HEADER DNA BINDING PROTEIN 07-APR-19 6RAR TITLE PMAR-LIG_PRES3-MN 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 STR. MIT 9302; SOURCE 15 ORGANISM_TAXID: 74545; 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 6RAR 1 LINK REVDAT 2 29-JAN-20 6RAR 1 JRNL REVDAT 1 10-JUL-19 6RAR 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. 1.79 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) : 1.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.6 REMARK 3 NUMBER OF REFLECTIONS : 57870 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.234 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 2875 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 24.2935 - 4.9117 0.96 3923 244 0.2173 0.2367 REMARK 3 2 4.9117 - 3.9038 0.97 3923 234 0.1847 0.2161 REMARK 3 3 3.9038 - 3.4118 0.95 3845 191 0.2038 0.2465 REMARK 3 4 3.4118 - 3.1006 0.96 3873 185 0.2239 0.2614 REMARK 3 5 3.1006 - 2.8787 0.98 3944 199 0.2577 0.3100 REMARK 3 6 2.8787 - 2.7092 0.98 3937 200 0.2663 0.2949 REMARK 3 7 2.7092 - 2.5737 0.97 3954 151 0.2592 0.2789 REMARK 3 8 2.5737 - 2.4618 0.98 3904 243 0.2643 0.3219 REMARK 3 9 2.4618 - 2.3671 0.98 3881 263 0.2629 0.3024 REMARK 3 10 2.3671 - 2.2855 0.94 3781 159 0.2605 0.3158 REMARK 3 11 2.2855 - 2.2141 0.85 3403 184 0.2737 0.3042 REMARK 3 12 2.2141 - 2.1508 0.77 3126 139 0.2731 0.2819 REMARK 3 13 2.1508 - 2.0942 0.64 2553 164 0.2901 0.2995 REMARK 3 14 2.0942 - 2.0432 0.48 1933 86 0.3014 0.3099 REMARK 3 15 2.0432 - 1.9967 0.39 1552 79 0.2909 0.3344 REMARK 3 16 1.9967 - 1.9543 0.32 1290 56 0.3103 0.2991 REMARK 3 17 1.9543 - 1.9152 0.24 953 45 0.3055 0.3401 REMARK 3 18 1.9152 - 1.8791 0.15 588 23 0.3140 0.3778 REMARK 3 19 1.8791 - 1.8455 0.09 346 12 0.3385 0.4421 REMARK 3 20 1.8455 - 1.8142 0.05 198 8 0.3578 0.3602 REMARK 3 21 1.8142 - 1.7850 0.02 88 10 0.3588 0.3855 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.430 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.10 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 : 0.018 4583 REMARK 3 ANGLE : 1.180 6341 REMARK 3 CHIRALITY : 0.055 686 REMARK 3 PLANARITY : 0.005 663 REMARK 3 DIHEDRAL : 11.512 3513 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 6RAR 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_1292101699. 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) : 0.991872 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 : 57936 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.785 REMARK 200 RESOLUTION RANGE LOW (A) : 68.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.6 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 59.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.56000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 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 (%): 67.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.73 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 51.65750 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: 8950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -80.0 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 HIS I 18 CE1 REMARK 470 GLU I 62 CD OE1 OE2 REMARK 470 LYS I 65 CD CE NZ REMARK 470 GLU I 72 CD REMARK 470 LYS I 76 CE NZ REMARK 470 LYS I 133 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 NZ REMARK 470 GLU I 208 CD OE1 OE2 REMARK 470 GLN I 227 CD REMARK 470 ASP I 228 CB CG OD1 OD2 REMARK 470 LYS I 231 CE NZ REMARK 470 LYS I 239 CD CE NZ REMARK 470 LYS I 259 CG CD CE NZ REMARK 470 LYS I 275 CG CD CE NZ REMARK 470 LYS I 279 NZ REMARK 470 LEU I 282 CB CG CD1 CD2 REMARK 470 LYS I 285 CD CE NZ REMARK 470 ASN I 294 ND2 REMARK 470 ASN I 310 ND2 REMARK 470 LYS I 311 CD CE NZ REMARK 470 LYS I 350 CG CD CE NZ REMARK 470 GLU I 393 CD REMARK 470 LYS I 398 CD REMARK 470 LYS I 400 CD CE NZ REMARK 470 LYS I 418 NZ REMARK 470 ARG I 434 CZ NH1 NH2 REMARK 470 PHE I 436 CG CD1 CD2 CE1 CE2 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 H42 DC B 7 H61 DA D 36 1.33 REMARK 500 HB2 GLU I 371 O HOH I 610 1.39 REMARK 500 HH12 ARG I 261 OE2 GLU I 331 1.50 REMARK 500 O GLU I 62 HZ2 LYS I 104 1.58 REMARK 500 O HOH B 140 O HOH B 153 1.84 REMARK 500 O HOH B 106 O HOH B 144 1.88 REMARK 500 OP1 DA D 36 O HOH D 401 1.90 REMARK 500 O HOH I 800 O HOH I 863 1.92 REMARK 500 O HOH I 750 O HOH I 850 1.99 REMARK 500 OE1 GLU I 16 O HOH I 601 2.02 REMARK 500 O ASP I 243 O HOH I 602 2.02 REMARK 500 O HOH B 107 O HOH B 138 2.03 REMARK 500 O HOH I 730 O HOH I 750 2.05 REMARK 500 O HOH I 806 O HOH I 867 2.05 REMARK 500 O HOH D 425 O HOH I 758 2.05 REMARK 500 O HOH B 129 O HOH B 152 2.05 REMARK 500 O HOH I 695 O HOH I 861 2.05 REMARK 500 OP1 DC D 32 O2P AMP D 300 2.06 REMARK 500 CB GLU I 371 O HOH I 610 2.06 REMARK 500 OE2 GLU I 125 O HOH I 603 2.08 REMARK 500 O HOH I 804 O HOH I 853 2.08 REMARK 500 OG1 THR I 87 O HOH I 604 2.11 REMARK 500 O HOH I 795 O HOH I 850 2.12 REMARK 500 O HOH B 134 O HOH I 616 2.12 REMARK 500 O HOH B 104 O HOH B 148 2.12 REMARK 500 OE1 GLU I 293 O HOH I 605 2.13 REMARK 500 C GLU I 371 O HOH I 610 2.14 REMARK 500 O HOH I 822 O HOH I 826 2.14 REMARK 500 O2 DT B 10 O HOH B 101 2.16 REMARK 500 O HOH I 674 O HOH I 864 2.16 REMARK 500 NH1 ARG I 261 OE2 GLU I 331 2.17 REMARK 500 O HOH B 124 O HOH B 126 2.18 REMARK 500 O HOH C 209 O HOH C 214 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DT B 2 C5 DT B 2 C7 -0.038 REMARK 500 DG B 11 O3' DG B 11 C3' -0.047 REMARK 500 DT B 21 C5 DT B 21 C7 -0.038 REMARK 500 DT C 23 C5 DT C 23 C7 -0.040 REMARK 500 DC D 32 P DC D 32 OP3 -0.122 REMARK 500 DT D 35 C5 DT D 35 C7 -0.036 REMARK 500 DT D 37 C5 DT D 37 C7 -0.044 REMARK 500 GLN I 179 CG GLN I 179 CD -0.224 REMARK 500 GLN I 179 CD GLN I 179 OE1 0.338 REMARK 500 GLN I 179 CD GLN I 179 NE2 -0.397 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' - C4' - C3' ANGL. DEV. = -2.7 DEGREES REMARK 500 DG B 12 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG B 14 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DC C 29 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 GLN I 179 CG - CD - OE1 ANGL. DEV. = -19.8 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 -127.05 -112.77 REMARK 500 PHE I 110 -64.59 -155.18 REMARK 500 SER I 124 -164.51 -127.36 REMARK 500 ALA I 132 -5.92 -58.83 REMARK 500 HIS I 154 49.29 -144.85 REMARK 500 SER I 223 -158.91 -140.38 REMARK 500 ASN I 263 35.80 -85.93 REMARK 500 SER I 281 -12.23 -40.80 REMARK 500 LYS I 431 -60.47 -105.89 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 I 889 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH I 890 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH I 891 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH I 892 DISTANCE = 6.22 ANGSTROMS REMARK 525 HOH I 893 DISTANCE = 6.46 ANGSTROMS REMARK 525 HOH I 894 DISTANCE = 6.48 ANGSTROMS REMARK 525 HOH I 895 DISTANCE = 8.12 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 MN C 101 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC C 31 O3' REMARK 620 2 DC D 32 OP3 64.5 REMARK 620 3 HOH I 611 O 84.7 148.6 REMARK 620 4 HOH I 613 O 97.2 78.6 100.1 REMARK 620 5 HOH I 680 O 162.8 98.5 112.4 81.3 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AMP D 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 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: 6RAU RELATED DB: PDB REMARK 900 IN THE SAME PAPER REMARK 900 RELATED ID: 6RCE RELATED DB: PDB REMARK 900 IN THE SAME PAPER REMARK 900 RELATED ID: 6RAS RELATED DB: PDB REMARK 900 IN THE SAME PAPER DBREF 6RAR B 1 21 PDB 6RAR 6RAR 1 21 DBREF 6RAR C 22 31 PDB 6RAR 6RAR 22 31 DBREF 6RAR D 32 42 PDB 6RAR 6RAR 32 42 DBREF1 6RAR I 5 436 UNP A0A0A2ACP7_PROMR DBREF2 6RAR 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 MN C 101 1 HET AMP D 300 34 HET SO4 I 501 5 HETNAM OMC O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM AMP ADENOSINE MONOPHOSPHATE HETNAM SO4 SULFATE ION FORMUL 2 OMC C10 H16 N3 O8 P FORMUL 5 MN MN 2+ FORMUL 6 AMP C10 H14 N5 O7 P FORMUL 7 SO4 O4 S 2- FORMUL 8 HOH *398(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 ALA I 132 1 9 HELIX 9 AA9 LYS I 133 ALA I 139 5 7 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 TRP I 338 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 VAL I 295 N LYS I 162 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 CYS I 252 N VAL I 216 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 LYS I 350 O GLU I 371 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 ARG I 429 N ARG I 410 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 1.56 LINK O3' DC C 31 MN MN C 101 1555 1555 2.16 LINK MN MN C 101 OP3 DC D 32 1555 1555 2.54 LINK MN MN C 101 O HOH I 611 1555 1555 2.33 LINK MN MN C 101 O HOH I 613 1555 1555 2.50 LINK MN MN C 101 O HOH I 680 1555 1555 1.99 SITE 1 AC1 7 DC C 31 DC D 32 LYS I 167 GLU I 319 SITE 2 AC1 7 HOH I 611 HOH I 613 HOH I 680 SITE 1 AC2 15 DC D 32 HOH D 403 HOH D 414 GLU I 165 SITE 2 AC2 15 ILE I 166 LYS I 167 LEU I 168 ARG I 172 SITE 3 AC2 15 GLU I 220 PHE I 249 LEU I 290 MET I 322 SITE 4 AC2 15 LYS I 324 LYS I 340 HOH I 613 SITE 1 AC3 4 HIS I 149 ASP I 150 ASN I 153 HIS I 154 CRYST1 67.304 103.315 68.543 90.00 90.79 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 0.014858 0.000000 0.000204 0.00000 SCALE2 0.000000 0.009679 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014591 0.00000