARK 3 L11: 1.9178 L22: 7.2109 REMARK 3 L33: 3.3879 L12: 0.6538 REMARK 3 L13: 1.0220 L23: 4.3228 REMARK 3 S TENSOR REMARK 3 S11: 0.0142 S12: -0.1867 S13: -0.0857 REMARK 3 S21: 0.1357 S22: -0.0337 S23: -0.2467 REMARK 3 S31: 0.0378 S32: 0.2117 S33: -0.1775 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 383 THROUGH 412 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.0959 -4.9792 -0.0823 REMARK 3 T TENSOR REMARK 3 T11: 0.1479 T22: 0.0784 REMARK 3 T33: 0.1406 T12: -0.0067 REMARK 3 T13: 0.0044 T23: 0.0131 REMARK 3 L TENSOR REMARK 3 L11: 5.5490 L22: 2.9298 REMARK 3 L33: 6.8649 L12: -1.1007 REMARK 3 L13: -1.8171 L23: 2.9236 REMARK 3 S TENSOR REMARK 3 S11: 0.1129 S12: -0.1939 S13: 0.2740 REMARK 3 S21: -0.0770 S22: -0.0063 S23: -0.0207 REMARK 3 S31: -0.4147 S32: -0.0042 S33: -0.1124 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 4XJ4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-JAN-15. REMARK 100 THE DEPOSITION ID IS D_1000205776. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-MAY-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55529 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.596 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL 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: 4XJ1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, SODIUM MALONATE, TRIS-HCL, REMARK 280 PH 8.0, VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 59.04500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.65000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 59.04500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.65000 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: 1650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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 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 A1126 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1178 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 MET A 1 REMARK 465 GLU A 203 REMARK 465 PHE A 204 REMARK 465 GLN A 205 REMARK 465 LYS A 206 REMARK 465 LYS A 207 REMARK 465 GLN A 208 REMARK 465 ILE A 209 REMARK 465 ALA A 210 REMARK 465 LEU A 211 REMARK 465 GLU A 212 REMARK 465 ALA A 213 REMARK 465 ASN A 214 REMARK 465 ARG A 215 REMARK 465 GLY A 239 REMARK 465 SER A 240 REMARK 465 GLY A 241 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 ARG A 2 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 27 CG CD OE1 OE2 REMARK 470 LYS A 59 CG CD CE NZ REMARK 470 GLU A 146 CG CD OE1 OE2 REMARK 470 LYS A 173 CG CD CE NZ REMARK 470 LYS A 184 CG CD CE NZ REMARK 470 GLU A 243 CG CD OE1 OE2 REMARK 470 GLU A 251 CG CD OE1 OE2 REMARK 470 GLU A 342 CG CD OE1 OE2 REMARK 470 GLU A 349 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 A 1151 O HOH A 1162 2.04 REMARK 500 O HOH A 1236 O HOH A 1269 2.12 REMARK 500 OE1 GLU A 324 O HOH A 1101 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 ASP A 16 18.67 -145.10 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 A1008 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 131 OD1 REMARK 620 2 ASP A 133 OD2 99.1 REMARK 620 3 3AT A1006 O1G 84.4 176.5 REMARK 620 4 3AT A1006 O1B 161.1 89.3 87.3 REMARK 620 5 3AT A1006 O1A 114.2 93.4 85.1 81.9 REMARK 620 6 HOH A1187 O 77.6 85.2 95.6 86.4 168.2 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 EDO A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 3AT A 1006 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 3AT A 1007 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 1008 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4XJ1 RELATED DB: PDB REMARK 900 RELATED ID: 4XJ3 RELATED DB: PDB REMARK 900 RELATED ID: 4XJ5 RELATED DB: PDB REMARK 900 RELATED ID: 4XJ6 RELATED DB: PDB DBREF 4XJ4 A 1 215 UNP Q9KVG7 DNCV_VIBCH 1 215 DBREF 4XJ4 A 242 412 UNP Q9KVG7 DNCV_VIBCH 242 412 SEQADV 4XJ4 GLY A 239 UNP Q9KVG7 LINKER SEQADV 4XJ4 SER A 240 UNP Q9KVG7 LINKER SEQADV 4XJ4 GLY A 241 UNP Q9KVG7 LINKER SEQRES 1 A 389 MET ARG MET THR TRP ASN PHE HIS GLN TYR TYR THR ASN SEQRES 2 A 389 ARG ASN ASP GLY LEU MET GLY LYS LEU VAL LEU THR ASP SEQRES 3 A 389 GLU GLU LYS ASN ASN LEU LYS ALA LEU ARG LYS ILE ILE SEQRES 4 A 389 ARG LEU ARG THR ARG ASP VAL PHE GLU GLU ALA LYS GLY SEQRES 5 A 389 ILE ALA LYS ALA VAL LYS LYS SER ALA LEU THR PHE GLU SEQRES 6 A 389 ILE ILE GLN GLU LYS VAL SER THR THR GLN ILE LYS HIS SEQRES 7 A 389 LEU SER ASP SER GLU GLN ARG GLU VAL ALA LYS LEU ILE SEQRES 8 A 389 TYR GLU MET ASP ASP ASP ALA ARG ASP GLU PHE LEU GLY SEQRES 9 A 389 LEU THR PRO ARG PHE TRP THR GLN GLY SER PHE GLN TYR SEQRES 10 A 389 ASP THR LEU ASN ARG PRO PHE GLN PRO GLY GLN GLU MET SEQRES 11 A 389 ASP ILE ASP ASP GLY THR TYR MET PRO MET PRO ILE PHE SEQRES 12 A 389 GLU SER GLU PRO LYS ILE GLY HIS SER LEU LEU ILE LEU SEQRES 13 A 389 LEU VAL ASP ALA SER LEU LYS SER LEU VAL ALA GLU ASN SEQRES 14 A 389 HIS GLY TRP LYS PHE GLU ALA LYS GLN THR CYS GLY ARG SEQRES 15 A 389 ILE LYS ILE GLU ALA GLU LYS THR HIS ILE ASP VAL PRO SEQRES 16 A 389 MET TYR ALA ILE PRO LYS ASP GLU PHE GLN LYS LYS GLN SEQRES 17 A 389 ILE ALA LEU GLU ALA ASN ARG GLY SER GLY SER GLU ASN SEQRES 18 A 389 VAL ASN LEU ALA LEU ARG GLU GLY ASP ARG LYS TRP ILE SEQRES 19 A 389 ASN SER ASP PRO LYS ILE VAL GLU ASP TRP PHE ASN ASP SEQRES 20 A 389 SER CYS ILE ARG ILE GLY LYS HIS LEU ARG LYS VAL CYS SEQRES 21 A 389 ARG PHE MET LYS ALA TRP ARG ASP ALA GLN TRP ASP VAL SEQRES 22 A 389 GLY GLY PRO SER SER ILE SER LEU MET ALA ALA THR VAL SEQRES 23 A 389 ASN ILE LEU ASP SER VAL ALA HIS ASP ALA SER ASP LEU SEQRES 24 A 389 GLY GLU THR MET LYS ILE ILE ALA LYS HIS LEU PRO SER SEQRES 25 A 389 GLU PHE ALA ARG GLY VAL GLU SER PRO ASP SER THR ASP SEQRES 26 A 389 GLU LYS PRO LEU PHE PRO PRO SER TYR LYS HIS GLY PRO SEQRES 27 A 389 ARG GLU MET ASP ILE MET SER LYS LEU GLU ARG LEU PRO SEQRES 28 A 389 GLU ILE LEU SER SER ALA GLU SER ALA ASP SER LYS SER SEQRES 29 A 389 GLU ALA LEU LYS LYS ILE ASN MET ALA PHE GLY ASN ARG SEQRES 30 A 389 VAL THR ASN SER GLU LEU ILE VAL LEU ALA LYS ALA HET EDO A1001 4 HET EDO A1002 4 HET EDO A1003 4 HET EDO A1004 4 HET EDO A1005 4 HET 3AT A1006 30 HET 3AT A1007 30 HET MG A1008 1 HETNAM EDO 1,2-ETHANEDIOL HETNAM 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETSYN EDO ETHYLENE GLYCOL HETSYN 3AT CORDYCEPIN TRIPHOSPHATE FORMUL 2 EDO 5(C2 H6 O2) FORMUL 7 3AT 2(C10 H16 N5 O12 P3) FORMUL 9 MG MG 2+ FORMUL 10 HOH *280(H2 O) HELIX 1 AA1 PHE A 7 ASN A 13 1 7 HELIX 2 AA2 GLY A 17 VAL A 23 1 7 HELIX 3 AA3 THR A 25 SER A 60 1 36 HELIX 4 AA4 THR A 63 SER A 72 1 10 HELIX 5 AA5 THR A 73 LEU A 79 5 7 HELIX 6 AA6 SER A 80 MET A 94 1 15 HELIX 7 AA7 ASP A 95 GLY A 104 1 10 HELIX 8 AA8 GLY A 113 GLN A 116 5 4 HELIX 9 AA9 GLY A 150 ASN A 169 1 20 HELIX 10 AB1 ASP A 260 GLY A 276 1 17 HELIX 11 AB2 LYS A 277 TRP A 294 1 18 HELIX 12 AB3 SER A 300 VAL A 315 1 16 HELIX 13 AB4 ASP A 321 ARG A 339 1 19 HELIX 14 AB5 PRO A 355 HIS A 359 5 5 HELIX 15 AB6 GLY A 360 SER A 382 1 23 HELIX 16 AB7 SER A 385 GLY A 398 1 14 HELIX 17 AB8 ASN A 403 ILE A 407 5 5 SHEET 1 AA1 2 MET A 3 ASN A 6 0 SHEET 2 AA1 2 VAL A 408 LYS A 411 -1 O VAL A 408 N ASN A 6 SHEET 1 AA2 5 ARG A 108 GLN A 112 0 SHEET 2 AA2 5 MET A 130 PRO A 139 -1 O ASP A 133 N GLN A 112 SHEET 3 AA2 5 THR A 190 VAL A 194 1 O ASP A 193 N ASP A 134 SHEET 4 AA2 5 GLY A 181 ILE A 185 -1 N GLY A 181 O VAL A 194 SHEET 5 AA2 5 TRP A 172 ALA A 176 -1 N LYS A 173 O LYS A 184 SHEET 1 AA3 5 ARG A 108 GLN A 112 0 SHEET 2 AA3 5 MET A 130 PRO A 139 -1 O ASP A 133 N GLN A 112 SHEET 3 AA3 5 MET A 196 ILE A 199 1 O TYR A 197 N MET A 138 SHEET 4 AA3 5 ASN A 246 ALA A 248 -1 O ALA A 248 N MET A 196 SHEET 5 AA3 5 TRP A 256 ASN A 258 -1 O ILE A 257 N LEU A 247 LINK OD1 ASP A 131 MG MG A1008 1555 1555 2.33 LINK OD2 ASP A 133 MG MG A1008 1555 1555 2.23 LINK O1G 3AT A1006 MG MG A1008 1555 1555 2.16 LINK O1B 3AT A1006 MG MG A1008 1555 1555 2.13 LINK O1A 3AT A1006 MG MG A1008 1555 1555 2.34 LINK MG MG A1008 O HOH A1187 1555 1555 2.06 SITE 1 AC1 6 LYS A 29 PHE A 115 ASP A 118 LEU A 120 SITE 2 AC1 6 ARG A 284 HOH A1199 SITE 1 AC2 6 ALA A 292 ASN A 394 MET A 395 GLY A 398 SITE 2 AC2 6 HOH A1230 HOH A1370 SITE 1 AC3 6 PHE A 7 TYR A 11 GLY A 323 LEU A 377 SITE 2 AC3 6 GLU A 381 ILE A 393 SITE 1 AC4 4 TRP A 5 GLU A 381 SER A 382 ALA A 383 SITE 1 AC5 6 PRO A 334 SER A 335 ALA A 338 GLU A 371 SITE 2 AC5 6 HOH A1246 HOH A1308 SITE 1 AC6 21 GLN A 112 GLY A 113 SER A 114 TYR A 117 SITE 2 AC6 21 ASP A 131 ASP A 133 LYS A 287 SER A 301 SITE 3 AC6 21 LEU A 352 3AT A1007 MG A1008 HOH A1187 SITE 4 AC6 21 HOH A1188 HOH A1198 HOH A1201 HOH A1203 SITE 5 AC6 21 HOH A1256 HOH A1260 HOH A1270 HOH A1291 SITE 6 AC6 21 HOH A1379 SITE 1 AC7 9 GLN A 112 ASP A 133 LYS A 177 THR A 179 SITE 2 AC7 9 ARG A 182 SER A 259 3AT A1006 HOH A1225 SITE 3 AC7 9 HOH A1380 SITE 1 AC8 4 ASP A 131 ASP A 133 3AT A1006 HOH A1187 CRYST1 118.090 51.300 71.540 90.00 93.85 90.00 C 1 2 1 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 0.008468 0.000000 0.000570 0.00000 SCALE2 0.000000 0.019493 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014010 0.00000