HEADER HYDROLASE 27-OCT-20 7DCY TITLE APO FORM OF MYCOPLASMA GENITALIUM RNASE R COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE R; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RNASE R,VACB PROTEIN HOMOLOG; COMPND 5 EC: 3.1.13.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOPLASMA GENITALIUM G37; SOURCE 3 ORGANISM_TAXID: 243273; SOURCE 4 STRAIN: G-37; SOURCE 5 GENE: RNR, VACB, MG104; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: K-12 KEYWDS RNA HYDROLASE, RNA 2'-O-METHYLATION SENSITIVE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.ABULA,X.QUAN,X.LI,T.YANG,T.LI,Q.CHEN,X.JI REVDAT 4 29-NOV-23 7DCY 1 REMARK REVDAT 3 19-MAY-21 7DCY 1 JRNL REVDAT 2 14-APR-21 7DCY 1 JRNL REVDAT 1 17-MAR-21 7DCY 0 JRNL AUTH A.ABULA,X.LI,X.QUAN,T.YANG,Y.LIU,H.GUO,T.LI,X.JI JRNL TITL MOLECULAR MECHANISM OF RNASE R SUBSTRATE SENSITIVITY FOR RNA JRNL TITL 2 RIBOSE METHYLATION. JRNL REF NUCLEIC ACIDS RES. V. 49 4738 2021 JRNL REFN ESSN 1362-4962 JRNL PMID 33788943 JRNL DOI 10.1093/NAR/GKAB202 REMARK 2 REMARK 2 RESOLUTION. 1.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10_2148 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 70582 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.230 REMARK 3 FREE R VALUE TEST SET COUNT : 3689 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 10.0000 - 5.8387 0.99 2780 168 0.1649 0.1683 REMARK 3 2 5.8387 - 4.6356 1.00 2680 131 0.1530 0.1708 REMARK 3 3 4.6356 - 4.0500 1.00 2629 153 0.1346 0.1650 REMARK 3 4 4.0500 - 3.6798 1.00 2617 137 0.1501 0.1651 REMARK 3 5 3.6798 - 3.4162 1.00 2635 142 0.1621 0.1728 REMARK 3 6 3.4162 - 3.2148 1.00 2601 139 0.1730 0.1989 REMARK 3 7 3.2148 - 3.0538 1.00 2604 141 0.1761 0.2201 REMARK 3 8 3.0538 - 2.9209 1.00 2585 141 0.1800 0.1999 REMARK 3 9 2.9209 - 2.8085 1.00 2569 151 0.1801 0.2051 REMARK 3 10 2.8085 - 2.7116 1.00 2576 146 0.1811 0.2151 REMARK 3 11 2.7116 - 2.6268 1.00 2576 150 0.1790 0.2431 REMARK 3 12 2.6268 - 2.5517 1.00 2545 170 0.1758 0.2171 REMARK 3 13 2.5517 - 2.4845 1.00 2540 145 0.1800 0.2193 REMARK 3 14 2.4845 - 2.4239 1.00 2583 138 0.1837 0.2392 REMARK 3 15 2.4239 - 2.3688 1.00 2532 148 0.1889 0.2147 REMARK 3 16 2.3688 - 2.3184 1.00 2573 127 0.1822 0.2348 REMARK 3 17 2.3184 - 2.2720 1.00 2584 149 0.1933 0.2688 REMARK 3 18 2.2720 - 2.2292 1.00 2588 119 0.1921 0.2250 REMARK 3 19 2.2292 - 2.1894 1.00 2534 148 0.1995 0.2518 REMARK 3 20 2.1894 - 2.1522 1.00 2574 148 0.2132 0.2267 REMARK 3 21 2.1522 - 2.1175 1.00 2533 141 0.2103 0.2412 REMARK 3 22 2.1175 - 2.0849 1.00 2556 155 0.2278 0.3131 REMARK 3 23 2.0849 - 2.0543 1.00 2567 129 0.2475 0.2774 REMARK 3 24 2.0543 - 2.0253 1.00 2531 144 0.2595 0.2794 REMARK 3 25 2.0253 - 1.9980 1.00 2569 118 0.2687 0.3046 REMARK 3 26 1.9980 - 1.9720 0.87 2232 111 0.2931 0.3046 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.670 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.011 5341 REMARK 3 ANGLE : 0.978 7250 REMARK 3 CHIRALITY : 0.065 836 REMARK 3 PLANARITY : 0.006 935 REMARK 3 DIHEDRAL : 14.336 3250 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 82 THROUGH 126 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.3365 43.3125 95.8783 REMARK 3 T TENSOR REMARK 3 T11: 0.2717 T22: 0.2858 REMARK 3 T33: 0.3991 T12: 0.0325 REMARK 3 T13: 0.0047 T23: 0.0274 REMARK 3 L TENSOR REMARK 3 L11: 0.1025 L22: 0.0988 REMARK 3 L33: 0.1246 L12: 0.0659 REMARK 3 L13: -0.0025 L23: -0.0023 REMARK 3 S TENSOR REMARK 3 S11: 0.0604 S12: 0.0732 S13: -0.3909 REMARK 3 S21: 0.1878 S22: -0.0517 S23: -0.1202 REMARK 3 S31: -0.0835 S32: 0.1958 S33: 0.0009 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 127 THROUGH 204 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.4710 54.3126 89.7450 REMARK 3 T TENSOR REMARK 3 T11: 0.2256 T22: 0.3150 REMARK 3 T33: 0.2676 T12: -0.0093 REMARK 3 T13: 0.0102 T23: -0.0104 REMARK 3 L TENSOR REMARK 3 L11: 0.3031 L22: 0.3697 REMARK 3 L33: 0.2405 L12: 0.1069 REMARK 3 L13: -0.0792 L23: 0.0620 REMARK 3 S TENSOR REMARK 3 S11: -0.0117 S12: 0.2226 S13: -0.0409 REMARK 3 S21: -0.0809 S22: 0.0177 S23: -0.0764 REMARK 3 S31: -0.0061 S32: 0.0026 S33: 0.0002 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 205 THROUGH 427 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.5550 47.7769 129.2260 REMARK 3 T TENSOR REMARK 3 T11: 0.2751 T22: 0.2106 REMARK 3 T33: 0.2388 T12: -0.0176 REMARK 3 T13: 0.0209 T23: 0.0221 REMARK 3 L TENSOR REMARK 3 L11: 0.6267 L22: 0.5543 REMARK 3 L33: 0.7994 L12: -0.0038 REMARK 3 L13: -0.2525 L23: -0.4041 REMARK 3 S TENSOR REMARK 3 S11: -0.0113 S12: -0.0452 S13: -0.0649 REMARK 3 S21: 0.1766 S22: 0.0639 S23: 0.0781 REMARK 3 S31: -0.0849 S32: -0.1323 S33: 0.0001 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 428 THROUGH 725 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.9928 52.6930 119.7523 REMARK 3 T TENSOR REMARK 3 T11: 0.2254 T22: 0.2550 REMARK 3 T33: 0.2657 T12: 0.0039 REMARK 3 T13: -0.0082 T23: -0.0037 REMARK 3 L TENSOR REMARK 3 L11: 0.6484 L22: 0.7874 REMARK 3 L33: 0.9276 L12: 0.6529 REMARK 3 L13: -0.4655 L23: -0.3574 REMARK 3 S TENSOR REMARK 3 S11: -0.0489 S12: -0.0916 S13: -0.1732 REMARK 3 S21: 0.0116 S22: 0.0175 S23: -0.1325 REMARK 3 S31: -0.0114 S32: 0.1841 S33: -0.0000 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 7DCY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-OCT-20. REMARK 100 THE DEPOSITION ID IS D_1300018691. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-OCT-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 : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 70690 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : 0.17500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 2.93100 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: 5XGU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM KCL, 100 MM HEPES (PH 6.8), 15% REMARK 280 PEG 5000MME, MICROBATCH, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 34.82600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 88.23800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.38400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 88.23800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.82600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.38400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 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 -21 REMARK 465 GLY A -20 REMARK 465 HIS A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 HIS A -6 REMARK 465 ILE A -5 REMARK 465 ASP A -4 REMARK 465 ASP A -3 REMARK 465 ASP A -2 REMARK 465 ASP A -1 REMARK 465 LYS A 0 REMARK 465 MET A 1 REMARK 465 LYS A 2 REMARK 465 VAL A 3 REMARK 465 LEU A 4 REMARK 465 THR A 5 REMARK 465 GLU A 6 REMARK 465 LEU A 7 REMARK 465 GLN A 8 REMARK 465 LYS A 9 REMARK 465 GLN A 10 REMARK 465 ILE A 11 REMARK 465 PHE A 12 REMARK 465 THR A 13 REMARK 465 ILE A 14 REMARK 465 VAL A 15 REMARK 465 LYS A 16 REMARK 465 LYS A 17 REMARK 465 GLU A 18 REMARK 465 ASN A 19 REMARK 465 GLY A 20 REMARK 465 LYS A 21 REMARK 465 PRO A 22 REMARK 465 ILE A 23 REMARK 465 PRO A 24 REMARK 465 PRO A 25 REMARK 465 GLY A 26 REMARK 465 ILE A 27 REMARK 465 VAL A 28 REMARK 465 VAL A 29 REMARK 465 ARG A 30 REMARK 465 MET A 31 REMARK 465 MET A 32 REMARK 465 GLU A 33 REMARK 465 ASN A 34 REMARK 465 SER A 35 REMARK 465 PRO A 36 REMARK 465 ASN A 37 REMARK 465 PHE A 38 REMARK 465 PRO A 39 REMARK 465 GLY A 40 REMARK 465 LYS A 41 REMARK 465 HIS A 42 REMARK 465 LEU A 43 REMARK 465 ILE A 44 REMARK 465 TYR A 45 REMARK 465 ARG A 46 REMARK 465 ALA A 47 REMARK 465 ILE A 48 REMARK 465 ASP A 49 REMARK 465 ASP A 50 REMARK 465 LEU A 51 REMARK 465 LEU A 52 REMARK 465 ASP A 53 REMARK 465 TRP A 54 REMARK 465 ALA A 55 REMARK 465 ILE A 56 REMARK 465 LEU A 57 REMARK 465 ARG A 58 REMARK 465 LYS A 59 REMARK 465 ALA A 60 REMARK 465 GLY A 61 REMARK 465 GLY A 62 REMARK 465 VAL A 63 REMARK 465 THR A 64 REMARK 465 ASN A 65 REMARK 465 GLN A 66 REMARK 465 LEU A 67 REMARK 465 LEU A 68 REMARK 465 VAL A 69 REMARK 465 ASN A 70 REMARK 465 TYR A 71 REMARK 465 GLU A 72 REMARK 465 PRO A 73 REMARK 465 ALA A 74 REMARK 465 GLU A 75 REMARK 465 PRO A 76 REMARK 465 LEU A 77 REMARK 465 LEU A 78 REMARK 465 ASP A 79 REMARK 465 LYS A 80 REMARK 465 LYS A 81 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 OG1 THR A 676 O HOH A 901 1.66 REMARK 500 O GLN A 607 O HOH A 902 1.97 REMARK 500 O HOH A 1296 O HOH A 1298 2.02 REMARK 500 O HOH A 1271 O HOH A 1340 2.09 REMARK 500 O HOH A 993 O HOH A 1274 2.11 REMARK 500 O HOH A 1267 O HOH A 1276 2.12 REMARK 500 NZ LYS A 550 O HOH A 903 2.16 REMARK 500 O HOH A 1194 O HOH A 1338 2.17 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 GLU A 161 CB GLU A 161 CG -0.133 REMARK 500 GLU A 161 CG GLU A 161 CD -0.130 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 GLU A 161 OE1 - CD - OE2 ANGL. DEV. = 11.3 DEGREES REMARK 500 MET A 336 CG - SD - CE ANGL. DEV. = -9.9 DEGREES REMARK 500 LYS A 686 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 PRO A 130 -119.74 -71.53 REMARK 500 ASP A 134 -71.37 69.38 REMARK 500 GLU A 161 47.48 71.22 REMARK 500 LEU A 283 58.70 -119.68 REMARK 500 THR A 323 -21.99 66.70 REMARK 500 GLN A 344 -83.82 -128.73 REMARK 500 ASP A 679 -9.11 83.86 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 A1375 DISTANCE = 5.99 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 MG A 801 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 276 OD2 REMARK 620 2 ASP A 285 OD1 170.4 REMARK 620 3 HOH A 934 O 84.4 93.0 REMARK 620 4 HOH A 953 O 87.5 83.3 90.2 REMARK 620 5 HOH A1013 O 93.4 96.2 107.1 162.7 REMARK 620 6 HOH A1266 O 92.4 88.0 166.3 76.4 86.3 REMARK 620 N 1 2 3 4 5 DBREF 7DCY A 1 725 UNP P47350 RNR_MYCGE 1 725 SEQADV 7DCY MET A -21 UNP P47350 EXPRESSION TAG SEQADV 7DCY GLY A -20 UNP P47350 EXPRESSION TAG SEQADV 7DCY HIS A -19 UNP P47350 EXPRESSION TAG SEQADV 7DCY HIS A -18 UNP P47350 EXPRESSION TAG SEQADV 7DCY HIS A -17 UNP P47350 EXPRESSION TAG SEQADV 7DCY HIS A -16 UNP P47350 EXPRESSION TAG SEQADV 7DCY HIS A -15 UNP P47350 EXPRESSION TAG SEQADV 7DCY HIS A -14 UNP P47350 EXPRESSION TAG SEQADV 7DCY HIS A -13 UNP P47350 EXPRESSION TAG SEQADV 7DCY HIS A -12 UNP P47350 EXPRESSION TAG SEQADV 7DCY HIS A -11 UNP P47350 EXPRESSION TAG SEQADV 7DCY HIS A -10 UNP P47350 EXPRESSION TAG SEQADV 7DCY SER A -9 UNP P47350 EXPRESSION TAG SEQADV 7DCY SER A -8 UNP P47350 EXPRESSION TAG SEQADV 7DCY GLY A -7 UNP P47350 EXPRESSION TAG SEQADV 7DCY HIS A -6 UNP P47350 EXPRESSION TAG SEQADV 7DCY ILE A -5 UNP P47350 EXPRESSION TAG SEQADV 7DCY ASP A -4 UNP P47350 EXPRESSION TAG SEQADV 7DCY ASP A -3 UNP P47350 EXPRESSION TAG SEQADV 7DCY ASP A -2 UNP P47350 EXPRESSION TAG SEQADV 7DCY ASP A -1 UNP P47350 EXPRESSION TAG SEQADV 7DCY LYS A 0 UNP P47350 EXPRESSION TAG SEQRES 1 A 747 MET GLY HIS HIS HIS HIS HIS HIS HIS HIS HIS HIS SER SEQRES 2 A 747 SER GLY HIS ILE ASP ASP ASP ASP LYS MET LYS VAL LEU SEQRES 3 A 747 THR GLU LEU GLN LYS GLN ILE PHE THR ILE VAL LYS LYS SEQRES 4 A 747 GLU ASN GLY LYS PRO ILE PRO PRO GLY ILE VAL VAL ARG SEQRES 5 A 747 MET MET GLU ASN SER PRO ASN PHE PRO GLY LYS HIS LEU SEQRES 6 A 747 ILE TYR ARG ALA ILE ASP ASP LEU LEU ASP TRP ALA ILE SEQRES 7 A 747 LEU ARG LYS ALA GLY GLY VAL THR ASN GLN LEU LEU VAL SEQRES 8 A 747 ASN TYR GLU PRO ALA GLU PRO LEU LEU ASP LYS LYS LEU SEQRES 9 A 747 GLN GLY ILE LEU THR LEU GLY ASN LYS ASN SER GLY PHE SEQRES 10 A 747 ILE ARG SER LEU ASP ASP ASP LYS THR VAL TYR TYR VAL SEQRES 11 A 747 HIS TYR SER ASN LEU THR GLY ALA LEU ASP GLY ASP LEU SEQRES 12 A 747 VAL GLU PHE CYS LYS LEU ASP LYS PRO GLN PHE GLY ASP SEQRES 13 A 747 LYS PHE ASP ALA ALA VAL ILE THR ILE LEU LYS ARG ALA SEQRES 14 A 747 ARG ILE LEU TYR ALA GLY ASN PHE LEU VAL ASP GLN ASN SEQRES 15 A 747 GLU PHE ALA LEU GLU TYR LYS ILE VAL ALA ASP ASN PRO SEQRES 16 A 747 ARG PHE TYR LEU THR MET ILE VAL ASN PRO ASP SER ILE SEQRES 17 A 747 PRO ASN ASN LEU ALA SER ASN THR LYS ILE ALA PHE GLN SEQRES 18 A 747 ILE ASP GLU TYR ASP PRO ASP ASN ASN LEU CYS LYS VAL SEQRES 19 A 747 SER VAL GLN GLN VAL LEU GLY ASN ASN ASP ASP PRO LEU SEQRES 20 A 747 ILE ASN ILE LYS ALA ILE MET LEU ASP ASN SER ILE VAL SEQRES 21 A 747 PHE GLU THR ASN ASP VAL VAL GLU GLN HIS ALA ASN LYS SEQRES 22 A 747 LEU SER PHE ASP THR GLU GLU GLN HIS LYS ALA TYR ARG SEQRES 23 A 747 GLN ASP LEU THR ASP LEU ALA PHE VAL THR VAL ASP PRO SEQRES 24 A 747 THR THR SER LYS ASP LEU ASP ASP ALA ILE TYR VAL LYS SEQRES 25 A 747 THR ILE PRO THR GLY PHE VAL LEU TYR VAL ALA ILE ALA SEQRES 26 A 747 ASP VAL ALA HIS TYR VAL ASN ARG ASN SER GLU ILE ASP SEQRES 27 A 747 ILE GLU ALA LYS HIS LYS THR SER SER ILE TYR LEU PRO SEQRES 28 A 747 GLY HIS TYR VAL VAL PRO MET LEU PRO GLU GLN LEU SER SEQRES 29 A 747 ASN GLN LEU CYS SER LEU ASN PRO ALA GLN LYS ARG TYR SEQRES 30 A 747 VAL VAL VAL CYS GLU ILE SER PHE ASP ASN GLN GLY ARG SEQRES 31 A 747 ILE LYS THR ASN LYS LEU TYR PRO ALA THR ILE ILE SER SEQRES 32 A 747 LYS ASN ARG PHE SER TYR ASP GLN VAL ASN LYS TRP LEU SEQRES 33 A 747 ASN ASN LYS SER GLU LEU ASN CYS ASP GLU THR VAL ILE SEQRES 34 A 747 ASN SER LEU LYS ALA ALA PHE THR LEU SER ASP LEU ILE SEQRES 35 A 747 GLN ALA GLN ARG GLN LYS ARG GLY THR ILE ASP LEU SER SEQRES 36 A 747 HIS LYS GLU THR GLU ILE VAL VAL ASP GLU HIS TYR PHE SEQRES 37 A 747 PRO ILE LYS ILE ASN PHE LEU VAL HIS ASP LYS ALA GLU SEQRES 38 A 747 THR MET ILE GLU ASN LEU MET VAL VAL ALA ASN GLU THR SEQRES 39 A 747 VAL ALA TRP VAL LEU THR ASN ASN LYS ILE ALA LEU PRO SEQRES 40 A 747 TYR ARG VAL HIS PRO ARG PRO SER LYS LYS LYS LEU GLN SEQRES 41 A 747 SER LEU ILE GLU THR VAL GLY GLU LEU ASN ILE THR LYS SEQRES 42 A 747 PRO GLN PHE ASN LEU ASP THR VAL THR SER SER GLN ILE SEQRES 43 A 747 ALA SER TRP LEU ASN GLU ASN LYS ASP ASN PRO SER TYR SEQRES 44 A 747 GLU ILE PHE VAL ILE LEU LEU LEU ARG THR LEU GLY LYS SEQRES 45 A 747 ALA PHE TYR SER VAL ASN PRO LEU MET HIS PHE SER ILE SEQRES 46 A 747 GLY SER ASN HIS TYR THR HIS PHE THR SER PRO ILE ARG SEQRES 47 A 747 ARG TYR ILE ASP LEU THR ILE HIS ARG LEU LEU TRP MET SEQRES 48 A 747 HIS LEU PHE THR PRO ASP GLN PHE THR ASP ASN GLU ARG SEQRES 49 A 747 ASP GLN LEU LYS GLN GLU LEU GLU LYS ILE ALA ASP THR SEQRES 50 A 747 VAL ASN ASP THR GLU ILE LYS ILE ILE ASN CYS GLU ARG SEQRES 51 A 747 ASN ALA ASN ASP TYR LEU THR THR LEU LEU LEU SER LYS SEQRES 52 A 747 GLN ILE GLY LYS THR PHE SER GLY PHE ILE SER ALA ILE SEQRES 53 A 747 THR SER PHE GLY ILE PHE MET ARG MET ASP GLU ASN ASN SEQRES 54 A 747 PHE ASP GLY LEU ILE LYS ILE THR THR ILE PRO ASP ASP SEQRES 55 A 747 PHE PHE ILE PHE GLU LYS GLU LYS MET VAL LEU LYS GLY SEQRES 56 A 747 ARG LYS THR ASN LYS VAL TYR LYS ILE GLY ASP ARG LEU SEQRES 57 A 747 GLU ALA LYS LEU SER GLU ILE ASP PHE ILE GLN LYS ARG SEQRES 58 A 747 ALA ILE LEU THR LEU ILE HET MG A 801 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG MG 2+ FORMUL 3 HOH *475(H2 O) HELIX 1 AA1 ASN A 90 ASN A 92 5 3 HELIX 2 AA2 HIS A 109 LEU A 113 5 5 HELIX 3 AA3 PRO A 183 ILE A 186 5 4 HELIX 4 AA4 ASP A 223 ASN A 235 1 13 HELIX 5 AA5 ASN A 242 LYS A 251 1 10 HELIX 6 AA6 ASP A 255 LYS A 261 5 7 HELIX 7 AA7 ASP A 304 VAL A 309 1 6 HELIX 8 AA8 SER A 313 THR A 323 1 11 HELIX 9 AA9 PRO A 338 ASN A 343 1 6 HELIX 10 AB1 TYR A 387 ASN A 395 1 9 HELIX 11 AB2 ASP A 403 GLY A 428 1 26 HELIX 12 AB3 ASP A 456 ASN A 480 1 25 HELIX 13 AB4 SER A 493 GLU A 506 1 14 HELIX 14 AB5 THR A 520 GLU A 530 1 11 HELIX 15 AB6 SER A 536 GLY A 549 1 14 HELIX 16 AB7 ARG A 577 LEU A 591 1 15 HELIX 17 AB8 THR A 593 PHE A 597 5 5 HELIX 18 AB9 THR A 598 SER A 640 1 43 HELIX 19 AC1 THR A 675 ILE A 677 5 3 SHEET 1 AA1 5 VAL A 105 VAL A 108 0 SHEET 2 AA1 5 GLY A 94 SER A 98 -1 N GLY A 94 O VAL A 108 SHEET 3 AA1 5 GLN A 83 LEU A 88 -1 N THR A 87 O PHE A 95 SHEET 4 AA1 5 LEU A 121 LYS A 126 -1 O VAL A 122 N GLY A 84 SHEET 5 AA1 5 ALA A 138 LYS A 145 -1 O ILE A 141 N GLU A 123 SHEET 1 AA2 5 ALA A 163 ALA A 170 0 SHEET 2 AA2 5 TYR A 151 ASN A 160 -1 N ASP A 158 O GLU A 165 SHEET 3 AA2 5 THR A 194 ASP A 204 -1 O ILE A 196 N GLY A 153 SHEET 4 AA2 5 LEU A 209 ASN A 220 -1 O GLN A 215 N ALA A 197 SHEET 5 AA2 5 THR A 178 VAL A 181 1 N ILE A 180 O CYS A 210 SHEET 1 AA3 5 GLN A 265 ASP A 266 0 SHEET 2 AA3 5 ILE A 369 ILE A 380 1 O PRO A 376 N GLN A 265 SHEET 3 AA3 5 LYS A 353 ASP A 364 -1 N SER A 362 O LYS A 370 SHEET 4 AA3 5 GLY A 295 ALA A 303 -1 N PHE A 296 O PHE A 363 SHEET 5 AA3 5 ASP A 285 ILE A 292 -1 N TYR A 288 O TYR A 299 SHEET 1 AA4 2 VAL A 273 ASP A 276 0 SHEET 2 AA4 2 ASN A 383 SER A 386 1 O PHE A 385 N THR A 274 SHEET 1 AA5 2 ILE A 326 LEU A 328 0 SHEET 2 AA5 2 TYR A 332 VAL A 334 -1 O TYR A 332 N LEU A 328 SHEET 1 AA6 2 THR A 437 VAL A 441 0 SHEET 2 AA6 2 PRO A 447 PHE A 452 -1 O ILE A 448 N VAL A 440 SHEET 1 AA7 2 TYR A 486 VAL A 488 0 SHEET 2 AA7 2 PHE A 552 SER A 554 -1 O PHE A 552 N VAL A 488 SHEET 1 AA8 6 THR A 646 THR A 655 0 SHEET 2 AA8 6 GLY A 658 MET A 663 -1 O ARG A 662 N PHE A 650 SHEET 3 AA8 6 ASP A 669 LYS A 673 -1 O ILE A 672 N ILE A 659 SHEET 4 AA8 6 ARG A 719 LEU A 724 1 O ALA A 720 N LEU A 671 SHEET 5 AA8 6 ARG A 705 ASP A 714 -1 N GLU A 712 O ILE A 721 SHEET 6 AA8 6 THR A 646 THR A 655 -1 N PHE A 647 O ALA A 708 SHEET 1 AA9 3 PHE A 682 GLU A 685 0 SHEET 2 AA9 3 VAL A 690 GLY A 693 -1 O VAL A 690 N GLU A 685 SHEET 3 AA9 3 VAL A 699 TYR A 700 -1 O TYR A 700 N LEU A 691 LINK OD2 ASP A 276 MG MG A 801 1555 1555 2.10 LINK OD1 ASP A 285 MG MG A 801 1555 1555 2.16 LINK MG MG A 801 O HOH A 934 1555 1555 2.21 LINK MG MG A 801 O HOH A 953 1555 1555 2.11 LINK MG MG A 801 O HOH A1013 1555 1555 1.86 LINK MG MG A 801 O HOH A1266 1555 1555 2.28 CRYST1 69.652 80.768 176.476 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.014357 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012381 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005666 0.00000