HEADER TRANSFERASE 14-APR-11 3AXT TITLE COMPLEX STRUCTURE OF TRNA METHYLTRANSFERASE TRM1 FROM AQUIFEX AEOLICUS TITLE 2 WITH S-ADENOSYL-L-METHIONINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE N(2),N(2)-DIMETHYLGUANOSINE TRNA METHYLTRANSFERASE COMPND 3 TRM1; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: TRNA 2,2-DIMETHYLGUANOSINE-26 METHYLTRANSFERASE, COMPND 6 TRNA(GUANINE-26,N(2)-N(2)) METHYLTRANSFERASE, TRNA(M(2,2)G26) COMPND 7 DIMETHYLTRANSFERASE; COMPND 8 EC: 2.1.1.32; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AQUIFEX AEOLICUS; SOURCE 3 ORGANISM_TAXID: 63363; SOURCE 4 GENE: TRM1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-21A KEYWDS STRUCTURAL GENOMICS, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, KEYWDS 2 RSGI, TRNA MODIFICATION ENZYME, GUANINE 26, N2, N2- KEYWDS 3 DIMETHYLTRANSFERASE, AQUIFEX AEOLICUS, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR IHSANAWATI,T.SENGOKU,S.YOKOYAMA,Y.BESSHO,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 01-NOV-23 3AXT 1 REMARK LINK REVDAT 2 15-MAY-13 3AXT 1 JRNL REVDAT 1 03-AUG-11 3AXT 0 JRNL AUTH T.AWAI,A.OCHI,IHSANAWATI,T.SENGOKU,A.HIRATA,Y.BESSHO, JRNL AUTH 2 S.YOKOYAMA,H.HORI JRNL TITL SUBSTRATE TRNA RECOGNITION MECHANISM OF A MULTISITE-SPECIFIC JRNL TITL 2 TRNA METHYLTRANSFERASE, AQUIFEX AEOLICUS TRM1, BASED ON THE JRNL TITL 3 X-RAY CRYSTAL STRUCTURE JRNL REF J.BIOL.CHEM. V. 286 35236 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21844194 JRNL DOI 10.1074/JBC.M111.253641 REMARK 2 REMARK 2 RESOLUTION. 2.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7_650) 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) : 2.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 16387 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.840 REMARK 3 FREE R VALUE TEST SET COUNT : 793 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 27.4165 - 4.5204 1.00 2707 149 0.1800 0.2135 REMARK 3 2 4.5204 - 3.5905 1.00 2620 130 0.1556 0.1845 REMARK 3 3 3.5905 - 3.1374 1.00 2594 127 0.1832 0.2124 REMARK 3 4 3.1374 - 2.8509 1.00 2577 134 0.2007 0.2476 REMARK 3 5 2.8509 - 2.6467 1.00 2574 123 0.2328 0.3194 REMARK 3 6 2.6467 - 2.4908 0.99 2522 130 0.2424 0.3082 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.95 REMARK 3 K_SOL : 0.37 REMARK 3 B_SOL : 44.24 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.99450 REMARK 3 B22 (A**2) : 1.52960 REMARK 3 B33 (A**2) : -4.52420 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.002 3295 REMARK 3 ANGLE : 0.560 4439 REMARK 3 CHIRALITY : 0.039 475 REMARK 3 PLANARITY : 0.002 558 REMARK 3 DIHEDRAL : 10.905 1263 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 1:86) REMARK 3 ORIGIN FOR THE GROUP (A): 12.7441 12.7634 49.4351 REMARK 3 T TENSOR REMARK 3 T11: 0.2403 T22: 0.2570 REMARK 3 T33: 0.2341 T12: -0.0988 REMARK 3 T13: -0.0698 T23: 0.1726 REMARK 3 L TENSOR REMARK 3 L11: 0.1043 L22: 0.1780 REMARK 3 L33: 0.1294 L12: 0.0902 REMARK 3 L13: -0.1071 L23: -0.0403 REMARK 3 S TENSOR REMARK 3 S11: 0.0783 S12: -0.0163 S13: -0.0493 REMARK 3 S21: 0.1752 S22: 0.0222 S23: 0.0516 REMARK 3 S31: 0.0397 S32: -0.1338 S33: 0.0105 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 87:110) REMARK 3 ORIGIN FOR THE GROUP (A): 14.9865 0.5741 47.1417 REMARK 3 T TENSOR REMARK 3 T11: 0.2806 T22: -0.0511 REMARK 3 T33: 0.1449 T12: -0.1193 REMARK 3 T13: -0.1937 T23: 0.2998 REMARK 3 L TENSOR REMARK 3 L11: 0.0096 L22: 0.0060 REMARK 3 L33: 0.0058 L12: 0.0086 REMARK 3 L13: -0.0060 L23: -0.0065 REMARK 3 S TENSOR REMARK 3 S11: 0.0197 S12: -0.0181 S13: -0.0377 REMARK 3 S21: 0.0053 S22: 0.0321 S23: 0.0302 REMARK 3 S31: 0.0306 S32: -0.0162 S33: 0.0226 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 111:147) REMARK 3 ORIGIN FOR THE GROUP (A): 19.8280 14.0784 35.3603 REMARK 3 T TENSOR REMARK 3 T11: 0.2491 T22: 0.2372 REMARK 3 T33: 0.2414 T12: -0.0549 REMARK 3 T13: -0.0753 T23: 0.0625 REMARK 3 L TENSOR REMARK 3 L11: 0.1628 L22: 0.0130 REMARK 3 L33: 0.1749 L12: -0.0230 REMARK 3 L13: 0.0878 L23: -0.0370 REMARK 3 S TENSOR REMARK 3 S11: 0.0424 S12: -0.0460 S13: -0.0015 REMARK 3 S21: 0.0262 S22: -0.0068 S23: 0.0057 REMARK 3 S31: 0.0719 S32: -0.0004 S33: -0.0459 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 148:229) REMARK 3 ORIGIN FOR THE GROUP (A): 20.2276 29.9870 40.1517 REMARK 3 T TENSOR REMARK 3 T11: 0.0870 T22: 0.1547 REMARK 3 T33: 0.1175 T12: -0.0045 REMARK 3 T13: 0.0074 T23: 0.0307 REMARK 3 L TENSOR REMARK 3 L11: 0.1931 L22: 0.0077 REMARK 3 L33: 0.1939 L12: -0.0284 REMARK 3 L13: 0.0292 L23: 0.0008 REMARK 3 S TENSOR REMARK 3 S11: 0.1182 S12: -0.0786 S13: 0.0502 REMARK 3 S21: 0.0016 S22: 0.0674 S23: 0.0501 REMARK 3 S31: -0.0522 S32: -0.1308 S33: -0.0106 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 230:272) REMARK 3 ORIGIN FOR THE GROUP (A): 20.4980 47.1323 36.0524 REMARK 3 T TENSOR REMARK 3 T11: 0.3131 T22: 0.1507 REMARK 3 T33: 0.2738 T12: 0.0042 REMARK 3 T13: 0.0648 T23: 0.0101 REMARK 3 L TENSOR REMARK 3 L11: 0.1111 L22: 0.5560 REMARK 3 L33: 0.5349 L12: 0.1387 REMARK 3 L13: -0.0029 L23: 0.4347 REMARK 3 S TENSOR REMARK 3 S11: 0.1470 S12: -0.0029 S13: 0.0996 REMARK 3 S21: 0.0081 S22: 0.2092 S23: 0.0498 REMARK 3 S31: -0.2920 S32: -0.0687 S33: -0.2026 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 273:335) REMARK 3 ORIGIN FOR THE GROUP (A): 8.1041 34.7953 48.7915 REMARK 3 T TENSOR REMARK 3 T11: 0.2499 T22: 0.3590 REMARK 3 T33: 0.2013 T12: 0.0265 REMARK 3 T13: 0.0651 T23: 0.0786 REMARK 3 L TENSOR REMARK 3 L11: 0.0822 L22: 0.2722 REMARK 3 L33: 0.0350 L12: -0.0902 REMARK 3 L13: -0.0345 L23: 0.0977 REMARK 3 S TENSOR REMARK 3 S11: 0.1150 S12: -0.1313 S13: 0.0530 REMARK 3 S21: 0.1238 S22: 0.0724 S23: 0.0379 REMARK 3 S31: -0.0721 S32: -0.2274 S33: -0.0760 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 336:387) REMARK 3 ORIGIN FOR THE GROUP (A): 8.6907 52.5674 56.7062 REMARK 3 T TENSOR REMARK 3 T11: 0.3576 T22: 0.3614 REMARK 3 T33: 0.2401 T12: 0.0873 REMARK 3 T13: 0.1229 T23: -0.0179 REMARK 3 L TENSOR REMARK 3 L11: 0.0608 L22: 0.1111 REMARK 3 L33: 0.2365 L12: 0.0799 REMARK 3 L13: 0.1143 L23: 0.1608 REMARK 3 S TENSOR REMARK 3 S11: 0.1309 S12: -0.0628 S13: 0.0603 REMARK 3 S21: -0.0517 S22: -0.0685 S23: 0.0081 REMARK 3 S31: 0.0195 S32: 0.0089 S33: 0.0187 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 3AXT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-APR-11. REMARK 100 THE DEPOSITION ID IS D_1000029829. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-NOV-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16410 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.491 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 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 : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2EJT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M NA-CITRATE, 2M (NH4)2SO4, PH 5.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.51900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.51900 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 27.21900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 70.46400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 27.21900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 70.46400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 59.51900 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 27.21900 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 70.46400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 59.51900 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 27.21900 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 70.46400 REMARK 290 SMTRY3 8 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: 3070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 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 -1.000000 0.000000 0.000000 54.43800 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 59.51900 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 420 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 426 LIES ON A SPECIAL POSITION. 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 LYS A 388 REMARK 465 LYS A 389 REMARK 465 LYS A 390 REMARK 465 GLN A 391 REMARK 465 GLY A 392 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 17 156.53 -47.99 REMARK 500 ALA A 62 -103.63 60.90 REMARK 500 ASN A 183 -161.06 -116.53 REMARK 500 LEU A 218 -104.74 57.50 REMARK 500 LYS A 336 73.94 51.67 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 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 247 SG REMARK 620 2 CYS A 250 SG 114.3 REMARK 620 3 CYS A 266 SG 97.8 106.1 REMARK 620 4 CYS A 269 SG 112.8 106.9 118.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 393 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 394 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 395 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 396 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAM A 397 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3AXS RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH SINEFUNGIN. REMARK 900 RELATED ID: AAE001000841.4 RELATED DB: TARGETDB DBREF 3AXT A 1 392 UNP O67010 TRM1_AQUAE 1 392 SEQRES 1 A 392 MET GLU ILE VAL GLN GLU GLY ILE ALA LYS ILE ILE VAL SEQRES 2 A 392 PRO GLU ILE PRO LYS THR VAL SER SER ASP MET PRO VAL SEQRES 3 A 392 PHE TYR ASN PRO ARG MET ARG VAL ASN ARG ASP LEU ALA SEQRES 4 A 392 VAL LEU GLY LEU GLU TYR LEU CYS LYS LYS LEU GLY ARG SEQRES 5 A 392 PRO VAL LYS VAL ALA ASP PRO LEU SER ALA SER GLY ILE SEQRES 6 A 392 ARG ALA ILE ARG PHE LEU LEU GLU THR SER CYS VAL GLU SEQRES 7 A 392 LYS ALA TYR ALA ASN ASP ILE SER SER LYS ALA ILE GLU SEQRES 8 A 392 ILE MET LYS GLU ASN PHE LYS LEU ASN ASN ILE PRO GLU SEQRES 9 A 392 ASP ARG TYR GLU ILE HIS GLY MET GLU ALA ASN PHE PHE SEQRES 10 A 392 LEU ARG LYS GLU TRP GLY PHE GLY PHE ASP TYR VAL ASP SEQRES 11 A 392 LEU ASP PRO PHE GLY THR PRO VAL PRO PHE ILE GLU SER SEQRES 12 A 392 VAL ALA LEU SER MET LYS ARG GLY GLY ILE LEU SER LEU SEQRES 13 A 392 THR ALA THR ASP THR ALA PRO LEU SER GLY THR TYR PRO SEQRES 14 A 392 LYS THR CYS MET ARG ARG TYR MET ALA ARG PRO LEU ARG SEQRES 15 A 392 ASN GLU PHE LYS HIS GLU VAL GLY ILE ARG ILE LEU ILE SEQRES 16 A 392 LYS LYS VAL ILE GLU LEU ALA ALA GLN TYR ASP ILE ALA SEQRES 17 A 392 MET ILE PRO ILE PHE ALA TYR SER HIS LEU HIS TYR PHE SEQRES 18 A 392 LYS LEU PHE PHE VAL LYS GLU ARG GLY VAL GLU LYS VAL SEQRES 19 A 392 ASP LYS LEU ILE GLU GLN PHE GLY TYR ILE GLN TYR CYS SEQRES 20 A 392 PHE ASN CYS MET ASN ARG GLU VAL VAL THR ASP LEU TYR SEQRES 21 A 392 LYS PHE LYS GLU LYS CYS PRO HIS CYS GLY SER LYS PHE SEQRES 22 A 392 HIS ILE GLY GLY PRO LEU TRP ILE GLY LYS LEU TRP ASP SEQRES 23 A 392 GLU GLU PHE THR ASN PHE LEU TYR GLU GLU ALA GLN LYS SEQRES 24 A 392 ARG GLU GLU ILE GLU LYS GLU THR LYS ARG ILE LEU LYS SEQRES 25 A 392 LEU ILE LYS GLU GLU SER GLN LEU GLN THR VAL GLY PHE SEQRES 26 A 392 TYR VAL LEU SER LYS LEU ALA GLU LYS VAL LYS LEU PRO SEQRES 27 A 392 ALA GLN PRO PRO ILE ARG ILE ALA VAL LYS PHE PHE ASN SEQRES 28 A 392 GLY VAL ARG THR HIS PHE VAL GLY ASP GLY PHE ARG THR SEQRES 29 A 392 ASN LEU SER PHE GLU GLU VAL MET LYS LYS MET GLU GLU SEQRES 30 A 392 LEU LYS GLU LYS GLN LYS GLU PHE LEU GLU LYS LYS LYS SEQRES 31 A 392 GLN GLY HET ZN A 401 1 HET SO4 A 393 5 HET SO4 A 394 5 HET SO4 A 395 5 HET SO4 A 396 5 HET SAM A 397 27 HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION HETNAM SAM S-ADENOSYLMETHIONINE FORMUL 2 ZN ZN 2+ FORMUL 3 SO4 4(O4 S 2-) FORMUL 7 SAM C15 H22 N6 O5 S FORMUL 8 HOH *53(H2 O) HELIX 1 1 ASN A 29 ARG A 31 5 3 HELIX 2 2 MET A 32 GLY A 51 1 20 HELIX 3 3 GLY A 64 THR A 74 1 11 HELIX 4 4 SER A 86 ASN A 100 1 15 HELIX 5 5 PRO A 103 ASP A 105 5 3 HELIX 6 6 GLU A 113 ARG A 119 1 7 HELIX 7 7 PRO A 137 PRO A 139 5 3 HELIX 8 8 PHE A 140 SER A 147 1 8 HELIX 9 9 ASP A 160 SER A 165 1 6 HELIX 10 10 TYR A 168 MET A 177 1 10 HELIX 11 11 PHE A 185 GLN A 204 1 20 HELIX 12 12 GLY A 230 GLU A 239 1 10 HELIX 13 13 ASP A 258 PHE A 262 5 5 HELIX 14 14 ASP A 286 GLN A 298 1 13 HELIX 15 15 GLU A 304 GLN A 319 1 16 HELIX 16 16 LEU A 328 LYS A 336 1 9 HELIX 17 17 PRO A 342 PHE A 350 1 9 HELIX 18 18 SER A 367 PHE A 385 1 19 SHEET 1 A 2 GLU A 2 GLU A 6 0 SHEET 2 A 2 ALA A 9 VAL A 13 -1 O VAL A 13 N GLU A 2 SHEET 1 B 7 TYR A 107 HIS A 110 0 SHEET 2 B 7 VAL A 77 ASN A 83 1 N ALA A 80 O GLU A 108 SHEET 3 B 7 VAL A 54 ASP A 58 1 N ASP A 58 O TYR A 81 SHEET 4 B 7 PHE A 126 LEU A 131 1 O TYR A 128 N ALA A 57 SHEET 5 B 7 MET A 148 ALA A 158 1 O SER A 155 N VAL A 129 SHEET 6 B 7 TYR A 220 ARG A 229 -1 O PHE A 221 N ALA A 158 SHEET 7 B 7 ILE A 207 HIS A 217 -1 N ILE A 212 O PHE A 224 SHEET 1 C 3 ARG A 253 VAL A 256 0 SHEET 2 C 3 PHE A 241 CYS A 247 -1 N GLN A 245 O GLU A 254 SHEET 3 C 3 PHE A 273 TRP A 280 -1 O LEU A 279 N GLY A 242 SHEET 1 D 3 TYR A 326 VAL A 327 0 SHEET 2 D 3 GLY A 361 ARG A 363 -1 O PHE A 362 N TYR A 326 SHEET 3 D 3 VAL A 353 ARG A 354 -1 N VAL A 353 O ARG A 363 SSBOND 1 CYS A 47 CYS A 76 1555 1555 2.03 LINK SG CYS A 247 ZN ZN A 401 1555 1555 2.30 LINK SG CYS A 250 ZN ZN A 401 1555 1555 2.27 LINK SG CYS A 266 ZN ZN A 401 1555 1555 2.31 LINK SG CYS A 269 ZN ZN A 401 1555 1555 2.28 CISPEP 1 GLY A 277 PRO A 278 0 0.56 SITE 1 AC1 4 CYS A 247 CYS A 250 CYS A 266 CYS A 269 SITE 1 AC2 5 SER A 21 SER A 22 ARG A 31 HIS A 219 SITE 2 AC2 5 ARG A 344 SITE 1 AC3 5 TYR A 168 PRO A 169 LYS A 170 THR A 171 SITE 2 AC3 5 HOH A 437 SITE 1 AC4 6 ALA A 162 TYR A 168 HIS A 219 PRO A 342 SITE 2 AC4 6 ARG A 344 HOH A 415 SITE 1 AC5 3 HIS A 110 GLY A 111 MET A 112 SITE 1 AC6 15 ARG A 36 LEU A 60 SER A 61 ALA A 62 SITE 2 AC6 15 ILE A 65 ARG A 66 ASP A 84 ILE A 85 SITE 3 AC6 15 MET A 112 GLU A 113 ALA A 114 ASP A 132 SITE 4 AC6 15 PHE A 134 HOH A 398 HOH A 399 CRYST1 54.438 140.928 119.038 90.00 90.00 90.00 C 2 2 21 8 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 0.018370 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007096 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008401 0.00000