HEADER OXIDOREDUCTASE 14-DEC-20 7B9P TITLE STRUCTURE OF RIBONUCLEOTIDE REDUCTASE FROM RHODOBACTER SPHAEROIDES COMPND MOL_ID: 1; COMPND 2 MOLECULE: VITAMIN B12-DEPENDENT RIBONUCLEOTIDE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.17.4.1; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: FROM THE FULL LENGTH PROTEIN WITH 1218 AA, THE C- COMPND 8 TERMINAL CRD DOMAIN WAS DELETED BY INSERTION OF A STOP CODON AT COMPND 9 POSTION 926. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOBACTER SPHAEROIDES (STRAIN ATCC 17023 / SOURCE 3 2.4.1 / NCIB 8253 / DSM 158); SOURCE 4 ORGANISM_TAXID: 272943; SOURCE 5 STRAIN: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158; SOURCE 6 ATCC: 17023; SOURCE 7 GENE: NRD, RSP_2495; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET28B(+) KEYWDS RIBONUCLEOTIDE REDUCTASE, THIYL RADICAL ENZYME, ALLOSTERIC EFFECTOR, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR P.WILK,C.FEILER,C.LODERER,F.KABINGER REVDAT 4 01-MAY-24 7B9P 1 REMARK REVDAT 3 10-AUG-22 7B9P 1 JRNL REVDAT 2 03-AUG-22 7B9P 1 JRNL REVDAT 1 12-JAN-22 7B9P 0 JRNL AUTH T.FIETZE,P.WILK,F.KABINGER,S.ANOOSHEH,A.HOFER,D.LUNDIN, JRNL AUTH 2 C.G.FEILER,M.S.WEISS,C.LODERER JRNL TITL HUG DOMAIN IS RESPONSIBLE FOR ACTIVE DIMER STABILIZATION IN JRNL TITL 2 AN NRDJD RIBONUCLEOTIDE REDUCTASE. JRNL REF BIOCHEMISTRY V. 61 1633 2022 JRNL REFN ISSN 0006-2960 JRNL PMID 35856337 JRNL DOI 10.1021/ACS.BIOCHEM.2C00173 REMARK 2 REMARK 2 RESOLUTION. 2.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16 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) : 2.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 62885 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) : 0.230 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.340 REMARK 3 FREE R VALUE TEST SET COUNT : 2098 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 47.8600 - 6.5210 1.00 4432 154 0.2260 0.2609 REMARK 3 2 6.5210 - 5.1779 1.00 4187 144 0.2359 0.2660 REMARK 3 3 5.1779 - 4.5239 1.00 4115 142 0.1921 0.2131 REMARK 3 4 4.5239 - 4.1106 1.00 4090 141 0.1751 0.2443 REMARK 3 5 4.1106 - 3.8161 1.00 4062 141 0.1953 0.2432 REMARK 3 6 3.8161 - 3.5912 1.00 4036 139 0.2079 0.2579 REMARK 3 7 3.5912 - 3.4114 1.00 4044 140 0.2396 0.3177 REMARK 3 8 3.4114 - 3.2629 1.00 4007 138 0.2658 0.2871 REMARK 3 9 3.2629 - 3.1373 1.00 4013 138 0.2858 0.3565 REMARK 3 10 3.1373 - 3.0291 1.00 4008 139 0.3011 0.3756 REMARK 3 11 3.0291 - 2.9344 1.00 3976 137 0.3086 0.3626 REMARK 3 12 2.9344 - 2.8505 1.00 4017 139 0.3321 0.3436 REMARK 3 13 2.8505 - 2.7755 1.00 3980 136 0.3771 0.3889 REMARK 3 14 2.7755 - 2.7078 1.00 3963 137 0.4000 0.4039 REMARK 3 15 2.7078 - 2.6462 0.96 3857 133 0.4381 0.4672 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) : 0.540 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 114.4 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 814 THROUGH 920 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.3441 52.4251 363.3871 REMARK 3 T TENSOR REMARK 3 T11: 0.7747 T22: 1.1964 REMARK 3 T33: 1.0849 T12: -0.0813 REMARK 3 T13: -0.0624 T23: 0.1521 REMARK 3 L TENSOR REMARK 3 L11: -0.0195 L22: 0.1117 REMARK 3 L33: 0.6471 L12: -0.0526 REMARK 3 L13: 0.4240 L23: -0.3245 REMARK 3 S TENSOR REMARK 3 S11: 0.1793 S12: 0.2617 S13: -0.0620 REMARK 3 S21: -0.0835 S22: 0.2317 S23: 0.5404 REMARK 3 S31: 0.1716 S32: -0.6858 S33: 0.0010 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 244 ) REMARK 3 ORIGIN FOR THE GROUP (A): 50.8831 54.2611 366.9506 REMARK 3 T TENSOR REMARK 3 T11: 0.7099 T22: 1.1444 REMARK 3 T33: 0.7712 T12: 0.1489 REMARK 3 T13: 0.1039 T23: 0.0405 REMARK 3 L TENSOR REMARK 3 L11: 2.0792 L22: 0.7704 REMARK 3 L33: 1.2075 L12: -0.7725 REMARK 3 L13: -0.0147 L23: -0.3332 REMARK 3 S TENSOR REMARK 3 S11: 0.1222 S12: 0.5056 S13: -0.0097 REMARK 3 S21: -0.0579 S22: -0.2805 S23: -0.2530 REMARK 3 S31: 0.0902 S32: 0.5344 S33: -0.0107 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 245 THROUGH 446 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.5312 63.7635 394.3827 REMARK 3 T TENSOR REMARK 3 T11: 0.6093 T22: 0.8804 REMARK 3 T33: 0.7078 T12: 0.1250 REMARK 3 T13: 0.0170 T23: 0.1362 REMARK 3 L TENSOR REMARK 3 L11: 1.2016 L22: 1.7810 REMARK 3 L33: 2.0033 L12: 0.0025 REMARK 3 L13: -0.1371 L23: 0.6779 REMARK 3 S TENSOR REMARK 3 S11: 0.0104 S12: -0.0398 S13: -0.1375 REMARK 3 S21: -0.3391 S22: 0.0080 S23: -0.0899 REMARK 3 S31: -0.2663 S32: -0.4016 S33: 0.0003 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 447 THROUGH 747 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.3768 41.8165 362.2143 REMARK 3 T TENSOR REMARK 3 T11: 0.8916 T22: 0.9894 REMARK 3 T33: 0.8626 T12: 0.0648 REMARK 3 T13: -0.0037 T23: -0.1345 REMARK 3 L TENSOR REMARK 3 L11: 2.0852 L22: 0.9492 REMARK 3 L33: 0.4613 L12: -0.6386 REMARK 3 L13: 0.4591 L23: 0.2229 REMARK 3 S TENSOR REMARK 3 S11: 0.1244 S12: 0.6415 S13: -0.4332 REMARK 3 S21: -0.3530 S22: 0.0008 S23: 0.0474 REMARK 3 S31: 0.5713 S32: 0.2645 S33: 0.0002 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 748 THROUGH 813 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.0422 85.6743 348.1618 REMARK 3 T TENSOR REMARK 3 T11: 0.8957 T22: 1.4687 REMARK 3 T33: 1.0072 T12: -0.2981 REMARK 3 T13: -0.1191 T23: 0.2162 REMARK 3 L TENSOR REMARK 3 L11: 2.7120 L22: 1.9197 REMARK 3 L33: 1.0281 L12: 0.7133 REMARK 3 L13: 0.8288 L23: -0.7064 REMARK 3 S TENSOR REMARK 3 S11: -0.3012 S12: -0.1246 S13: 0.4804 REMARK 3 S21: 0.8196 S22: 0.1799 S23: -0.5633 REMARK 3 S31: -0.4152 S32: 0.5858 S33: 0.2929 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 7B9P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1292111331. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JAN-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 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 : 62949 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.646 REMARK 200 RESOLUTION RANGE LOW (A) : 47.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 19.29 REMARK 200 R MERGE (I) : 0.16900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 19.70 REMARK 200 R MERGE FOR SHELL (I) : 7.68400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: ENSEMBLE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 76.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PRECIPITANT: 30% PEG 1500, 20% REMARK 280 GLYCEROL PROTEIN SOLUTION: 45 MG/ML PROTEIN + 100 UM DATP REMARK 280 HANGING DROP EXPERIMENT: 1.0 UL PROTEIN SOLUTION + 1.0 UL REMARK 280 PRECIPITANT OVER 500 UL PRECIPITANT, PH 8.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 242.85133 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 121.42567 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 182.13850 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 60.71283 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 303.56417 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 242.85133 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 121.42567 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 60.71283 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 182.13850 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 303.56417 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 68090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 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 350 BIOMT1 2 0.500000 -0.866025 0.000000 70.37400 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 121.89134 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 789.26683 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 ASP A 31 REMARK 465 GLY A 32 REMARK 465 THR A 33 REMARK 465 VAL A 34 REMARK 465 GLU A 785 REMARK 465 ASP A 786 REMARK 465 PHE A 787 REMARK 465 CYS A 788 REMARK 465 LYS A 789 REMARK 465 GLY A 790 REMARK 465 ALA A 791 REMARK 465 LEU A 792 REMARK 465 GLY A 793 REMARK 465 ILE A 794 REMARK 465 PRO A 795 REMARK 465 ALA A 796 REMARK 465 ASP A 797 REMARK 465 LYS A 798 REMARK 465 LEU A 799 REMARK 465 ALA A 800 REMARK 465 LEU A 921 REMARK 465 ALA A 922 REMARK 465 SER A 923 REMARK 465 ALA A 924 REMARK 465 LEU A 925 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 532 CD 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 NH1 ARG A 422 O HOH A 1101 2.07 REMARK 500 OH TYR A 15 O HOH A 1102 2.08 REMARK 500 OE1 GLN A 366 O HOH A 1103 2.14 REMARK 500 O ARG A 912 OG SER A 915 2.17 REMARK 500 OD2 ASP A 640 O HOH A 1104 2.18 REMARK 500 O HOH A 1142 O HOH A 1231 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 OH TYR A 367 NE2 HIS A 442 10667 2.14 REMARK 500 OE1 GLU A 301 NH2 ARG A 363 10667 2.16 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 LEU A 806 CA - CB - CG ANGL. DEV. = 14.1 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 VAL A 101 -158.32 -131.35 REMARK 500 ASN A 158 -55.54 -125.59 REMARK 500 ALA A 500 -109.75 46.48 REMARK 500 ASP A 504 86.16 -54.52 REMARK 500 LEU A 592 -11.79 -142.26 REMARK 500 PRO A 639 26.66 -76.76 REMARK 500 ASP A 640 112.33 -168.56 REMARK 500 VAL A 670 134.09 -170.18 REMARK 500 ALA A 758 34.22 -88.46 REMARK 500 ALA A 771 48.73 -104.68 REMARK 500 PHE A 772 86.48 47.05 REMARK 500 VAL A 777 -60.78 -133.02 REMARK 500 GLN A 780 -72.52 -81.70 REMARK 500 TRP A 781 -40.66 -26.27 REMARK 500 LEU A 783 75.42 -40.49 REMARK 500 PHE A 804 -138.53 69.58 REMARK 500 LEU A 806 59.81 -91.40 REMARK 500 ARG A 808 126.42 -36.95 REMARK 500 MET A 828 9.81 59.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU A 765 ALA A 766 144.43 REMARK 500 ASP A 773 ILE A 774 148.46 REMARK 500 ASP A 805 LEU A 806 -142.97 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 A1002 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DTP A1001 O1G REMARK 620 2 DTP A1001 O3G 68.7 REMARK 620 3 DTP A1001 O1A 77.4 91.5 REMARK 620 N 1 2 DBREF 7B9P A 1 925 UNP Q3J3H6 Q3J3H6_RHOS4 1 925 SEQRES 1 A 925 MET LYS ILE GLU ARG LYS PHE THR THR ALA GLU GLY GLY SEQRES 2 A 925 ALA TYR GLY GLY VAL GLY PHE THR THR THR VAL SER GLU SEQRES 3 A 925 ILE ARG ASN PRO ASP GLY THR VAL VAL PHE ARG ASN GLU SEQRES 4 A 925 SER VAL GLU VAL PRO GLU GLY TRP SER GLN VAL ALA SER SEQRES 5 A 925 ASP VAL LEU ALA GLN LYS TYR PHE ARG LYS ALA GLY VAL SEQRES 6 A 925 PRO ALA ARG LEU LYS ARG VAL LYS GLU LYS GLY VAL PRO SEQRES 7 A 925 ASP PHE LEU TRP ARG SER VAL PRO ASP GLU ALA GLU LEU SEQRES 8 A 925 ALA LYS LEU PRO GLU GLU GLU ARG PHE VAL GLY GLU THR SEQRES 9 A 925 SER ALA ARG GLN VAL PHE ASP ARG LEU ALA GLY ALA TRP SEQRES 10 A 925 ALA TYR TRP GLY TRP LYS GLY GLY TYR PHE SER THR GLU SEQRES 11 A 925 ALA ASP ALA ARG ALA TYR TYR ASP GLU MET ARG HIS MET SEQRES 12 A 925 LEU ALA ARG GLN MET ALA ALA PRO ASN SER PRO GLN TRP SEQRES 13 A 925 PHE ASN THR GLY LEU HIS TRP ALA TYR GLY ILE ASP GLY SEQRES 14 A 925 PRO SER GLN GLY HIS PHE TYR VAL ASP HIS ALA THR GLY SEQRES 15 A 925 LYS LEU GLN LYS SER ASP SER ALA TYR GLU HIS PRO GLN SEQRES 16 A 925 PRO HIS ALA CYS PHE ILE GLN SER VAL GLN ASP ASP LEU SEQRES 17 A 925 VAL ASN GLU GLY GLY ILE MET ASP LEU TRP VAL ARG GLU SEQRES 18 A 925 ALA ARG LEU PHE LYS TYR GLY SER GLY THR GLY THR ASN SEQRES 19 A 925 PHE SER SER LEU ARG GLY GLU GLY GLU LYS LEU SER GLY SEQRES 20 A 925 GLY GLY LYS SER SER GLY LEU MET GLY PHE LEU LYS ILE SEQRES 21 A 925 GLY ASP ARG ALA ALA GLY ALA ILE LYS SER GLY GLY THR SEQRES 22 A 925 THR ARG ARG ALA ALA LYS MET VAL ILE CYS ASP MET ASP SEQRES 23 A 925 HIS PRO ASP ILE GLU GLN PHE ILE ASN TRP LYS VAL ILE SEQRES 24 A 925 GLU GLU GLN LYS VAL ALA SER LEU VAL ALA GLY SER LYS SEQRES 25 A 925 GLN HIS GLU ALA LYS LEU ASN ASP ILE PHE ALA ALA ILE SEQRES 26 A 925 ARG SER PHE ASP GLY SER ILE GLU GLY ALA THR ASP PRO SEQRES 27 A 925 ALA GLY ASN ALA GLY LEU LYS THR ALA ILE ARG ALA ALA SEQRES 28 A 925 LYS LYS ALA MET ILE PRO GLU THR TYR ILE ASN ARG VAL SEQRES 29 A 925 LEU GLN TYR ALA ARG GLN GLY PHE SER SER ILE GLU PHE SEQRES 30 A 925 PRO THR TYR ASP THR ASP TRP ASP SER GLU ALA TYR THR SEQRES 31 A 925 THR VAL SER GLY GLN ASN SER ASN ASN SER VAL ARG VAL SEQRES 32 A 925 THR ASP ALA PHE LEU GLN ALA VAL LYS ASP ASP ALA ASP SEQRES 33 A 925 TRP ALA LEU VAL ARG ARG THR ASP GLY LYS VAL ALA LYS SEQRES 34 A 925 THR ILE LYS ALA ARG GLU LEU TRP ASP GLN VAL GLY HIS SEQRES 35 A 925 ALA ALA TRP ALA CYS ALA ASP PRO GLY ILE GLN PHE HIS SEQRES 36 A 925 ASP THR VAL ASN ALA TRP HIS THR CYS PRO GLU ASP GLY SEQRES 37 A 925 GLN ILE ARG GLY SER ASN PRO CYS SER GLU TYR MET PHE SEQRES 38 A 925 LEU ASP ASP THR ALA CYS ASN LEU ALA SER MET ASN LEU SEQRES 39 A 925 LEU THR PHE PHE GLU ALA GLY ARG PHE ASP ALA GLU GLY SEQRES 40 A 925 TYR VAL HIS ALA THR ARG LEU TRP THR VAL THR LEU GLU SEQRES 41 A 925 ILE SER VAL MET MET ALA GLN PHE PRO SER LYS GLU ILE SEQRES 42 A 925 ALA GLN LEU SER TYR ASP PHE ARG THR LEU GLY LEU GLY SEQRES 43 A 925 TYR ALA ASN ILE GLY GLY LEU LEU MET ASN MET GLY LEU SEQRES 44 A 925 GLY TYR ASP SER SER GLU GLY ARG ALA LEU CYS GLY ALA SEQRES 45 A 925 LEU SER ALA ILE MET THR GLY VAL ALA TYR ALA THR SER SEQRES 46 A 925 ALA GLU MET ALA GLY GLU LEU GLY ALA PHE SER GLY TYR SEQRES 47 A 925 GLU ARG ASN ALA GLY HIS MET LEU ARG VAL ILE ARG ASN SEQRES 48 A 925 HIS ARG THR ALA ALA HIS GLY HIS THR THR GLY TYR GLU SEQRES 49 A 925 GLY VAL ASN VAL SER PRO VAL ALA LEU ASP GLN VAL ASN SEQRES 50 A 925 CYS PRO ASP PRO ARG LEU VAL ALA LEU ALA LYS SER SER SEQRES 51 A 925 TRP ASP GLU ALA LEU ARG LEU GLY GLU ALA HIS GLY TYR SEQRES 52 A 925 ARG ASN ALA GLN VAL THR VAL ILE ALA PRO THR GLY THR SEQRES 53 A 925 ILE GLY LEU VAL MET ASP CYS ASP THR THR GLY ILE GLU SEQRES 54 A 925 PRO ASP PHE ALA LEU VAL LYS PHE LYS LYS LEU ALA GLY SEQRES 55 A 925 GLY GLY TYR PHE LYS ILE ILE ASN ARG SER VAL PRO ALA SEQRES 56 A 925 ALA LEU GLU THR LEU GLY TYR ALA SER ALA GLN ILE SER SEQRES 57 A 925 GLN ILE VAL ALA TYR ALA VAL GLY HIS GLY THR LEU ALA SEQRES 58 A 925 ASN CYS PRO THR ILE SER HIS SER ALA LEU VAL GLY HIS SEQRES 59 A 925 GLY PHE GLY ALA ARG GLU ILE GLU LYS ILE GLU ALA ALA SEQRES 60 A 925 LEU PRO SER ALA PHE ASP ILE ARG PHE VAL PHE ASN GLN SEQRES 61 A 925 TRP THR LEU GLY GLU ASP PHE CYS LYS GLY ALA LEU GLY SEQRES 62 A 925 ILE PRO ALA ASP LYS LEU ALA ASP PRO THR PHE ASP LEU SEQRES 63 A 925 LEU ARG HIS LEU GLY PHE THR ARG ALA GLN ILE GLU ALA SEQRES 64 A 925 ALA ASN ASP HIS VAL CYS GLY THR MET THR LEU GLU GLY SEQRES 65 A 925 ALA PRO HIS LEU LYS ALA GLU HIS LEU PRO VAL PHE ASP SEQRES 66 A 925 CYS ALA ASN PRO CYS GLY LYS LYS GLY LYS ARG TYR LEU SEQRES 67 A 925 SER VAL GLU SER HIS ILE HIS MET MET ALA ALA ALA GLN SEQRES 68 A 925 SER PHE ILE SER GLY ALA ILE SER LYS THR ILE ASN MET SEQRES 69 A 925 PRO ASN SER ALA THR ILE ALA GLU THR LEU ALA ALA TYR SEQRES 70 A 925 GLU LEU SER HIS SER LEU GLY ILE LYS ALA ASN ALA LEU SEQRES 71 A 925 TYR ARG ASP GLY SER LYS LEU SER GLN PRO LEU ALA SER SEQRES 72 A 925 ALA LEU HET DTP A1001 30 HET MG A1002 1 HETNAM DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 DTP C10 H16 N5 O12 P3 FORMUL 3 MG MG 2+ FORMUL 4 HOH *137(H2 O) HELIX 1 AA1 SER A 48 TYR A 59 1 12 HELIX 2 AA2 PRO A 78 TRP A 82 5 5 HELIX 3 AA3 ASP A 87 ALA A 92 1 6 HELIX 4 AA4 SER A 105 GLY A 124 1 20 HELIX 5 AA5 THR A 129 ARG A 146 1 18 HELIX 6 AA6 ASN A 152 THR A 159 1 8 HELIX 7 AA7 GLY A 160 TYR A 165 1 6 HELIX 8 AA8 GLY A 213 GLY A 228 1 16 HELIX 9 AA9 GLY A 253 ILE A 268 1 16 HELIX 10 AB1 LYS A 269 THR A 273 5 5 HELIX 11 AB2 ASP A 289 ASN A 295 1 7 HELIX 12 AB3 ASN A 295 SER A 327 1 33 HELIX 13 AB4 SER A 331 THR A 336 1 6 HELIX 14 AB5 ASN A 341 ALA A 354 1 14 HELIX 15 AB6 PRO A 357 GLY A 371 1 15 HELIX 16 AB7 SER A 386 VAL A 392 1 7 HELIX 17 AB8 THR A 404 ASP A 414 1 11 HELIX 18 AB9 ALA A 433 CYS A 447 1 15 HELIX 19 AC1 HIS A 455 TRP A 461 1 7 HELIX 20 AC2 CYS A 464 GLY A 468 5 5 HELIX 21 AC3 ASP A 504 ALA A 526 1 23 HELIX 22 AC4 SER A 530 ARG A 541 1 12 HELIX 23 AC5 ASN A 549 MET A 557 1 9 HELIX 24 AC6 SER A 563 GLY A 593 1 31 HELIX 25 AC7 TYR A 598 ARG A 600 5 3 HELIX 26 AC8 ASN A 601 HIS A 617 1 17 HELIX 27 AC9 ASP A 640 GLY A 662 1 23 HELIX 28 AD1 THR A 676 MET A 681 1 6 HELIX 29 AD2 ARG A 711 LEU A 720 1 10 HELIX 30 AD3 ALA A 723 GLY A 736 1 14 HELIX 31 AD4 SER A 747 GLY A 753 1 7 HELIX 32 AD5 ARG A 759 ALA A 766 1 8 HELIX 33 AD6 THR A 813 CYS A 825 1 13 HELIX 34 AD7 LYS A 837 ASP A 845 5 9 HELIX 35 AD8 SER A 859 SER A 872 1 14 HELIX 36 AD9 THR A 889 LEU A 903 1 15 SHEET 1 AA1 2 PHE A 20 ILE A 27 0 SHEET 2 AA1 2 PHE A 36 PRO A 44 -1 O VAL A 43 N THR A 21 SHEET 1 AA2 2 VAL A 65 PRO A 66 0 SHEET 2 AA2 2 PHE A 100 VAL A 101 -1 O VAL A 101 N VAL A 65 SHEET 1 AA3 2 LEU A 69 ARG A 71 0 SHEET 2 AA3 2 SER A 84 PRO A 86 -1 O VAL A 85 N LYS A 70 SHEET 1 AA4 3 ALA A 149 PRO A 151 0 SHEET 2 AA4 3 LEU A 489 ASN A 493 -1 O SER A 491 N ALA A 150 SHEET 3 AA4 3 GLY A 544 ALA A 548 1 O GLY A 546 N ALA A 490 SHEET 1 AA5 2 PHE A 175 VAL A 177 0 SHEET 2 AA5 2 LEU A 184 LYS A 186 -1 O GLN A 185 N TYR A 176 SHEET 1 AA6 7 THR A 485 CYS A 487 0 SHEET 2 AA6 7 CYS A 199 ILE A 201 -1 N CYS A 199 O CYS A 487 SHEET 3 AA6 7 GLY A 230 ASN A 234 1 O GLY A 232 N PHE A 200 SHEET 4 AA6 7 LYS A 279 ASP A 284 1 O ILE A 282 N THR A 233 SHEET 5 AA6 7 ASN A 398 VAL A 403 1 O ASN A 398 N LYS A 279 SHEET 6 AA6 7 GLY A 451 PHE A 454 1 O GLY A 451 N VAL A 401 SHEET 7 AA6 7 ALA A 907 ASN A 908 -1 O ASN A 908 N ILE A 452 SHEET 1 AA7 2 ASP A 416 VAL A 420 0 SHEET 2 AA7 2 VAL A 427 LYS A 432 -1 O LYS A 429 N LEU A 419 SHEET 1 AA8 2 PHE A 498 GLU A 499 0 SHEET 2 AA8 2 ARG A 502 PHE A 503 -1 O ARG A 502 N GLU A 499 SHEET 1 AA9 2 VAL A 695 LYS A 699 0 SHEET 2 AA9 2 TYR A 705 ILE A 709 -1 O ILE A 708 N LYS A 696 SHEET 1 AB1 2 ILE A 882 MET A 884 0 SHEET 2 AB1 2 LEU A 910 ARG A 912 1 O TYR A 911 N MET A 884 SSBOND 1 CYS A 199 CYS A 487 1555 1555 2.06 LINK O1G DTP A1001 MG MG A1002 1555 1555 2.27 LINK O3G DTP A1001 MG MG A1002 1555 1555 2.19 LINK O1A DTP A1001 MG MG A1002 1555 1555 1.98 CISPEP 1 ASP A 449 PRO A 450 0 3.46 CRYST1 140.748 140.748 364.277 90.00 90.00 120.00 P 65 2 2 12 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 0.007105 0.004102 0.000000 0.00000 SCALE2 0.000000 0.008204 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002745 0.00000