HEADER DNA BINDING PROTEIN 08-APR-19 6RAU TITLE POSTS3_PMAR_LIG4_WT 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 (5'- COMPND 9 D(*AP*TP*TP*GP*CP*GP*AP*CP*CP*CP*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)- COMPND 10 3'); COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: ATP-DEPENDENT DNA LIGASE; COMPND 15 CHAIN: I; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: DNA LAUNCH VECTOR PDE-GFP2; SOURCE 4 ORGANISM_TAXID: 415098; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: DNA LAUNCH VECTOR PDE-GFP2; SOURCE 8 ORGANISM_TAXID: 415098; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: PROCHLOROCOCCUS MARINUS; SOURCE 11 ORGANISM_TAXID: 1219; SOURCE 12 GENE: EU96_0746; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 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 01-MAY-24 6RAU 1 REMARK REVDAT 2 29-JAN-20 6RAU 1 JRNL REVDAT 1 10-JUL-19 6RAU 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. 1.99 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) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 62231 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.840 REMARK 3 FREE R VALUE TEST SET COUNT : 3014 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 24.1744 - 5.5545 0.99 2768 122 0.1690 0.1849 REMARK 3 2 5.5545 - 4.4175 0.98 2695 138 0.1410 0.1616 REMARK 3 3 4.4175 - 3.8617 0.99 2719 148 0.1444 0.1790 REMARK 3 4 3.8617 - 3.5098 0.98 2665 131 0.1721 0.2194 REMARK 3 5 3.5098 - 3.2589 0.98 2672 152 0.1868 0.2175 REMARK 3 6 3.2589 - 3.0671 0.98 2676 151 0.2014 0.2543 REMARK 3 7 3.0671 - 2.9138 0.99 2724 110 0.2250 0.2658 REMARK 3 8 2.9138 - 2.7871 0.99 2713 133 0.2347 0.2953 REMARK 3 9 2.7871 - 2.6800 0.97 2640 144 0.2291 0.2707 REMARK 3 10 2.6800 - 2.5876 0.99 2698 162 0.2337 0.2725 REMARK 3 11 2.5876 - 2.5068 0.99 2676 139 0.2360 0.3124 REMARK 3 12 2.5068 - 2.4352 0.99 2700 122 0.2336 0.3341 REMARK 3 13 2.4352 - 2.3712 0.99 2706 112 0.2384 0.2778 REMARK 3 14 2.3712 - 2.3133 1.00 2701 133 0.2333 0.2927 REMARK 3 15 2.3133 - 2.2608 0.98 2700 128 0.2414 0.2402 REMARK 3 16 2.2608 - 2.2127 0.99 2632 156 0.2459 0.2857 REMARK 3 17 2.2127 - 2.1685 0.99 2692 147 0.2466 0.3177 REMARK 3 18 2.1685 - 2.1276 0.99 2668 157 0.2575 0.3026 REMARK 3 19 2.1276 - 2.0896 0.99 2679 125 0.2715 0.3099 REMARK 3 20 2.0896 - 2.0542 0.99 2701 119 0.2826 0.3570 REMARK 3 21 2.0542 - 2.0211 0.99 2699 128 0.2945 0.3212 REMARK 3 22 2.0211 - 1.9900 0.99 2693 157 0.3045 0.3453 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.860 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.80 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 : 0.017 4588 REMARK 3 ANGLE : 1.364 6351 REMARK 3 CHIRALITY : 0.087 686 REMARK 3 PLANARITY : 0.008 664 REMARK 3 DIHEDRAL : 22.641 1805 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 9 ) REMARK 3 ORIGIN FOR THE GROUP (A): 104.0073 104.5144 31.0570 REMARK 3 T TENSOR REMARK 3 T11: 0.3112 T22: 0.4553 REMARK 3 T33: 0.5179 T12: 0.0284 REMARK 3 T13: 0.0037 T23: 0.0614 REMARK 3 L TENSOR REMARK 3 L11: 6.0758 L22: 1.4988 REMARK 3 L33: 1.0511 L12: 0.1119 REMARK 3 L13: -0.6940 L23: -0.3065 REMARK 3 S TENSOR REMARK 3 S11: -0.5820 S12: -0.1275 S13: 0.8080 REMARK 3 S21: -0.0525 S22: 0.2939 S23: -0.1506 REMARK 3 S31: -0.0312 S32: 0.0584 S33: 0.2736 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 10 THROUGH 21 ) REMARK 3 ORIGIN FOR THE GROUP (A): 70.4812 107.0047 30.1852 REMARK 3 T TENSOR REMARK 3 T11: 0.2611 T22: 0.4073 REMARK 3 T33: 0.4437 T12: 0.0326 REMARK 3 T13: -0.0085 T23: 0.0252 REMARK 3 L TENSOR REMARK 3 L11: 2.2269 L22: 1.5781 REMARK 3 L33: 1.3467 L12: 0.6014 REMARK 3 L13: 0.9411 L23: 0.4246 REMARK 3 S TENSOR REMARK 3 S11: -0.1491 S12: -0.1227 S13: -0.2907 REMARK 3 S21: 0.0445 S22: 0.1743 S23: 0.5513 REMARK 3 S31: -0.0701 S32: -0.4528 S33: -0.0232 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 22 THROUGH 26 ) REMARK 3 ORIGIN FOR THE GROUP (A): 60.2540 106.0776 33.2347 REMARK 3 T TENSOR REMARK 3 T11: 0.2877 T22: 0.6580 REMARK 3 T33: 0.6764 T12: 0.0043 REMARK 3 T13: 0.0223 T23: -0.0489 REMARK 3 L TENSOR REMARK 3 L11: 7.5833 L22: 4.1239 REMARK 3 L33: 6.1692 L12: -1.2030 REMARK 3 L13: -1.6727 L23: 1.9798 REMARK 3 S TENSOR REMARK 3 S11: -0.7311 S12: -0.1944 S13: 1.1400 REMARK 3 S21: 0.5971 S22: 0.0300 S23: 0.8438 REMARK 3 S31: -0.0429 S32: 0.3339 S33: 0.6934 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 27 THROUGH 42 ) REMARK 3 ORIGIN FOR THE GROUP (A): 93.4078 105.8915 29.8031 REMARK 3 T TENSOR REMARK 3 T11: 0.2787 T22: 0.3602 REMARK 3 T33: 0.3778 T12: -0.0278 REMARK 3 T13: 0.0323 T23: 0.0152 REMARK 3 L TENSOR REMARK 3 L11: 1.2944 L22: 1.9209 REMARK 3 L33: 0.7973 L12: -0.6641 REMARK 3 L13: 0.3821 L23: -0.2450 REMARK 3 S TENSOR REMARK 3 S11: -0.1026 S12: 0.2544 S13: -0.0370 REMARK 3 S21: 0.0095 S22: -0.0148 S23: -0.2890 REMARK 3 S31: -0.0143 S32: 0.1839 S33: 0.0999 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'I' AND (RESID 5 THROUGH 146 ) REMARK 3 ORIGIN FOR THE GROUP (A): 83.8811 87.3472 23.2385 REMARK 3 T TENSOR REMARK 3 T11: 0.4086 T22: 0.2715 REMARK 3 T33: 0.4492 T12: -0.0069 REMARK 3 T13: -0.0323 T23: -0.0677 REMARK 3 L TENSOR REMARK 3 L11: 2.7765 L22: 1.5198 REMARK 3 L33: 2.4596 L12: -0.2510 REMARK 3 L13: 0.5256 L23: -0.4583 REMARK 3 S TENSOR REMARK 3 S11: 0.0988 S12: 0.1514 S13: -0.6062 REMARK 3 S21: -0.2363 S22: -0.0528 S23: 0.1244 REMARK 3 S31: 0.4194 S32: -0.0631 S33: -0.0376 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'I' AND (RESID 147 THROUGH 333 ) REMARK 3 ORIGIN FOR THE GROUP (A): 87.9461 121.6856 13.3223 REMARK 3 T TENSOR REMARK 3 T11: 0.4610 T22: 0.3206 REMARK 3 T33: 0.2591 T12: -0.0010 REMARK 3 T13: 0.0244 T23: 0.0296 REMARK 3 L TENSOR REMARK 3 L11: 2.1965 L22: 1.6539 REMARK 3 L33: 3.2078 L12: 0.3107 REMARK 3 L13: 1.1763 L23: 0.8243 REMARK 3 S TENSOR REMARK 3 S11: 0.0051 S12: 0.0859 S13: 0.0448 REMARK 3 S21: -0.2083 S22: -0.0562 S23: 0.1108 REMARK 3 S31: -0.1469 S32: -0.2325 S33: 0.0480 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'I' AND (RESID 334 THROUGH 436 ) REMARK 3 ORIGIN FOR THE GROUP (A): 84.0064 114.3808 43.7044 REMARK 3 T TENSOR REMARK 3 T11: 0.4269 T22: 0.3241 REMARK 3 T33: 0.2353 T12: -0.0087 REMARK 3 T13: -0.0062 T23: -0.0257 REMARK 3 L TENSOR REMARK 3 L11: 1.7802 L22: 2.7089 REMARK 3 L33: 2.4668 L12: 0.1670 REMARK 3 L13: -0.5945 L23: -0.4606 REMARK 3 S TENSOR REMARK 3 S11: -0.0032 S12: -0.2135 S13: 0.0745 REMARK 3 S21: 0.4576 S22: 0.0126 S23: 0.1226 REMARK 3 S31: -0.1991 S32: -0.0926 S33: 0.0016 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 6RAU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-APR-19. REMARK 100 THE DEPOSITION ID IS D_1292101701. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-FEB-17 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 : MASSIF-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62306 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : 0.09900 REMARK 200 FOR THE DATA SET : 9.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.15400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.100 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: HOME-MADE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG BUFFER, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 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 51.24850 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -93.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, 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 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 I 1 REMARK 465 ARG I 2 REMARK 465 GLN I 3 REMARK 465 LYS I 4 REMARK 465 LYS I 437 REMARK 465 ALA I 438 REMARK 465 GLY I 439 REMARK 465 GLU I 440 REMARK 465 LYS I 441 REMARK 465 VAL I 442 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 I 26 CD REMARK 470 GLU I 33 CD REMARK 470 GLU I 62 CD OE1 OE2 REMARK 470 GLU I 72 CD REMARK 470 LYS I 76 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 NZ REMARK 470 LYS I 231 CE NZ REMARK 470 LYS I 259 CG CD CE NZ REMARK 470 LEU I 282 CG CD1 CD2 REMARK 470 LYS I 285 CD 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 CD CE NZ REMARK 470 LYS I 414 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 O HOH I 698 O HOH I 850 1.90 REMARK 500 OP2 DG B 9 O HOH B 101 1.94 REMARK 500 O3 SO4 I 503 O HOH I 601 1.96 REMARK 500 O HOH I 780 O HOH I 863 1.96 REMARK 500 OE1 GLU I 220 O2' AMP I 501 1.97 REMARK 500 OE1 GLU I 125 O HOH I 602 2.00 REMARK 500 OP2 DC C 30 O HOH C 101 2.01 REMARK 500 O3 SO4 I 503 O HOH I 603 2.06 REMARK 500 NH1 ARG I 261 OD1 ASN I 263 2.07 REMARK 500 O4 DT B 15 O HOH B 102 2.07 REMARK 500 O PHE I 436 O HOH I 604 2.08 REMARK 500 OP2 DA B 8 O HOH B 103 2.11 REMARK 500 OE1 GLU I 125 O HOH I 605 2.14 REMARK 500 O1P AMP I 501 O HOH I 606 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 DC B 7 C4 DC B 7 C5 0.050 REMARK 500 DT B 10 O3' DT B 10 C3' -0.055 REMARK 500 DG B 11 O3' DG B 11 C3' -0.058 REMARK 500 DG B 12 C2 DG B 12 N3 0.051 REMARK 500 DG B 14 P DG B 14 O5' 0.064 REMARK 500 DC C 29 O3' DC C 29 C3' -0.105 REMARK 500 DC C 31 C2' DC C 31 C1' 0.083 REMARK 500 DC C 31 N1 DC C 31 C2 0.080 REMARK 500 DC C 32 N1 DC C 32 C6 0.040 REMARK 500 DA C 33 P DA C 33 O5' 0.074 REMARK 500 DT C 37 C5 DT C 37 C7 -0.045 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 7 O4' - C1' - C2' ANGL. DEV. = 3.1 DEGREES REMARK 500 DT B 10 N3 - C4 - O4 ANGL. DEV. = 3.7 DEGREES REMARK 500 DG B 11 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG B 12 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DT C 23 N3 - C4 - O4 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC C 31 O4' - C1' - N1 ANGL. DEV. = 6.7 DEGREES REMARK 500 DC C 32 O4' - C1' - C2' ANGL. DEV. = 3.8 DEGREES REMARK 500 DA C 33 O5' - P - OP2 ANGL. DEV. = -6.1 DEGREES REMARK 500 DA C 41 O4' - C4' - C3' ANGL. DEV. = -2.9 DEGREES REMARK 500 ARG I 21 NE - CZ - NH2 ANGL. DEV. = -4.2 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 -117.24 -125.00 REMARK 500 PHE I 110 -67.33 -155.47 REMARK 500 CYS I 121 22.15 -148.98 REMARK 500 SER I 124 -162.91 -123.32 REMARK 500 SER I 124 -163.63 -123.32 REMARK 500 HIS I 154 46.70 -143.54 REMARK 500 SER I 223 -156.35 -136.45 REMARK 500 ASN I 263 37.99 -95.01 REMARK 500 LYS I 431 -63.09 -103.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 AMP I 501 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AMP I 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 I 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 I 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 I 504 DBREF 6RAU B 1 21 PDB 6RAU 6RAU 1 21 DBREF 6RAU C 22 42 PDB 6RAU 6RAU 22 42 DBREF1 6RAU I 2 442 UNP A0A0A2ACP7_PROMR DBREF2 6RAU I A0A0A2ACP7 2 442 SEQADV 6RAU GLY I 1 UNP A0A0A2ACP EXPRESSION TAG 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 21 DA DT DT DG DC DG DA DC DC DC DC DA DC SEQRES 2 C 21 DT DA DT DC DG DG DA DA SEQRES 1 I 442 GLY ARG GLN LYS GLU LEU PHE LYS GLU GLU ILE ILE HIS SEQRES 2 I 442 GLN LEU GLU LEU HIS PRO SER ARG LEU ASP LYS GLU LYS SEQRES 3 I 442 ILE ILE SER GLU ALA MET GLU ASP GLY ILE ASP ASP PHE SEQRES 4 I 442 PHE GLU GLY ILE ARG MET ALA LEU ASP PRO LEU VAL THR SEQRES 5 I 442 PHE GLY VAL LYS ILE VAL PRO GLU LYS GLU SER GLU LYS SEQRES 6 I 442 SER GLN ASN PHE LEU TRP GLU ASP PHE ARG LYS LEU ALA SEQRES 7 I 442 ASN LYS LEU MET GLN ARG GLU LEU THR GLY HIS ALA ALA SEQRES 8 I 442 ARG ASP ALA ILE LEU THR ALA MET GLU SER ALA THR LYS SEQRES 9 I 442 GLU GLU TRP ASN GLY PHE TYR ARG ARG VAL LEU ILE LYS SEQRES 10 I 442 ASP LEU ARG CYS GLY VAL SER GLU LYS THR ILE ASN LYS SEQRES 11 I 442 ILE ALA LYS LYS PHE PRO LYS TYR ALA ILE PRO ILE PHE SEQRES 12 I 442 SER CYS PRO LEU ALA HIS ASP SER ALA ASN HIS GLU LYS SEQRES 13 I 442 LYS MET ILE GLY LYS LYS GLN ILE GLU ILE LYS LEU ASP SEQRES 14 I 442 GLY VAL ARG VAL LEU THR ILE ILE ARG GLN ASN LYS VAL SEQRES 15 I 442 GLU MET PHE SER ARG ASN GLY LYS GLN PHE HIS ASN PHE SEQRES 16 I 442 GLY HIS ILE ILE LEU GLU ILE GLU ASN VAL LEU LYS GLU SEQRES 17 I 442 ASP PRO ALA PRO TYR ASP LEU VAL LEU ASP GLY GLU VAL SEQRES 18 I 442 MET SER ALA ASN PHE GLN ASP LEU MET LYS GLN VAL HIS SEQRES 19 I 442 ARG LYS ASP GLY LYS GLN THR LYS ASP ALA VAL LEU HIS SEQRES 20 I 442 LEU PHE ASP LEU CYS PRO LEU GLU ASN PHE GLN LYS GLY SEQRES 21 I 442 ARG TRP ASN THR LYS GLN THR ALA ARG SER LEU LEU VAL SEQRES 22 I 442 LYS LYS TRP VAL ALA LYS HIS SER LEU LEU LEU LYS HIS SEQRES 23 I 442 ILE GLN THR LEU GLU TRP GLU ASN VAL ASP LEU ASP THR SEQRES 24 I 442 ILE GLN GLY GLN LYS ARG PHE VAL GLU LEU ASN LYS SER SEQRES 25 I 442 ALA VAL GLU GLY GLY TYR GLU GLY VAL MET ILE LYS ASP SEQRES 26 I 442 PRO ASP GLY MET TYR GLU CYS LYS ARG THR HIS SER TRP SEQRES 27 I 442 LEU LYS ALA LYS PRO PHE ILE GLU VAL THR LEU LYS VAL SEQRES 28 I 442 VAL SER VAL GLU GLU GLY THR GLY ARG ASN LYS GLY ARG SEQRES 29 I 442 LEU GLY ALA ILE LEU VAL GLU GLY GLU ASP ASP GLY TYR SEQRES 30 I 442 GLU TYR SER LEU SER CYS GLY SER GLY PHE SER ASP ILE SEQRES 31 I 442 GLN ARG GLU GLU TYR TRP SER LYS ARG LYS HIS LEU LEU SEQRES 32 I 442 GLY GLN LEU VAL GLU ILE ARG ALA ASP ALA LYS THR LYS SEQRES 33 I 442 SER LYS ASP GLY VAL ALA PHE SER LEU ARG PHE PRO ARG SEQRES 34 I 442 PHE LYS CYS PHE ARG GLY PHE LYS ALA GLY GLU LYS VAL HET AMP I 501 34 HET SO4 I 502 5 HET SO4 I 503 5 HET SO4 I 504 5 HETNAM AMP ADENOSINE MONOPHOSPHATE HETNAM SO4 SULFATE ION FORMUL 4 AMP C10 H14 N5 O7 P FORMUL 5 SO4 3(O4 S 2-) FORMUL 8 HOH *374(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 HIS I 280 1 16 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 LYS I 340 N HIS I 149 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 ILE I 176 O GLU I 183 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 PHE I 249 N ASP I 218 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 VAL I 370 O LEU I 381 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 SER I 424 N THR I 415 SITE 1 AC1 15 DC C 32 HOH C 107 GLU I 165 ILE I 166 SITE 2 AC1 15 LYS I 167 LEU I 168 ARG I 172 GLU I 220 SITE 3 AC1 15 PHE I 249 LEU I 290 MET I 322 LYS I 324 SITE 4 AC1 15 LYS I 340 HOH I 606 HOH I 620 SITE 1 AC2 2 ARG I 178 GLN I 179 SITE 1 AC3 5 LYS I 274 GLU I 291 TRP I 292 HOH I 601 SITE 2 AC3 5 HOH I 603 SITE 1 AC4 4 HIS I 149 ASP I 150 ASN I 153 HIS I 154 CRYST1 66.725 102.497 68.356 90.00 91.44 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 0.014987 0.000000 0.000378 0.00000 SCALE2 0.000000 0.009756 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014634 0.00000