HEADER HYDROLASE/RNA 18-NOV-20 7DID TITLE MYCOPLASMA GENITALIUM RNASE R IN COMPLEX WITH RIBOSE METHYLATED TITLE 2 SINGLE-STRANDED RNA 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; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: RNA (5'-R(*AP*AP*AP*A)-3'); COMPND 10 CHAIN: C; COMPND 11 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; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: MYCOPLASMA GENITALIUM G37; SOURCE 12 ORGANISM_TAXID: 243273 KEYWDS RNA HYDROLASE, 2'-O-METHYLATION SENSITIVE, HYDROLASE, HYDROLASE-RNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.ABULA,X.QUAN,X.LI,T.YANG,T.LI,Q.CHEN,X.JI REVDAT 4 29-NOV-23 7DID 1 REMARK REVDAT 3 19-MAY-21 7DID 1 JRNL REVDAT 2 14-APR-21 7DID 1 JRNL REVDAT 1 17-MAR-21 7DID 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. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 78276 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.550 REMARK 3 FREE R VALUE TEST SET COUNT : 1995 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 29.9700 - 4.5735 0.99 5710 149 0.1665 0.1941 REMARK 3 2 4.5735 - 3.6321 1.00 5549 146 0.1532 0.1720 REMARK 3 3 3.6321 - 3.1736 1.00 5501 142 0.1760 0.2122 REMARK 3 4 3.1736 - 2.8837 1.00 5452 143 0.1941 0.2277 REMARK 3 5 2.8837 - 2.6771 1.00 5464 143 0.1945 0.2439 REMARK 3 6 2.6771 - 2.5194 1.00 5440 141 0.1880 0.2199 REMARK 3 7 2.5194 - 2.3933 1.00 5421 143 0.1932 0.2309 REMARK 3 8 2.3933 - 2.2891 1.00 5434 142 0.2001 0.2558 REMARK 3 9 2.2891 - 2.2010 1.00 5409 141 0.2119 0.2687 REMARK 3 10 2.2010 - 2.1251 1.00 5373 141 0.2291 0.2619 REMARK 3 11 2.1251 - 2.0587 1.00 5434 142 0.2550 0.3167 REMARK 3 12 2.0587 - 1.9998 1.00 5389 141 0.2808 0.3185 REMARK 3 13 1.9998 - 1.9472 1.00 5422 142 0.3054 0.3421 REMARK 3 14 1.9472 - 1.9000 0.98 5283 139 0.3518 0.4059 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.760 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.03 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 : 0.012 5405 REMARK 3 ANGLE : 1.009 7347 REMARK 3 CHIRALITY : 0.067 851 REMARK 3 PLANARITY : 0.006 929 REMARK 3 DIHEDRAL : 15.548 3261 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 82 THROUGH 170 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.6253 -7.5705 4.3733 REMARK 3 T TENSOR REMARK 3 T11: 0.2636 T22: 0.2715 REMARK 3 T33: 0.3204 T12: 0.0099 REMARK 3 T13: -0.0171 T23: -0.0195 REMARK 3 L TENSOR REMARK 3 L11: 1.8547 L22: 1.2160 REMARK 3 L33: 0.9071 L12: 0.9037 REMARK 3 L13: 0.5549 L23: -0.5208 REMARK 3 S TENSOR REMARK 3 S11: -0.0175 S12: -0.0181 S13: 0.4113 REMARK 3 S21: 0.1117 S22: -0.0031 S23: 0.2356 REMARK 3 S31: -0.1909 S32: -0.1471 S33: 0.0002 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 171 THROUGH 250 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.5075 -14.2212 8.3352 REMARK 3 T TENSOR REMARK 3 T11: 0.2195 T22: 0.2810 REMARK 3 T33: 0.2666 T12: -0.0273 REMARK 3 T13: -0.0031 T23: 0.0008 REMARK 3 L TENSOR REMARK 3 L11: 1.0869 L22: 0.7546 REMARK 3 L33: 1.3868 L12: 0.1932 REMARK 3 L13: -0.9704 L23: 0.5322 REMARK 3 S TENSOR REMARK 3 S11: 0.0652 S12: 0.1054 S13: 0.0620 REMARK 3 S21: -0.0084 S22: -0.0224 S23: -0.0932 REMARK 3 S31: -0.0629 S32: 0.1217 S33: 0.0061 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 251 THROUGH 427 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.7136 -5.5739 47.7015 REMARK 3 T TENSOR REMARK 3 T11: 0.3781 T22: 0.2628 REMARK 3 T33: 0.2826 T12: 0.0149 REMARK 3 T13: -0.0469 T23: -0.0356 REMARK 3 L TENSOR REMARK 3 L11: 1.8730 L22: 2.0500 REMARK 3 L33: 2.0706 L12: 0.3245 REMARK 3 L13: 0.4216 L23: 0.3288 REMARK 3 S TENSOR REMARK 3 S11: -0.0727 S12: -0.2231 S13: -0.0142 REMARK 3 S21: 0.3693 S22: 0.0124 S23: -0.1185 REMARK 3 S31: 0.1671 S32: 0.0886 S33: -0.0011 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 428 THROUGH 725 ) REMARK 3 ORIGIN FOR THE GROUP (A): -26.9130 -11.8598 31.4631 REMARK 3 T TENSOR REMARK 3 T11: 0.2375 T22: 0.2814 REMARK 3 T33: 0.2761 T12: 0.0132 REMARK 3 T13: -0.0151 T23: 0.0090 REMARK 3 L TENSOR REMARK 3 L11: 1.0404 L22: 1.1405 REMARK 3 L33: 1.2809 L12: 0.8202 REMARK 3 L13: 0.5090 L23: 0.5117 REMARK 3 S TENSOR REMARK 3 S11: -0.0876 S12: -0.1096 S13: 0.2896 REMARK 3 S21: 0.0444 S22: 0.0112 S23: 0.2381 REMARK 3 S31: -0.0623 S32: -0.2615 S33: -0.0003 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 5 THROUGH 8 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.4070 -9.6636 38.8457 REMARK 3 T TENSOR REMARK 3 T11: 0.8362 T22: 0.7602 REMARK 3 T33: 1.4781 T12: -0.0739 REMARK 3 T13: -0.2465 T23: 0.1492 REMARK 3 L TENSOR REMARK 3 L11: 0.0074 L22: 0.0269 REMARK 3 L33: 0.0146 L12: -0.0194 REMARK 3 L13: 0.0024 L23: -0.0092 REMARK 3 S TENSOR REMARK 3 S11: 0.0705 S12: -0.0451 S13: -0.5163 REMARK 3 S21: 0.2965 S22: 0.2138 S23: -0.5677 REMARK 3 S31: 1.0012 S32: 0.6208 S33: -0.0003 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 7DID COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1300019168. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUL-19 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 : 78483 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.20 REMARK 200 R MERGE (I) : 0.14800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 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 (%): 56.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 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 34.64300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 87.86750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.39200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 87.86750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.64300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.39200 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 O2' A C 8 O HOH C 101 2.03 REMARK 500 NH2 ARG A 148 OG SER A 236 2.10 REMARK 500 O HOH A 1125 O HOH A 1278 2.13 REMARK 500 OH TYR A 107 OD1 ASP A 134 2.17 REMARK 500 NH2 ARG A 174 O HOH A 901 2.18 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 ASP A 100 171.10 -55.82 REMARK 500 LYS A 129 154.15 -45.80 REMARK 500 ASP A 134 -66.73 69.85 REMARK 500 THR A 323 -24.93 70.06 REMARK 500 GLN A 344 -75.57 -124.98 REMARK 500 ASN A 396 30.00 48.32 REMARK 500 HIS A 489 103.53 -164.22 REMARK 500 ASP A 679 -11.41 82.52 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 A1384 DISTANCE = 6.08 ANGSTROMS REMARK 525 HOH A1385 DISTANCE = 6.10 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 135.4 REMARK 620 3 HOH A 976 O 106.4 116.7 REMARK 620 4 HOH A 979 O 82.5 81.8 96.8 REMARK 620 5 HOH A 997 O 70.5 67.7 173.4 88.6 REMARK 620 6 A C 8 O3' 129.5 66.8 86.0 145.8 91.6 REMARK 620 7 A C 8 O2' 67.3 130.7 78.2 146.0 95.3 68.0 REMARK 620 N 1 2 3 4 5 6 DBREF 7DID A 1 725 UNP P47350 RNR_MYCGE 1 725 DBREF 7DID C 5 8 PDB 7DID 7DID 5 8 SEQADV 7DID MET A -21 UNP P47350 EXPRESSION TAG SEQADV 7DID GLY A -20 UNP P47350 EXPRESSION TAG SEQADV 7DID HIS A -19 UNP P47350 EXPRESSION TAG SEQADV 7DID HIS A -18 UNP P47350 EXPRESSION TAG SEQADV 7DID HIS A -17 UNP P47350 EXPRESSION TAG SEQADV 7DID HIS A -16 UNP P47350 EXPRESSION TAG SEQADV 7DID HIS A -15 UNP P47350 EXPRESSION TAG SEQADV 7DID HIS A -14 UNP P47350 EXPRESSION TAG SEQADV 7DID HIS A -13 UNP P47350 EXPRESSION TAG SEQADV 7DID HIS A -12 UNP P47350 EXPRESSION TAG SEQADV 7DID HIS A -11 UNP P47350 EXPRESSION TAG SEQADV 7DID HIS A -10 UNP P47350 EXPRESSION TAG SEQADV 7DID SER A -9 UNP P47350 EXPRESSION TAG SEQADV 7DID SER A -8 UNP P47350 EXPRESSION TAG SEQADV 7DID GLY A -7 UNP P47350 EXPRESSION TAG SEQADV 7DID HIS A -6 UNP P47350 EXPRESSION TAG SEQADV 7DID ILE A -5 UNP P47350 EXPRESSION TAG SEQADV 7DID ASP A -4 UNP P47350 EXPRESSION TAG SEQADV 7DID ASP A -3 UNP P47350 EXPRESSION TAG SEQADV 7DID ASP A -2 UNP P47350 EXPRESSION TAG SEQADV 7DID ASP A -1 UNP P47350 EXPRESSION TAG SEQADV 7DID LYS A 0 UNP P47350 EXPRESSION TAG SEQADV 7DID ALA A 284 UNP P47350 ASP 284 ENGINEERED MUTATION 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 ALA 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 SEQRES 1 C 4 A A A2M A HET A2M C 7 23 HET MG A 801 1 HETNAM A2M 2'-O-METHYLADENOSINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM MG MAGNESIUM ION FORMUL 2 A2M C11 H16 N5 O7 P FORMUL 3 MG MG 2+ FORMUL 4 HOH *493(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 LEU A 252 1 11 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 6 GLN A 83 LEU A 88 0 SHEET 2 AA1 6 GLY A 94 SER A 98 -1 O PHE A 95 N THR A 87 SHEET 3 AA1 6 VAL A 105 VAL A 108 -1 O TYR A 106 N ILE A 96 SHEET 4 AA1 6 PHE A 136 LYS A 145 1 O PHE A 136 N TYR A 107 SHEET 5 AA1 6 LEU A 121 LYS A 126 -1 N GLU A 123 O ILE A 141 SHEET 6 AA1 6 GLN A 83 LEU A 88 -1 N GLY A 84 O VAL A 122 SHEET 1 AA2 5 ALA A 163 ALA A 170 0 SHEET 2 AA2 5 TYR A 151 ASN A 160 -1 N LEU A 156 O LYS A 167 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 LEU A 298 O ILE A 361 SHEET 5 AA3 5 ASP A 285 ILE A 292 -1 N ALA A 286 O ALA A 301 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 LYS A 709 O THR A 723 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 O3' A C 6 P A2M C 7 1555 1555 1.60 LINK O3' A2M C 7 P A C 8 1555 1555 1.61 LINK OD2 ASP A 276 MG MG A 801 1555 1555 2.19 LINK OD1 ASP A 285 MG MG A 801 1555 1555 2.21 LINK MG MG A 801 O HOH A 976 1555 1555 1.82 LINK MG MG A 801 O HOH A 979 1555 1555 2.40 LINK MG MG A 801 O HOH A 997 1555 1555 2.59 LINK MG MG A 801 O3' A C 8 1555 1555 2.32 LINK MG MG A 801 O2' A C 8 1555 1555 2.51 CRYST1 69.286 80.784 175.735 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 0.014433 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012379 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005690 0.00000