HEADER TRANSFERASE 13-APR-11 3AXS TITLE COMPLEX STRUCTURE OF TRNA METHYLTRANSFERASE TRM1 FROM AQUIFEX AEOLICUS TITLE 2 WITH SINEFUNGIN 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, TRM1, AQUIFEX AEOLICUS, TRNA MODIFICATION ENZYME, NPPSFA, KEYWDS 3 NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, KEYWDS 4 TRNA, 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 3AXS 1 REMARK LINK REVDAT 2 15-MAY-13 3AXS 1 JRNL REVDAT 1 03-AUG-11 3AXS 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. 2.16 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) : 2.16 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 24710 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) : 0.186 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.840 REMARK 3 FREE R VALUE TEST SET COUNT : 1197 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 30.5328 - 4.4922 1.00 2761 153 0.1762 0.1923 REMARK 3 2 4.4922 - 3.5674 1.00 2674 129 0.1575 0.1703 REMARK 3 3 3.5674 - 3.1169 1.00 2655 132 0.1970 0.2318 REMARK 3 4 3.1169 - 2.8322 1.00 2614 142 0.2087 0.2319 REMARK 3 5 2.8322 - 2.6293 1.00 2625 120 0.2029 0.3360 REMARK 3 6 2.6293 - 2.4744 1.00 2589 139 0.2023 0.2707 REMARK 3 7 2.4744 - 2.3505 1.00 2618 134 0.2077 0.2554 REMARK 3 8 2.3505 - 2.2482 1.00 2602 126 0.2065 0.2733 REMARK 3 9 2.2482 - 2.1617 0.92 2375 122 0.2111 0.2405 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.30 REMARK 3 SHRINKAGE RADIUS : 1.06 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 35.90 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.490 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.16 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.39800 REMARK 3 B22 (A**2) : 9.22430 REMARK 3 B33 (A**2) : -6.82630 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 : 0.005 3290 REMARK 3 ANGLE : 0.866 4431 REMARK 3 CHIRALITY : 0.055 475 REMARK 3 PLANARITY : 0.003 556 REMARK 3 DIHEDRAL : 13.389 1256 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 1:86) REMARK 3 ORIGIN FOR THE GROUP (A): 12.8184 12.8115 49.4696 REMARK 3 T TENSOR REMARK 3 T11: 0.2352 T22: 0.2926 REMARK 3 T33: 0.2712 T12: -0.0565 REMARK 3 T13: -0.0171 T23: 0.1241 REMARK 3 L TENSOR REMARK 3 L11: 0.5936 L22: 1.0472 REMARK 3 L33: 0.8142 L12: -0.1354 REMARK 3 L13: -0.6415 L23: 0.3576 REMARK 3 S TENSOR REMARK 3 S11: 0.0725 S12: 0.1202 S13: -0.0959 REMARK 3 S21: 0.1219 S22: -0.0153 S23: 0.1136 REMARK 3 S31: 0.0422 S32: -0.1583 S33: -0.0525 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 87:110) REMARK 3 ORIGIN FOR THE GROUP (A): 15.0548 0.5680 47.0762 REMARK 3 T TENSOR REMARK 3 T11: 0.4287 T22: 0.1927 REMARK 3 T33: 0.4136 T12: -0.0835 REMARK 3 T13: -0.0920 T23: 0.1726 REMARK 3 L TENSOR REMARK 3 L11: 1.7881 L22: 0.5663 REMARK 3 L33: 1.1368 L12: 0.9379 REMARK 3 L13: -0.0304 L23: 0.1547 REMARK 3 S TENSOR REMARK 3 S11: 0.1062 S12: 0.1163 S13: -0.8765 REMARK 3 S21: -0.1975 S22: 0.3948 S23: -0.0869 REMARK 3 S31: 1.0619 S32: 0.1217 S33: -0.1326 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 111:168) REMARK 3 ORIGIN FOR THE GROUP (A): 19.8355 18.0605 37.3907 REMARK 3 T TENSOR REMARK 3 T11: 0.1472 T22: 0.2189 REMARK 3 T33: 0.1987 T12: 0.0031 REMARK 3 T13: -0.0168 T23: 0.0375 REMARK 3 L TENSOR REMARK 3 L11: 0.6028 L22: 0.8338 REMARK 3 L33: 0.6336 L12: 0.3957 REMARK 3 L13: -0.1396 L23: 0.2261 REMARK 3 S TENSOR REMARK 3 S11: 0.0103 S12: -0.1196 S13: -0.1254 REMARK 3 S21: 0.0179 S22: 0.0494 S23: -0.0012 REMARK 3 S31: 0.0097 S32: -0.1949 S33: -0.0362 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 169:205) REMARK 3 ORIGIN FOR THE GROUP (A): 24.7304 34.2292 39.4038 REMARK 3 T TENSOR REMARK 3 T11: 0.1836 T22: 0.1628 REMARK 3 T33: 0.1486 T12: 0.0104 REMARK 3 T13: 0.0676 T23: 0.0220 REMARK 3 L TENSOR REMARK 3 L11: 0.5337 L22: 0.4630 REMARK 3 L33: 1.1755 L12: 0.1666 REMARK 3 L13: 0.1573 L23: -0.0354 REMARK 3 S TENSOR REMARK 3 S11: 0.1472 S12: 0.0365 S13: -0.0984 REMARK 3 S21: 0.0078 S22: 0.2380 S23: -0.0194 REMARK 3 S31: -0.3069 S32: 0.0208 S33: -0.1201 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 206:229) REMARK 3 ORIGIN FOR THE GROUP (A): 13.8682 26.8616 40.0361 REMARK 3 T TENSOR REMARK 3 T11: 0.1957 T22: 0.3212 REMARK 3 T33: 0.2584 T12: 0.0263 REMARK 3 T13: 0.0114 T23: 0.0867 REMARK 3 L TENSOR REMARK 3 L11: 0.5409 L22: 0.0957 REMARK 3 L33: 0.4825 L12: -0.0305 REMARK 3 L13: -0.2994 L23: 0.1081 REMARK 3 S TENSOR REMARK 3 S11: 0.0939 S12: -0.0923 S13: -0.0488 REMARK 3 S21: 0.0115 S22: -0.0185 S23: -0.0307 REMARK 3 S31: -0.0278 S32: -0.3904 S33: -0.0523 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 230:272) REMARK 3 ORIGIN FOR THE GROUP (A): 20.5763 47.1489 36.1024 REMARK 3 T TENSOR REMARK 3 T11: 0.4344 T22: 0.1831 REMARK 3 T33: 0.2728 T12: 0.0483 REMARK 3 T13: 0.0898 T23: 0.0263 REMARK 3 L TENSOR REMARK 3 L11: 0.3992 L22: 0.8682 REMARK 3 L33: 2.9235 L12: -0.3643 REMARK 3 L13: -0.1482 L23: 0.6238 REMARK 3 S TENSOR REMARK 3 S11: 0.1582 S12: -0.0217 S13: 0.0853 REMARK 3 S21: -0.2769 S22: 0.1202 S23: -0.0663 REMARK 3 S31: -0.9614 S32: -0.1974 S33: -0.1481 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 273:335) REMARK 3 ORIGIN FOR THE GROUP (A): 8.3082 34.8839 48.9243 REMARK 3 T TENSOR REMARK 3 T11: 0.2515 T22: 0.3017 REMARK 3 T33: 0.1761 T12: 0.0967 REMARK 3 T13: 0.0852 T23: 0.0605 REMARK 3 L TENSOR REMARK 3 L11: 0.0907 L22: 1.5996 REMARK 3 L33: 1.2298 L12: -0.2792 REMARK 3 L13: -0.1718 L23: 0.3215 REMARK 3 S TENSOR REMARK 3 S11: 0.1139 S12: -0.0990 S13: 0.0493 REMARK 3 S21: 0.2002 S22: 0.1255 S23: 0.2207 REMARK 3 S31: -0.2796 S32: -0.3766 S33: -0.1132 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 336:367) REMARK 3 ORIGIN FOR THE GROUP (A): 8.6354 46.9299 55.6355 REMARK 3 T TENSOR REMARK 3 T11: 0.5022 T22: 0.3574 REMARK 3 T33: 0.2821 T12: 0.1584 REMARK 3 T13: 0.1141 T23: 0.0300 REMARK 3 L TENSOR REMARK 3 L11: 1.0617 L22: 0.7370 REMARK 3 L33: 0.8348 L12: -0.3037 REMARK 3 L13: -1.0016 L23: 0.4811 REMARK 3 S TENSOR REMARK 3 S11: 0.1281 S12: -0.2114 S13: -0.1341 REMARK 3 S21: -0.1241 S22: 0.0364 S23: 0.2726 REMARK 3 S31: -0.6392 S32: 0.0733 S33: -0.0626 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 368:387) REMARK 3 ORIGIN FOR THE GROUP (A): 9.3088 60.4169 58.4784 REMARK 3 T TENSOR REMARK 3 T11: 0.5791 T22: 0.1480 REMARK 3 T33: 0.3330 T12: 0.2452 REMARK 3 T13: 0.5360 T23: -0.2598 REMARK 3 L TENSOR REMARK 3 L11: 0.6557 L22: 1.1982 REMARK 3 L33: 1.5404 L12: -0.5431 REMARK 3 L13: -0.3834 L23: 1.3368 REMARK 3 S TENSOR REMARK 3 S11: 0.2417 S12: 0.1693 S13: 0.4792 REMARK 3 S21: -0.6021 S22: -0.3224 S23: 0.3999 REMARK 3 S31: -0.2059 S32: -0.1095 S33: -0.0399 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 3AXS 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_1000029828. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-MAY-08 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 : BL-5A 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 : 24738 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.162 REMARK 200 RESOLUTION RANGE LOW (A) : 30.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 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) : 2.17 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 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: PDB ENTRY 2YXA 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, 2.1M (NH4)2SO4, PH REMARK 280 5.5, 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: 2990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 457 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 461 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: 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 O HOH A 434 O HOH A 434 3655 2.15 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 ALA A 62 -109.99 56.97 REMARK 500 ASN A 183 -163.89 -113.68 REMARK 500 LEU A 218 -105.88 40.71 REMARK 500 LYS A 336 81.93 43.45 REMARK 500 LYS A 379 -38.83 78.68 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 113.5 REMARK 620 3 CYS A 266 SG 105.0 101.4 REMARK 620 4 CYS A 269 SG 104.7 114.5 117.6 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 SFG A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 393 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3AXT RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH S-ADENOSYL-L-METHIONINE REMARK 900 RELATED ID: AAE001000841.5 RELATED DB: TARGETDB DBREF 3AXS 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 SFG A 501 27 HET SO4 A 502 5 HET SO4 A 503 5 HET SO4 A 504 5 HET SO4 A 506 5 HET SO4 A 393 5 HETNAM ZN ZINC ION HETNAM SFG SINEFUNGIN HETNAM SO4 SULFATE ION HETSYN SFG ADENOSYL-ORNITHINE FORMUL 2 ZN ZN 2+ FORMUL 3 SFG C15 H23 N7 O5 FORMUL 4 SO4 5(O4 S 2-) FORMUL 9 HOH *94(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 LYS A 120 1 8 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 LYS A 299 1 14 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 82 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 225 N LEU A 154 SHEET 7 B 7 ILE A 207 HIS A 217 -1 N TYR A 215 O LYS A 222 SHEET 1 C 3 ARG A 253 VAL A 256 0 SHEET 2 C 3 PHE A 241 TYR A 246 -1 N GLN A 245 O GLU A 254 SHEET 3 C 3 HIS A 274 TRP A 280 -1 O GLY A 276 N ILE A 244 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 2.23 LINK SG CYS A 250 ZN ZN A 401 1555 1555 2.24 LINK SG CYS A 266 ZN ZN A 401 1555 1555 2.37 LINK SG CYS A 269 ZN ZN A 401 1555 1555 2.23 CISPEP 1 GLY A 277 PRO A 278 0 2.14 SITE 1 AC1 4 CYS A 247 CYS A 250 CYS A 266 CYS A 269 SITE 1 AC2 16 ARG A 36 LEU A 60 SER A 61 ALA A 62 SITE 2 AC2 16 ILE A 65 ARG A 66 ASP A 84 ILE A 85 SITE 3 AC2 16 MET A 112 GLU A 113 ALA A 114 ASP A 132 SITE 4 AC2 16 PHE A 134 HOH A 395 HOH A 399 HOH A 487 SITE 1 AC3 6 SER A 21 SER A 22 ARG A 31 LEU A 218 SITE 2 AC3 6 HIS A 219 ARG A 344 SITE 1 AC4 5 ALA A 162 TYR A 168 HIS A 219 ARG A 344 SITE 2 AC4 5 HOH A 436 SITE 1 AC5 6 TYR A 168 PRO A 169 LYS A 170 THR A 171 SITE 2 AC5 6 HOH A 410 HOH A 481 SITE 1 AC6 3 HIS A 110 GLY A 111 MET A 112 SITE 1 AC7 4 ARG A 182 LYS A 186 LYS A 305 ARG A 309 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