HEADER TRANSFERASE/TRANSFERASE INHIBITOR 13-MAR-15 4YQD TITLE CRYSTAL STRUCTURE OF TRMD, A M1G37 TRNA METHYLTRANSFERASE WITH SAM- TITLE 2 COMPETITIVE COMPOUNDS CAVEAT 4YQD THE DISTANCE BETWEEN RESIDUE A GLY 161 AND RESIDUE A ALA 165 CAVEAT 2 4YQD IS 19.72 ANGSTROM. BUT THERE ARE ONLY 2 RESIDUES (NOT CAVEAT 3 4YQD ENOUGH SEQUENCE) TO COVER THE GAP REGION. 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, SAM-BINDING, KNOT, TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.A.ELKINS,W.G.BONNETTE,K.P.MADAUSS REVDAT 2 27-SEP-23 4YQD 1 REMARK REVDAT 1 11-NOV-15 4YQD 0 JRNL AUTH P.A.ELKINS,W.G.BONNETTE,K.P.MADAUSS 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. 1.45 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.1 REMARK 3 NUMBER OF REFLECTIONS : 46676 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.280 REMARK 3 FREE R VALUE TEST SET COUNT : 1998 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 39.8448 - 3.4942 1.00 3889 174 0.1568 0.1600 REMARK 3 2 3.4942 - 2.7737 1.00 3750 168 0.1634 0.1757 REMARK 3 3 2.7737 - 2.4231 1.00 3733 167 0.1553 0.1947 REMARK 3 4 2.4231 - 2.2016 1.00 3731 167 0.1506 0.1889 REMARK 3 5 2.2016 - 2.0438 1.00 3697 165 0.1434 0.1971 REMARK 3 6 2.0438 - 1.9233 1.00 3675 164 0.1456 0.1840 REMARK 3 7 1.9233 - 1.8270 1.00 3705 165 0.1483 0.1996 REMARK 3 8 1.8270 - 1.7474 1.00 3680 165 0.1582 0.1937 REMARK 3 9 1.7474 - 1.6802 1.00 3666 163 0.1669 0.1958 REMARK 3 10 1.6802 - 1.6222 1.00 3666 165 0.1867 0.2264 REMARK 3 11 1.6222 - 1.5715 0.91 3326 149 0.2217 0.3131 REMARK 3 12 1.5715 - 1.5265 0.58 2154 96 0.2438 0.3099 REMARK 3 13 1.5265 - 1.4864 0.33 1217 54 0.2562 0.2792 REMARK 3 14 1.4864 - 1.4501 0.22 789 36 0.2555 0.3060 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) : 21.730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.58 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.20 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 : 0.006 2027 REMARK 3 ANGLE : 1.089 2748 REMARK 3 CHIRALITY : 0.067 297 REMARK 3 PLANARITY : 0.005 361 REMARK 3 DIHEDRAL : 13.365 770 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 4YQD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000207791. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAY-11 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 : ALS REMARK 200 BEAMLINE : 5.0.2 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 : UNKNOWN REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46707 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 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 (%) : 86.2 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 23.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.64100 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 (%): 54.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 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 47.18800 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 27.24400 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 59.33200 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 47.18800 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 27.24400 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 59.33200 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 47.18800 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 27.24400 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 59.33200 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 47.18800 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 27.24400 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 59.33200 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 47.18800 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 27.24400 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 59.33200 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 47.18800 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 27.24400 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 59.33200 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 54.48801 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 118.66400 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 54.48801 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 118.66400 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 54.48801 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 118.66400 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 54.48801 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 118.66400 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 54.48801 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 118.66400 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 54.48801 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 118.66400 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: 7100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 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 576 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 593 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 599 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 607 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 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER 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 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 LYS A 163 REMARK 465 GLN A 164 REMARK 465 GLU A 167A REMARK 465 GLU A 167B REMARK 465 ASP A 167C 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 SER A 166 OG REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 130 CA CB 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 2.01 REMARK 500 O HOH A 405 O HOH A 589 2.17 REMARK 500 NH2 ARG A 39 O HOH A 402 2.19 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 414 O HOH A 422 17554 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 LYS A 45 CE LYS A 45 NZ -0.156 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 54.81 -67.82 REMARK 500 TYR A 115 -142.34 59.91 REMARK 500 SER A 166 -156.24 -144.93 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 4GZ 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: 4YQ9 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 4YQD A 1 246 UNP P43912 TRMD_HAEIN 1 246 SEQADV 4YQD MET A -19 UNP P43912 INITIATING METHIONINE SEQADV 4YQD GLY A -18 UNP P43912 EXPRESSION TAG SEQADV 4YQD SER A -17 UNP P43912 EXPRESSION TAG SEQADV 4YQD SER A -16 UNP P43912 EXPRESSION TAG SEQADV 4YQD HIS A -15 UNP P43912 EXPRESSION TAG SEQADV 4YQD HIS A -14 UNP P43912 EXPRESSION TAG SEQADV 4YQD HIS A -13 UNP P43912 EXPRESSION TAG SEQADV 4YQD HIS A -12 UNP P43912 EXPRESSION TAG SEQADV 4YQD HIS A -11 UNP P43912 EXPRESSION TAG SEQADV 4YQD HIS A -10 UNP P43912 EXPRESSION TAG SEQADV 4YQD SER A -9 UNP P43912 EXPRESSION TAG SEQADV 4YQD SER A -8 UNP P43912 EXPRESSION TAG SEQADV 4YQD GLY A -7 UNP P43912 EXPRESSION TAG SEQADV 4YQD LEU A -6 UNP P43912 EXPRESSION TAG SEQADV 4YQD VAL A -5 UNP P43912 EXPRESSION TAG SEQADV 4YQD PRO A -4 UNP P43912 EXPRESSION TAG SEQADV 4YQD ARG A -3 UNP P43912 EXPRESSION TAG SEQADV 4YQD GLY A -2 UNP P43912 EXPRESSION TAG SEQADV 4YQD SER A -1 UNP P43912 EXPRESSION TAG SEQADV 4YQD HIS A 0 UNP P43912 EXPRESSION TAG SEQRES 1 A 266 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 266 LEU VAL PRO ARG GLY SER HIS MET TRP ILE GLY VAL ILE SEQRES 3 A 266 SER LEU PHE PRO GLU MET PHE LYS ALA ILE THR GLU PHE SEQRES 4 A 266 GLY VAL THR GLY ARG ALA VAL LYS HIS ASN LEU LEU LYS SEQRES 5 A 266 VAL GLU CYS TRP ASN PRO ARG ASP PHE THR PHE ASP LYS SEQRES 6 A 266 HIS LYS THR VAL ASP ASP ARG PRO TYR GLY GLY GLY PRO SEQRES 7 A 266 GLY MET LEU MET MET VAL GLN PRO LEU ARG ASP ALA ILE SEQRES 8 A 266 HIS THR ALA LYS ALA ALA ALA GLY GLU GLY ALA LYS VAL SEQRES 9 A 266 ILE TYR LEU SER PRO GLN GLY ARG LYS LEU ASP GLN GLY SEQRES 10 A 266 GLY VAL THR GLU LEU ALA GLN ASN GLN LYS LEU ILE LEU SEQRES 11 A 266 VAL CYS GLY ARG TYR GLU GLY ILE ASP GLU ARG LEU ILE SEQRES 12 A 266 GLN THR GLU ILE ASP GLU GLU TRP SER ILE GLY ASP TYR SEQRES 13 A 266 VAL LEU THR GLY GLY GLU LEU PRO ALA MET THR LEU ILE SEQRES 14 A 266 ASP ALA VAL ALA ARG PHE ILE PRO GLY VAL LEU GLY LYS SEQRES 15 A 266 GLN ALA SER ALA GLU GLU ASP SER PHE ALA ASP GLY LEU SEQRES 16 A 266 LEU ASP CYS PRO HIS TYR THR ARG PRO GLU VAL LEU GLU SEQRES 17 A 266 GLY LEU THR VAL PRO PRO VAL LEU MET SER GLY HIS HIS SEQRES 18 A 266 GLU GLU ILE ARG LYS TRP ARG LEU LYS GLN SER LEU GLN SEQRES 19 A 266 ARG THR TRP LEU ARG ARG PRO GLU LEU LEU GLU GLY LEU SEQRES 20 A 266 ALA LEU THR ASP GLU GLN ARG LYS LEU LEU LYS GLU ALA SEQRES 21 A 266 GLN ALA GLU HIS ASN SER HET 4GZ A 301 29 HETNAM 4GZ 6-{[(1-{2-[(3-METHYLBENZOYL)AMINO]ETHYL}CYCLOHEXYL) HETNAM 2 4GZ METHYL]AMINO}PYRIDINE-3-CARBOXAMIDE FORMUL 2 4GZ C23 H30 N4 O2 FORMUL 3 HOH *208(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 PRO A 193 SER A 198 5 6 HELIX 10 AB1 HIS A 200 ARG A 220 1 21 HELIX 11 AB2 ARG A 220 GLY A 226 1 7 HELIX 12 AB3 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 110 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 3.01 SITE 1 AC1 19 TYR A 86 LEU A 87 SER A 88 PRO A 89 SITE 2 AC1 19 GLN A 90 GLY A 113 ARG A 114 TYR A 115 SITE 3 AC1 19 GLU A 116 SER A 132 ILE A 133 GLY A 134 SITE 4 AC1 19 TYR A 136 LEU A 138 PRO A 144 ALA A 165 SITE 5 AC1 19 LEU A 175 ASP A 177 HOH A 527 CRYST1 94.376 94.376 177.996 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 0.010596 0.006118 0.000000 0.00000 SCALE2 0.000000 0.012235 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005618 0.00000