HEADER DNA BINDING PROTEIN 11-APR-19 6RCE TITLE PMAR-LIG_PRES3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*TP*TP*CP*CP*GP*AP*CP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*T)- COMPND 4 3'); COMPND 5 CHAIN: B; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA/RNA (5'-D(*AP*TP*TP*GP*CP*GP*AP*C)-R(P*(OMC))-D(P*C)- COMPND 9 3'); COMPND 10 CHAIN: C; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3'); COMPND 14 CHAIN: D; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: ATP-DEPENDENT DNA LIGASE; COMPND 18 CHAIN: I; COMPND 19 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 MOL_ID: 4; SOURCE 14 ORGANISM_SCIENTIFIC: PROCHLOROCOCCUS MARINUS; SOURCE 15 ORGANISM_TAXID: 1219; SOURCE 16 GENE: EU96_0746; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNA LIGASE, ATP-DEPENDENT, LIGASE-DNA CO-CRYSTAL STRUCTURE, KEYWDS 2 DETERMINANTS IN DNA BINDING, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.K.S.LEIROS,A.WILLIAMSON REVDAT 3 24-JAN-24 6RCE 1 REMARK REVDAT 2 29-JAN-20 6RCE 1 JRNL REVDAT 1 10-JUL-19 6RCE 0 JRNL AUTH A.WILLIAMSON,H.S.LEIROS JRNL TITL STRUCTURAL INTERMEDIATES OF A DNA-LIGASE COMPLEX ILLUMINATE JRNL TITL 2 THE ROLE OF THE CATALYTIC METAL ION AND MECHANISM OF JRNL TITL 3 PHOSPHODIESTER BOND FORMATION. JRNL REF NUCLEIC ACIDS RES. V. 47 7147 2019 JRNL REFN ESSN 1362-4962 JRNL PMID 31312841 JRNL DOI 10.1093/NAR/GKZ596 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 84.7 REMARK 3 NUMBER OF REFLECTIONS : 57815 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.231 REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.660 REMARK 3 FREE R VALUE TEST SET COUNT : 2694 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 24.2630 - 5.1770 0.97 3426 127 0.2258 0.2856 REMARK 3 2 5.1770 - 4.1157 0.98 3358 182 0.1841 0.2072 REMARK 3 3 4.1157 - 3.5973 0.98 3370 163 0.1947 0.2509 REMARK 3 4 3.5973 - 3.2693 0.96 3270 189 0.2058 0.2351 REMARK 3 5 3.2693 - 3.0354 0.98 3376 151 0.2274 0.2751 REMARK 3 6 3.0354 - 2.8567 0.98 3314 191 0.2455 0.2806 REMARK 3 7 2.8567 - 2.7139 0.97 3319 159 0.2623 0.3353 REMARK 3 8 2.7139 - 2.5959 0.98 3391 156 0.2507 0.3072 REMARK 3 9 2.5959 - 2.4961 0.99 3326 195 0.2538 0.3159 REMARK 3 10 2.4961 - 2.4100 0.98 3316 196 0.2609 0.3351 REMARK 3 11 2.4100 - 2.3347 0.97 3331 172 0.2654 0.3036 REMARK 3 12 2.3347 - 2.2680 0.96 3273 171 0.2681 0.3331 REMARK 3 13 2.2680 - 2.2084 0.95 3248 159 0.2791 0.3044 REMARK 3 14 2.2084 - 2.1545 0.95 3261 131 0.2791 0.3089 REMARK 3 15 2.1545 - 2.1056 0.86 2942 121 0.2930 0.3334 REMARK 3 16 2.1056 - 2.0608 0.64 2203 97 0.2943 0.3196 REMARK 3 17 2.0608 - 2.0196 0.45 1537 71 0.3022 0.3436 REMARK 3 18 2.0196 - 1.9815 0.33 1147 39 0.3116 0.3620 REMARK 3 19 1.9815 - 1.9461 0.21 713 24 0.3045 0.2529 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.430 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.70 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 : 0.016 4573 REMARK 3 ANGLE : 1.367 6326 REMARK 3 CHIRALITY : 0.063 685 REMARK 3 PLANARITY : 0.005 661 REMARK 3 DIHEDRAL : 11.494 3509 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 5 ) REMARK 3 ORIGIN FOR THE GROUP (A): 112.0884 106.8110 33.4406 REMARK 3 T TENSOR REMARK 3 T11: 0.3034 T22: 0.4524 REMARK 3 T33: 0.7017 T12: 0.0638 REMARK 3 T13: 0.0081 T23: -0.0077 REMARK 3 L TENSOR REMARK 3 L11: 5.4301 L22: 5.2026 REMARK 3 L33: 9.6546 L12: 0.5728 REMARK 3 L13: 0.5128 L23: 2.8512 REMARK 3 S TENSOR REMARK 3 S11: -0.9486 S12: -1.7712 S13: 0.8304 REMARK 3 S21: 0.2535 S22: 0.7308 S23: 0.0441 REMARK 3 S31: -0.4448 S32: -0.2427 S33: 0.2376 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 6 THROUGH 20 ) REMARK 3 ORIGIN FOR THE GROUP (A): 78.6405 106.4946 29.9837 REMARK 3 T TENSOR REMARK 3 T11: 0.1497 T22: 0.2856 REMARK 3 T33: 0.2457 T12: -0.0134 REMARK 3 T13: 0.0120 T23: 0.0517 REMARK 3 L TENSOR REMARK 3 L11: 0.1919 L22: 3.1231 REMARK 3 L33: 2.2956 L12: 0.8184 REMARK 3 L13: 0.2466 L23: -0.0123 REMARK 3 S TENSOR REMARK 3 S11: -0.1347 S12: 0.2543 S13: -0.0505 REMARK 3 S21: -0.0957 S22: -0.0509 S23: 0.0840 REMARK 3 S31: -0.0790 S32: -0.0106 S33: 0.1675 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 22 THROUGH 26 ) REMARK 3 ORIGIN FOR THE GROUP (A): 60.6602 106.3465 33.7567 REMARK 3 T TENSOR REMARK 3 T11: 0.2266 T22: 0.7323 REMARK 3 T33: 0.6472 T12: 0.0119 REMARK 3 T13: 0.0156 T23: -0.1428 REMARK 3 L TENSOR REMARK 3 L11: 4.7900 L22: 3.5327 REMARK 3 L33: 9.0966 L12: 2.1132 REMARK 3 L13: -2.6455 L23: 3.2895 REMARK 3 S TENSOR REMARK 3 S11: -0.9246 S12: -1.4330 S13: 1.3530 REMARK 3 S21: 0.4390 S22: 0.1254 S23: 0.5893 REMARK 3 S31: -0.2825 S32: 0.4650 S33: 0.7629 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 34 THROUGH 42 ) REMARK 3 ORIGIN FOR THE GROUP (A): 104.6369 103.6211 32.6082 REMARK 3 T TENSOR REMARK 3 T11: 0.1803 T22: 0.3411 REMARK 3 T33: 0.3019 T12: 0.0236 REMARK 3 T13: -0.0506 T23: 0.0300 REMARK 3 L TENSOR REMARK 3 L11: 4.5239 L22: 4.1124 REMARK 3 L33: 0.8407 L12: -1.2101 REMARK 3 L13: 0.5771 L23: 0.0029 REMARK 3 S TENSOR REMARK 3 S11: -0.2165 S12: 0.6214 S13: 0.1811 REMARK 3 S21: -0.0057 S22: -0.1237 S23: -0.6779 REMARK 3 S31: 0.1038 S32: 0.1855 S33: 0.1564 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'I' AND (RESID 5 THROUGH 138) REMARK 3 ORIGIN FOR THE GROUP (A): 84.1138 86.7162 24.0563 REMARK 3 T TENSOR REMARK 3 T11: 0.3160 T22: 0.1848 REMARK 3 T33: 0.3302 T12: -0.0087 REMARK 3 T13: -0.0361 T23: -0.0577 REMARK 3 L TENSOR REMARK 3 L11: 5.0304 L22: 1.8388 REMARK 3 L33: 2.1511 L12: -0.1458 REMARK 3 L13: -0.0421 L23: -0.3504 REMARK 3 S TENSOR REMARK 3 S11: -0.0036 S12: 0.1871 S13: -0.5989 REMARK 3 S21: -0.2248 S22: -0.0044 S23: 0.0754 REMARK 3 S31: 0.4597 S32: -0.1258 S33: 0.0405 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'I' AND (RESID 139 THROUGH 315 ) REMARK 3 ORIGIN FOR THE GROUP (A): 87.6547 121.0914 13.2166 REMARK 3 T TENSOR REMARK 3 T11: 0.3223 T22: 0.2214 REMARK 3 T33: 0.1695 T12: 0.0147 REMARK 3 T13: 0.0031 T23: 0.0209 REMARK 3 L TENSOR REMARK 3 L11: 1.5497 L22: 1.7901 REMARK 3 L33: 2.4140 L12: 0.3817 REMARK 3 L13: 0.5790 L23: 0.5618 REMARK 3 S TENSOR REMARK 3 S11: -0.0075 S12: 0.2097 S13: 0.0048 REMARK 3 S21: -0.3442 S22: 0.0210 S23: 0.0855 REMARK 3 S31: -0.1618 S32: -0.1161 S33: -0.0192 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'I' AND (RESID 316 THROUGH 436 ) REMARK 3 ORIGIN FOR THE GROUP (A): 86.2943 115.6392 40.4257 REMARK 3 T TENSOR REMARK 3 T11: 0.2837 T22: 0.2140 REMARK 3 T33: 0.1746 T12: -0.0236 REMARK 3 T13: -0.0580 T23: -0.0245 REMARK 3 L TENSOR REMARK 3 L11: 1.5939 L22: 2.3455 REMARK 3 L33: 3.8726 L12: 0.5797 REMARK 3 L13: -1.3209 L23: -1.4811 REMARK 3 S TENSOR REMARK 3 S11: 0.0899 S12: -0.2704 S13: 0.0767 REMARK 3 S21: 0.4828 S22: -0.0396 S23: 0.0555 REMARK 3 S31: -0.2798 S32: 0.0478 S33: -0.0177 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 21 THROUGH 21 ) REMARK 3 ORIGIN FOR THE GROUP (A): 56.0429 98.9593 33.6002 REMARK 3 T TENSOR REMARK 3 T11: 0.3094 T22: 0.7714 REMARK 3 T33: 0.7566 T12: 0.2443 REMARK 3 T13: 0.1742 T23: 0.1050 REMARK 3 L TENSOR REMARK 3 L11: 6.9137 L22: 7.9365 REMARK 3 L33: 8.0574 L12: -7.3041 REMARK 3 L13: 5.9793 L23: -7.1153 REMARK 3 S TENSOR REMARK 3 S11: -0.6851 S12: -1.3816 S13: -0.2105 REMARK 3 S21: 0.6496 S22: 0.2804 S23: -0.9946 REMARK 3 S31: 0.4131 S32: 0.5011 S33: 0.3384 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 32 THROUGH 33 ) REMARK 3 ORIGIN FOR THE GROUP (A): 88.0952 113.9469 30.8753 REMARK 3 T TENSOR REMARK 3 T11: 0.1856 T22: 0.2334 REMARK 3 T33: 0.1218 T12: 0.0014 REMARK 3 T13: 0.0373 T23: -0.0091 REMARK 3 L TENSOR REMARK 3 L11: 3.9576 L22: 3.6892 REMARK 3 L33: 8.8050 L12: -3.0221 REMARK 3 L13: 5.1115 L23: -2.1669 REMARK 3 S TENSOR REMARK 3 S11: -0.1935 S12: -0.3948 S13: 0.1043 REMARK 3 S21: 0.5568 S22: -0.2780 S23: -0.8842 REMARK 3 S31: -0.3280 S32: 1.1076 S33: 0.4729 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 6RCE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-APR-19. REMARK 100 THE DEPOSITION ID IS D_1292101778. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-AUG-18 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 : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9919 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57869 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.946 REMARK 200 RESOLUTION RANGE LOW (A) : 69.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.0 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 39.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.94600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6RAU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 17-18% PEG 8K, 100 MM AMMONIUM REMARK 280 SULFATE, 100 MM BIS-TRIS PH 5.5, VAPOR DIFFUSION, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 51.50350 REMARK 290 SMTRY3 2 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: 8650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -71.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, D, I 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 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 DC B 7 C1' REMARK 470 GLU I 62 CD OE1 OE2 REMARK 470 GLU I 72 CD REMARK 470 LYS I 76 CD CE NZ REMARK 470 LYS I 134 NZ REMARK 470 GLU I 155 CD OE1 OE2 REMARK 470 LYS I 156 CE NZ REMARK 470 LYS I 181 CB CG CD CE NZ REMARK 470 LYS I 231 CE NZ REMARK 470 ARG I 235 CZ REMARK 470 LYS I 242 CD CE NZ REMARK 470 LYS I 259 CG CD CE NZ REMARK 470 LYS I 275 CE NZ REMARK 470 LEU I 282 CG CD1 CD2 REMARK 470 LYS I 285 CD CE NZ REMARK 470 ASN I 294 ND2 REMARK 470 LYS I 304 CE NZ REMARK 470 LYS I 311 CD CE NZ REMARK 470 LYS I 350 NZ REMARK 470 LEU I 369 CD1 CD2 REMARK 470 LYS I 398 CD REMARK 470 LYS I 400 CG CD CE NZ REMARK 470 LYS I 418 CE NZ REMARK 470 ARG I 434 CZ 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 HZ3 LYS I 340 O HOH I 606 1.34 REMARK 500 HG SER I 151 O LYS I 340 1.56 REMARK 500 HZ1 LYS I 274 O HOH I 602 1.58 REMARK 500 O ARG I 360 O HOH I 601 1.87 REMARK 500 O HOH I 961 O HOH I 968 1.96 REMARK 500 NZ LYS I 274 O HOH I 602 1.97 REMARK 500 O HOH I 968 O HOH I 978 1.98 REMARK 500 OE1 GLU I 125 O HOH I 603 1.99 REMARK 500 OE2 GLU I 371 O HOH I 604 2.01 REMARK 500 O HOH I 978 O HOH I 980 2.02 REMARK 500 OP1 DC D 32 O2P AMP D 300 2.02 REMARK 500 OP2 DA B 8 O HOH B 101 2.03 REMARK 500 O HOH I 849 O HOH I 880 2.04 REMARK 500 NZ LYS I 157 O HOH I 605 2.05 REMARK 500 O HOH I 981 O HOH I 988 2.06 REMARK 500 O HOH I 815 O HOH I 962 2.09 REMARK 500 O HOH C 104 O HOH C 120 2.10 REMARK 500 O HOH I 976 O HOH I 985 2.11 REMARK 500 O HOH I 987 O HOH I 992 2.11 REMARK 500 O HOH I 884 O HOH I 903 2.11 REMARK 500 NZ LYS I 340 O HOH I 606 2.13 REMARK 500 O HOH I 888 O HOH I 907 2.15 REMARK 500 O HOH B 115 O HOH I 896 2.17 REMARK 500 O HOH D 426 O HOH D 429 2.19 REMARK 500 O HOH I 861 O HOH I 909 2.19 REMARK 500 O HOH B 124 O HOH B 131 2.19 REMARK 500 O HOH I 699 O HOH I 848 2.19 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 O5' DA C 22 O3' DA D 42 1455 2.14 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 DT B 10 O3' DT B 10 C3' -0.036 REMARK 500 DG B 11 O3' DG B 11 C3' -0.057 REMARK 500 DC D 32 P DC D 32 OP3 -0.133 REMARK 500 DC D 32 O3' DC D 32 C3' -0.043 REMARK 500 DA D 41 O4' DA D 41 C4' 0.062 REMARK 500 GLU I 16 C LEU I 17 N 0.141 REMARK 500 GLN I 179 CG GLN I 179 CD -0.199 REMARK 500 GLN I 179 CD GLN I 179 OE1 0.208 REMARK 500 GLN I 179 CD GLN I 179 NE2 0.305 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 DC B 3 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DC B 4 O4' - C4' - C3' ANGL. DEV. = -2.7 DEGREES REMARK 500 DC B 4 C5' - C4' - C3' ANGL. DEV. = 7.3 DEGREES REMARK 500 DC B 4 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 DG B 11 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG B 13 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG B 17 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DC B 18 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 DC C 26 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC C 29 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 DC C 29 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 DC D 32 O5' - P - OP1 ANGL. DEV. = -6.5 DEGREES REMARK 500 DG D 39 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG D 40 O4' - C4' - C3' ANGL. DEV. = -2.7 DEGREES REMARK 500 DA D 41 O4' - C4' - C3' ANGL. DEV. = -5.9 DEGREES REMARK 500 GLU I 16 N - CA - CB ANGL. DEV. = 12.7 DEGREES REMARK 500 LEU I 17 CB - CG - CD1 ANGL. DEV. = -11.8 DEGREES REMARK 500 GLN I 179 CB - CG - CD ANGL. DEV. = -20.1 DEGREES REMARK 500 GLN I 179 OE1 - CD - NE2 ANGL. DEV. = 14.3 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 GLN I 67 -122.57 -109.59 REMARK 500 PHE I 110 -62.77 -150.90 REMARK 500 CYS I 121 18.91 -143.19 REMARK 500 HIS I 154 44.49 -142.76 REMARK 500 SER I 223 -166.25 -119.90 REMARK 500 ASN I 263 47.38 -97.66 REMARK 500 HIS I 280 39.56 -140.18 REMARK 500 LYS I 431 -63.43 -105.15 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 B 143 DISTANCE = 8.72 ANGSTROMS REMARK 525 HOH I 979 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH I 980 DISTANCE = 6.01 ANGSTROMS REMARK 525 HOH I 981 DISTANCE = 6.06 ANGSTROMS REMARK 525 HOH I 982 DISTANCE = 6.45 ANGSTROMS REMARK 525 HOH I 983 DISTANCE = 6.69 ANGSTROMS REMARK 525 HOH I 984 DISTANCE = 6.85 ANGSTROMS REMARK 525 HOH I 985 DISTANCE = 7.39 ANGSTROMS REMARK 525 HOH I 986 DISTANCE = 7.49 ANGSTROMS REMARK 525 HOH I 987 DISTANCE = 7.54 ANGSTROMS REMARK 525 HOH I 988 DISTANCE = 7.62 ANGSTROMS REMARK 525 HOH I 989 DISTANCE = 7.66 ANGSTROMS REMARK 525 HOH I 990 DISTANCE = 7.71 ANGSTROMS REMARK 525 HOH I 991 DISTANCE = 7.76 ANGSTROMS REMARK 525 HOH I 992 DISTANCE = 8.21 ANGSTROMS REMARK 525 HOH I 993 DISTANCE = 9.28 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AMP D 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 I 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6RAR RELATED DB: PDB REMARK 900 IS IN THE SAME PUBLICATION REMARK 900 RELATED ID: 6RAS RELATED DB: PDB REMARK 900 IS IN THE SAME PUBLICATION REMARK 900 RELATED ID: 6RAU RELATED DB: PDB REMARK 900 IS IN THE SAME PUBLICATION DBREF 6RCE B 1 21 PDB 6RCE 6RCE 1 21 DBREF 6RCE C 22 31 PDB 6RCE 6RCE 22 31 DBREF 6RCE D 32 42 PDB 6RCE 6RCE 32 42 DBREF1 6RCE I 5 436 UNP A0A0A2ACP7_PROMR DBREF2 6RCE I A0A0A2ACP7 5 436 SEQRES 1 B 21 DT DT DC DC DG DA DC DA DG DT DG DG DG SEQRES 2 B 21 DG DT DC DG DC DA DA DT SEQRES 1 C 10 DA DT DT DG DC DG DA DC OMC DC SEQRES 1 D 11 DC DA DC DT DA DT DC DG DG DA DA SEQRES 1 I 432 GLU LEU PHE LYS GLU GLU ILE ILE HIS GLN LEU GLU LEU SEQRES 2 I 432 HIS PRO SER ARG LEU ASP LYS GLU LYS ILE ILE SER GLU SEQRES 3 I 432 ALA MET GLU ASP GLY ILE ASP ASP PHE PHE GLU GLY ILE SEQRES 4 I 432 ARG MET ALA LEU ASP PRO LEU VAL THR PHE GLY VAL LYS SEQRES 5 I 432 ILE VAL PRO GLU LYS GLU SER GLU LYS SER GLN ASN PHE SEQRES 6 I 432 LEU TRP GLU ASP PHE ARG LYS LEU ALA ASN LYS LEU MET SEQRES 7 I 432 GLN ARG GLU LEU THR GLY HIS ALA ALA ARG ASP ALA ILE SEQRES 8 I 432 LEU THR ALA MET GLU SER ALA THR LYS GLU GLU TRP ASN SEQRES 9 I 432 GLY PHE TYR ARG ARG VAL LEU ILE LYS ASP LEU ARG CYS SEQRES 10 I 432 GLY VAL SER GLU LYS THR ILE ASN LYS ILE ALA LYS LYS SEQRES 11 I 432 PHE PRO LYS TYR ALA ILE PRO ILE PHE SER CYS PRO LEU SEQRES 12 I 432 ALA HIS ASP SER ALA ASN HIS GLU LYS LYS MET ILE GLY SEQRES 13 I 432 LYS LYS GLN ILE GLU ILE LYS LEU ASP GLY VAL ARG VAL SEQRES 14 I 432 LEU THR ILE ILE ARG GLN ASN LYS VAL GLU MET PHE SER SEQRES 15 I 432 ARG ASN GLY LYS GLN PHE HIS ASN PHE GLY HIS ILE ILE SEQRES 16 I 432 LEU GLU ILE GLU ASN VAL LEU LYS GLU ASP PRO ALA PRO SEQRES 17 I 432 TYR ASP LEU VAL LEU ASP GLY GLU VAL MET SER ALA ASN SEQRES 18 I 432 PHE GLN ASP LEU MET LYS GLN VAL HIS ARG LYS ASP GLY SEQRES 19 I 432 LYS GLN THR LYS ASP ALA VAL LEU HIS LEU PHE ASP LEU SEQRES 20 I 432 CYS PRO LEU GLU ASN PHE GLN LYS GLY ARG TRP ASN THR SEQRES 21 I 432 LYS GLN THR ALA ARG SER LEU LEU VAL LYS LYS TRP VAL SEQRES 22 I 432 ALA LYS HIS SER LEU LEU LEU LYS HIS ILE GLN THR LEU SEQRES 23 I 432 GLU TRP GLU ASN VAL ASP LEU ASP THR ILE GLN GLY GLN SEQRES 24 I 432 LYS ARG PHE VAL GLU LEU ASN LYS SER ALA VAL GLU GLY SEQRES 25 I 432 GLY TYR GLU GLY VAL MET ILE LYS ASP PRO ASP GLY MET SEQRES 26 I 432 TYR GLU CYS LYS ARG THR HIS SER TRP LEU LYS ALA LYS SEQRES 27 I 432 PRO PHE ILE GLU VAL THR LEU LYS VAL VAL SER VAL GLU SEQRES 28 I 432 GLU GLY THR GLY ARG ASN LYS GLY ARG LEU GLY ALA ILE SEQRES 29 I 432 LEU VAL GLU GLY GLU ASP ASP GLY TYR GLU TYR SER LEU SEQRES 30 I 432 SER CYS GLY SER GLY PHE SER ASP ILE GLN ARG GLU GLU SEQRES 31 I 432 TYR TRP SER LYS ARG LYS HIS LEU LEU GLY GLN LEU VAL SEQRES 32 I 432 GLU ILE ARG ALA ASP ALA LYS THR LYS SER LYS ASP GLY SEQRES 33 I 432 VAL ALA PHE SER LEU ARG PHE PRO ARG PHE LYS CYS PHE SEQRES 34 I 432 ARG GLY PHE HET OMC C 30 34 HET AMP D 300 34 HET SO4 I 501 5 HETNAM OMC O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE HETNAM AMP ADENOSINE MONOPHOSPHATE HETNAM SO4 SULFATE ION FORMUL 2 OMC C10 H16 N3 O8 P FORMUL 5 AMP C10 H14 N5 O7 P FORMUL 6 SO4 O4 S 2- FORMUL 7 HOH *492(H2 O) HELIX 1 AA1 PHE I 7 HIS I 18 1 12 HELIX 2 AA2 SER I 20 ASP I 34 1 15 HELIX 3 AA3 ILE I 36 ASP I 48 1 13 HELIX 4 AA4 LEU I 70 GLN I 83 1 14 HELIX 5 AA5 THR I 87 ALA I 102 1 16 HELIX 6 AA6 THR I 103 PHE I 110 1 8 HELIX 7 AA7 PHE I 110 ILE I 116 1 7 HELIX 8 AA8 SER I 124 LYS I 133 1 10 HELIX 9 AA9 LYS I 134 ALA I 139 5 6 HELIX 10 AB1 ALA I 152 MET I 158 5 7 HELIX 11 AB2 PHE I 195 ASP I 209 1 15 HELIX 12 AB3 ASN I 225 HIS I 234 1 10 HELIX 13 AB4 LEU I 254 GLY I 260 1 7 HELIX 14 AB5 LYS I 265 LYS I 279 1 15 HELIX 15 AB6 THR I 299 GLY I 316 1 18 HELIX 16 AB7 THR I 358 LYS I 362 5 5 HELIX 17 AB8 SER I 388 LYS I 398 1 11 HELIX 18 AB9 LYS I 398 LEU I 403 1 6 SHEET 1 AA1 5 LEU I 147 ASP I 150 0 SHEET 2 AA1 5 ARG I 334 ALA I 341 1 O THR I 335 N LEU I 147 SHEET 3 AA1 5 GLY I 320 LYS I 324 -1 N ILE I 323 O LEU I 339 SHEET 4 AA1 5 LYS I 161 LYS I 167 -1 N GLN I 163 O LYS I 324 SHEET 5 AA1 5 GLU I 293 ASP I 296 -1 O GLU I 293 N ILE I 164 SHEET 1 AA2 6 GLN I 191 PHE I 192 0 SHEET 2 AA2 6 LYS I 181 PHE I 185 -1 N MET I 184 O PHE I 192 SHEET 3 AA2 6 VAL I 171 ARG I 178 -1 N ARG I 178 O LYS I 181 SHEET 4 AA2 6 LEU I 215 MET I 222 -1 O LEU I 215 N ILE I 177 SHEET 5 AA2 6 VAL I 245 PRO I 253 -1 O HIS I 247 N GLU I 220 SHEET 6 AA2 6 ILE I 287 THR I 289 1 O GLN I 288 N LEU I 248 SHEET 1 AA3 2 ARG I 261 TRP I 262 0 SHEET 2 AA3 2 TYR I 330 GLU I 331 -1 O TYR I 330 N TRP I 262 SHEET 1 AA4 5 TYR I 377 CYS I 383 0 SHEET 2 AA4 5 LEU I 365 ASP I 374 -1 N GLY I 372 O TYR I 379 SHEET 3 AA4 5 ILE I 345 GLU I 356 -1 N VAL I 352 O LEU I 369 SHEET 4 AA4 5 LEU I 406 ALA I 411 -1 O ALA I 411 N ILE I 345 SHEET 5 AA4 5 ARG I 429 PHE I 433 -1 O CYS I 432 N GLU I 408 SHEET 1 AA5 2 ALA I 413 THR I 415 0 SHEET 2 AA5 2 SER I 424 ARG I 426 -1 O ARG I 426 N ALA I 413 LINK O3' DC C 29 P OMC C 30 1555 1555 1.61 LINK O3' OMC C 30 P DC C 31 1555 1555 1.61 LINK OP1 DC D 32 P AMP D 300 1555 1555 1.50 SITE 1 AC1 18 DC D 32 HOH D 403 HOH D 410 ALA I 148 SITE 2 AC1 18 GLU I 165 ILE I 166 LYS I 167 LEU I 168 SITE 3 AC1 18 ARG I 172 GLU I 220 PHE I 249 LEU I 290 SITE 4 AC1 18 MET I 322 LYS I 324 LYS I 340 HOH I 606 SITE 5 AC1 18 HOH I 628 HOH I 735 SITE 1 AC2 4 HIS I 149 ASP I 150 ASN I 153 HIS I 154 CRYST1 67.137 103.007 68.581 90.00 91.01 90.00 P 1 21 1 2 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 0.014895 0.000000 0.000263 0.00000 SCALE2 0.000000 0.009708 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014584 0.00000