HEADER TRANSFERASE/TRANSFERASE INHIBITOR 13-MAR-15 4YQ9 TITLE CRYSTAL STRUCTURE OF TRMD, A M1G37 TRNA METHYLTRANSFERASE WITH SAM- TITLE 2 COMPETITIVE COMPOUNDS COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA (GUANINE-N(1)-)-METHYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: M1G-METHYLTRANSFERASE,TRNA [GM37] METHYLTRANSFERASE; COMPND 5 EC: 2.1.1.228; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HAEMOPHILUS INFLUENZAE (STRAIN ATCC 51907 / DSM SOURCE 3 11121 / KW20 / RD); SOURCE 4 ORGANISM_TAXID: 71421; SOURCE 5 STRAIN: ATCC 51907 / DSM 11121 / KW20 / RD; SOURCE 6 GENE: TRMD, HI_0202; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21*(DE3)PGRO7; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS TRMD, HAEMOPHILUS INFLUENZAE, DIMERIZATION, MODELS, TRNA KEYWDS 2 METHYLTRANSFERASES, S-ADENOSYL METHIONINE, SAM-BINDING, KNOT, KEYWDS 3 TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.A.ELKINS,W.G.BONNETTE,J.A.STUCKEY REVDAT 3 27-SEP-23 4YQ9 1 REMARK REVDAT 2 13-NOV-19 4YQ9 1 KEYWDS REMARK ATOM REVDAT 1 16-MAR-16 4YQ9 0 JRNL AUTH P.A.ELKINS,W.G.BONNETTE JRNL TITL CRYSTAL STRUCTURE OF TRMD, A M1G37 TRNA METHYLTRANSFERASE JRNL TITL 2 WITH SAM-COMPETITIVE COMPOUNDS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 37765 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.740 REMARK 3 FREE R VALUE TEST SET COUNT : 1789 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 37.2551 - 3.8549 0.98 2869 143 0.1614 0.1899 REMARK 3 2 3.8549 - 3.0602 1.00 2810 140 0.1548 0.1560 REMARK 3 3 3.0602 - 2.6735 1.00 2799 139 0.1792 0.2125 REMARK 3 4 2.6735 - 2.4291 1.00 2769 137 0.1704 0.1943 REMARK 3 5 2.4291 - 2.2550 1.00 2765 138 0.1656 0.2105 REMARK 3 6 2.2550 - 2.1221 1.00 2765 138 0.1527 0.1821 REMARK 3 7 2.1221 - 2.0158 1.00 2756 137 0.1566 0.1904 REMARK 3 8 2.0158 - 1.9281 1.00 2753 137 0.1591 0.1718 REMARK 3 9 1.9281 - 1.8538 1.00 2764 137 0.1621 0.1788 REMARK 3 10 1.8538 - 1.7899 1.00 2731 136 0.1695 0.1882 REMARK 3 11 1.7899 - 1.7339 1.00 2744 137 0.1737 0.2093 REMARK 3 12 1.7339 - 1.6843 1.00 2733 135 0.1788 0.2109 REMARK 3 13 1.6843 - 1.6400 1.00 2718 135 0.1886 0.1974 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.56 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 2043 REMARK 3 ANGLE : 1.340 2778 REMARK 3 CHIRALITY : 0.071 306 REMARK 3 PLANARITY : 0.007 369 REMARK 3 DIHEDRAL : 12.595 802 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 -6:34) REMARK 3 ORIGIN FOR THE GROUP (A): -26.8123 22.4783 -2.5530 REMARK 3 T TENSOR REMARK 3 T11: 0.1749 T22: 0.1643 REMARK 3 T33: 0.2002 T12: -0.0725 REMARK 3 T13: 0.0198 T23: -0.0089 REMARK 3 L TENSOR REMARK 3 L11: 2.8739 L22: 2.1691 REMARK 3 L33: 3.9517 L12: 0.5474 REMARK 3 L13: -0.2666 L23: -0.8981 REMARK 3 S TENSOR REMARK 3 S11: -0.0836 S12: -0.0371 S13: -0.4018 REMARK 3 S21: -0.0328 S22: 0.0692 S23: 0.3083 REMARK 3 S31: 0.5371 S32: -0.5092 S33: 0.0186 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 35:132) REMARK 3 ORIGIN FOR THE GROUP (A): -23.1514 34.1992 -16.6774 REMARK 3 T TENSOR REMARK 3 T11: 0.1276 T22: 0.1193 REMARK 3 T33: 0.1063 T12: -0.0201 REMARK 3 T13: -0.0374 T23: -0.0067 REMARK 3 L TENSOR REMARK 3 L11: 1.3775 L22: 1.9851 REMARK 3 L33: 3.5752 L12: -1.1781 REMARK 3 L13: -1.2293 L23: 1.1385 REMARK 3 S TENSOR REMARK 3 S11: 0.0280 S12: 0.0537 S13: 0.0098 REMARK 3 S21: -0.1904 S22: -0.0357 S23: 0.1037 REMARK 3 S31: -0.1494 S32: -0.2170 S33: 0.0050 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 133:161) REMARK 3 ORIGIN FOR THE GROUP (A): -27.0335 34.3267 -1.0656 REMARK 3 T TENSOR REMARK 3 T11: 0.0842 T22: 0.1575 REMARK 3 T33: 0.0998 T12: -0.0157 REMARK 3 T13: -0.0011 T23: -0.0090 REMARK 3 L TENSOR REMARK 3 L11: 2.9811 L22: 4.4477 REMARK 3 L33: 2.7809 L12: 1.2406 REMARK 3 L13: -0.0737 L23: -0.5456 REMARK 3 S TENSOR REMARK 3 S11: 0.0489 S12: -0.1087 S13: -0.0636 REMARK 3 S21: 0.2074 S22: -0.0387 S23: 0.3081 REMARK 3 S31: 0.0207 S32: -0.3662 S33: -0.0114 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 171:190) REMARK 3 ORIGIN FOR THE GROUP (A): -29.4126 39.9541 22.8464 REMARK 3 T TENSOR REMARK 3 T11: 0.1238 T22: 0.1924 REMARK 3 T33: 0.1691 T12: 0.0317 REMARK 3 T13: 0.0053 T23: 0.0030 REMARK 3 L TENSOR REMARK 3 L11: 4.8285 L22: 8.5017 REMARK 3 L33: 4.1466 L12: -4.7444 REMARK 3 L13: 1.7569 L23: -5.3985 REMARK 3 S TENSOR REMARK 3 S11: 0.1732 S12: -0.0818 S13: -0.1965 REMARK 3 S21: -0.2426 S22: 0.2606 S23: 0.5212 REMARK 3 S31: 0.1706 S32: -0.2584 S33: -0.4294 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 191:245) REMARK 3 ORIGIN FOR THE GROUP (A): -38.9724 48.3979 20.6857 REMARK 3 T TENSOR REMARK 3 T11: 0.1331 T22: 0.2382 REMARK 3 T33: 0.1757 T12: 0.0448 REMARK 3 T13: -0.0010 T23: -0.0157 REMARK 3 L TENSOR REMARK 3 L11: 4.5288 L22: 3.0049 REMARK 3 L33: 3.5497 L12: -1.4812 REMARK 3 L13: 0.0172 L23: -0.7885 REMARK 3 S TENSOR REMARK 3 S11: -0.1489 S12: -0.4258 S13: 0.0236 REMARK 3 S21: 0.1899 S22: 0.1845 S23: 0.2911 REMARK 3 S31: -0.1350 S32: -0.2313 S33: -0.0375 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 4YQ9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000207787. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : UNKNOWN REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42204 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 0.55800 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: PHASER REMARK 200 STARTING MODEL: 1P9P REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION:( 12/MG/ML IN 100MM REMARK 280 HEPES PH 7.5, 150MM NACL, 10MM MGCL2 2MM DTT) WELL SOLUTION: (20% REMARK 280 PEG3,350 AND 0.2M POTASSIUM CITRATE TRIBASIC MONOHYDRATE). 4UL REMARK 280 OF S-ADENOSYL METHIONINE IN WATER WERE ADDED TO 100UL OF PROTEIN REMARK 280 AND ALLOWED TO INCUBATE ON ICE FOR 1 HOUR BEFORE PROTEIN WAS REMARK 280 MIXED WITH WELL AT 1:1 RATIO.SEEDING USED TO IMPROVE CRYSTALS. REMARK 280 COMPOUND STOCK SOLUTIONS (EITHER 100MM OR 1M STOCKS) WERE ADDED REMARK 280 UP TO A FINAL DROP CONCENTRATION OF 4.8% DMSO. CRYSTALS WERE REMARK 280 SOAKED FOR 4-6 HOURS. 20% GLYCEROL IN WELL SOLUTION WAS USED AS REMARK 280 CRYOPROTECTANT FOR A QUICK DIP OF CRYSTAL IN LIQUID N2., VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 47.36900 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 27.34850 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 59.24200 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 47.36900 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 27.34850 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 59.24200 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 47.36900 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 27.34850 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 59.24200 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 47.36900 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 27.34850 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 59.24200 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 47.36900 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 27.34850 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 59.24200 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 47.36900 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 27.34850 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 59.24200 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 54.69701 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 118.48400 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 54.69701 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 118.48400 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 54.69701 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 118.48400 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 54.69701 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 118.48400 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 54.69701 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 118.48400 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 54.69701 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 118.48400 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: 6970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 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 582 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 597 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 618 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 630 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 GLY A -7 REMARK 465 LYS A 162 REMARK 465 GLN A 163 REMARK 465 ALA A 164 REMARK 465 SER A 165 REMARK 465 ALA A 166 REMARK 465 GLU A 167 REMARK 465 GLU A 168 REMARK 465 ASP A 169 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER A -1 OG REMARK 470 LYS A 45 CE NZ REMARK 470 GLU A 80 CG CD OE1 OE2 REMARK 470 HIS A 200 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 225 CG CD OE1 OE2 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 O ASN A 245 O HOH A 401 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 628 O HOH A 632 6555 2.15 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 MET A 146 CG - SD - CE ANGL. DEV. = -9.7 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 SER A -1 35.87 -98.83 REMARK 500 TYR A 115 -134.98 61.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 4GO A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4YPW RELATED DB: PDB REMARK 900 RELATED ID: 4YPX RELATED DB: PDB REMARK 900 RELATED ID: 4YPZ RELATED DB: PDB REMARK 900 RELATED ID: 4YQ0 RELATED DB: PDB REMARK 900 RELATED ID: 4YQ1 RELATED DB: PDB REMARK 900 RELATED ID: 4YQ2 RELATED DB: PDB REMARK 900 RELATED ID: 4YQ3 RELATED DB: PDB REMARK 900 RELATED ID: 4YQ4 RELATED DB: PDB REMARK 900 RELATED ID: 4YQ5 RELATED DB: PDB REMARK 900 RELATED ID: 4YQ6 RELATED DB: PDB REMARK 900 RELATED ID: 4YQ7 RELATED DB: PDB REMARK 900 RELATED ID: 4YQ8 RELATED DB: PDB REMARK 900 RELATED ID: 4YQA RELATED DB: PDB REMARK 900 RELATED ID: 4YQB RELATED DB: PDB REMARK 900 RELATED ID: 4YQC RELATED DB: PDB REMARK 900 RELATED ID: 4YQD RELATED DB: PDB REMARK 900 RELATED ID: 4YQG RELATED DB: PDB REMARK 900 RELATED ID: 4YQI RELATED DB: PDB REMARK 900 RELATED ID: 4YQJ RELATED DB: PDB REMARK 900 RELATED ID: 4YQK RELATED DB: PDB REMARK 900 RELATED ID: 4YQL RELATED DB: PDB REMARK 900 RELATED ID: 4YQN RELATED DB: PDB REMARK 900 RELATED ID: 4YQO RELATED DB: PDB REMARK 900 RELATED ID: 4YQP RELATED DB: PDB REMARK 900 RELATED ID: 4YQQ RELATED DB: PDB REMARK 900 RELATED ID: 4YQR RELATED DB: PDB REMARK 900 RELATED ID: 4YQS RELATED DB: PDB REMARK 900 RELATED ID: 4YQT RELATED DB: PDB REMARK 900 RELATED ID: 4YPY RELATED DB: PDB DBREF 4YQ9 A 1 246 UNP P43912 TRMD_HAEIN 1 246 SEQADV 4YQ9 GLY A -7 UNP P43912 EXPRESSION TAG SEQADV 4YQ9 LEU A -6 UNP P43912 EXPRESSION TAG SEQADV 4YQ9 VAL A -5 UNP P43912 EXPRESSION TAG SEQADV 4YQ9 PRO A -4 UNP P43912 EXPRESSION TAG SEQADV 4YQ9 ARG A -3 UNP P43912 EXPRESSION TAG SEQADV 4YQ9 GLY A -2 UNP P43912 EXPRESSION TAG SEQADV 4YQ9 SER A -1 UNP P43912 EXPRESSION TAG SEQADV 4YQ9 HIS A 0 UNP P43912 EXPRESSION TAG SEQRES 1 A 254 GLY LEU VAL PRO ARG GLY SER HIS MET TRP ILE GLY VAL SEQRES 2 A 254 ILE SER LEU PHE PRO GLU MET PHE LYS ALA ILE THR GLU SEQRES 3 A 254 PHE GLY VAL THR GLY ARG ALA VAL LYS HIS ASN LEU LEU SEQRES 4 A 254 LYS VAL GLU CYS TRP ASN PRO ARG ASP PHE THR PHE ASP SEQRES 5 A 254 LYS HIS LYS THR VAL ASP ASP ARG PRO TYR GLY GLY GLY SEQRES 6 A 254 PRO GLY MET LEU MET MET VAL GLN PRO LEU ARG ASP ALA SEQRES 7 A 254 ILE HIS THR ALA LYS ALA ALA ALA GLY GLU GLY ALA LYS SEQRES 8 A 254 VAL ILE TYR LEU SER PRO GLN GLY ARG LYS LEU ASP GLN SEQRES 9 A 254 GLY GLY VAL THR GLU LEU ALA GLN ASN GLN LYS LEU ILE SEQRES 10 A 254 LEU VAL CYS GLY ARG TYR GLU GLY ILE ASP GLU ARG LEU SEQRES 11 A 254 ILE GLN THR GLU ILE ASP GLU GLU TRP SER ILE GLY ASP SEQRES 12 A 254 TYR VAL LEU THR GLY GLY GLU LEU PRO ALA MET THR LEU SEQRES 13 A 254 ILE ASP ALA VAL ALA ARG PHE ILE PRO GLY VAL LEU GLY SEQRES 14 A 254 LYS GLN ALA SER ALA GLU GLU ASP SER PHE ALA ASP GLY SEQRES 15 A 254 LEU LEU ASP CYS PRO HIS TYR THR ARG PRO GLU VAL LEU SEQRES 16 A 254 GLU GLY LEU THR VAL PRO PRO VAL LEU MET SER GLY HIS SEQRES 17 A 254 HIS GLU GLU ILE ARG LYS TRP ARG LEU LYS GLN SER LEU SEQRES 18 A 254 GLN ARG THR TRP LEU ARG ARG PRO GLU LEU LEU GLU GLY SEQRES 19 A 254 LEU ALA LEU THR ASP GLU GLN ARG LYS LEU LEU LYS GLU SEQRES 20 A 254 ALA GLN ALA GLU HIS ASN SER HET 4GO A 301 20 HETNAM 4GO 6-(CYCLOPENTYLAMINO)PYRIDINE-3-CARBOXAMIDE FORMUL 2 4GO C11 H15 N3 O FORMUL 3 HOH *236(H2 O) HELIX 1 AA1 PHE A 9 MET A 12 5 4 HELIX 2 AA2 PHE A 13 GLU A 18 1 6 HELIX 3 AA3 PHE A 19 HIS A 28 1 10 HELIX 4 AA4 ASN A 37 THR A 42 5 6 HELIX 5 AA5 MET A 63 GLY A 79 1 17 HELIX 6 AA6 ASP A 95 ALA A 103 1 9 HELIX 7 AA7 ASP A 119 ILE A 127 1 9 HELIX 8 AA8 GLY A 141 ARG A 154 1 14 HELIX 9 AA9 SER A 170 GLY A 174 5 5 HELIX 10 AB1 PRO A 193 SER A 198 5 6 HELIX 11 AB2 HIS A 200 ARG A 220 1 21 HELIX 12 AB3 ARG A 220 GLY A 226 1 7 HELIX 13 AB4 THR A 230 SER A 246 1 17 SHEET 1 AA1 6 LEU A 31 TRP A 36 0 SHEET 2 AA1 6 MET A 1 ILE A 6 1 N ILE A 3 O LYS A 32 SHEET 3 AA1 6 LYS A 107 VAL A 111 1 O LEU A 108 N GLY A 4 SHEET 4 AA1 6 LYS A 83 LEU A 87 1 N ILE A 85 O ILE A 109 SHEET 5 AA1 6 GLU A 129 SER A 132 1 O TRP A 131 N TYR A 86 SHEET 6 AA1 6 ARG A 92 LYS A 93 1 N ARG A 92 O SER A 132 SHEET 1 AA2 2 ASP A 50 ASP A 51 0 SHEET 2 AA2 2 LEU A 61 MET A 62 -1 O LEU A 61 N ASP A 51 SHEET 1 AA3 2 VAL A 186 LEU A 187 0 SHEET 2 AA3 2 LEU A 190 THR A 191 -1 O LEU A 190 N LEU A 187 CISPEP 1 ARG A 183 PRO A 184 0 3.23 SITE 1 AC1 12 LEU A 87 SER A 88 PRO A 89 GLY A 113 SITE 2 AC1 12 TYR A 115 GLY A 117 SER A 132 ILE A 133 SITE 3 AC1 12 GLY A 134 TYR A 136 LEU A 138 PRO A 144 CRYST1 94.738 94.738 177.726 90.00 90.00 120.00 H 3 2 18 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 0.010555 0.006094 0.000000 0.00000 SCALE2 0.000000 0.012188 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005627 0.00000