HEADER TRANSFERASE 05-APR-07 2YTZ TITLE COMPLEX STRUCTURE OF TRM1 FROM PYROCOCCUS HORIKOSHII WITH S-ADENOSYL- TITLE 2 L-HOMOCYSTEIN IN THE ORTHORHOMBIC CRYSTAL-LATTICE COMPND MOL_ID: 1; COMPND 2 MOLECULE: N(2),N(2)-DIMETHYLGUANOSINE TRNA METHYLTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 1-378; COMPND 5 SYNONYM: TRNA(GUANINE-26,N(2)-N(2) METHYLTRANSFERASE, TRNA 2,2- COMPND 6 DIMETHYLGUANOSINE-26 METHYLTRANSFERASE, TRNA(M(2,2)G26) COMPND 7 DIMETHYLTRANSFERASE; COMPND 8 EC: 2.1.1.32; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 53953; SOURCE 4 GENE: TRM1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS (DE3)-RIL; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS TRNA MODIFICATION ENZYME, GUANINE-26, N(2)-N(2)-DIMETHYLTRANSFERASE, KEYWDS 2 STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL KEYWDS 3 AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 4 INITIATIVE, RSGI, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR IHSANAWATI,M.SHIROUZU,Y.BESSHO,S.YOKOYAMA,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 4 25-OCT-23 2YTZ 1 REMARK REVDAT 3 24-FEB-09 2YTZ 1 VERSN REVDAT 2 21-OCT-08 2YTZ 1 JRNL REMARK REVDAT 1 09-OCT-07 2YTZ 0 JRNL AUTH IHSANAWATI,M.NISHIMOTO,K.HIGASHIJIMA,M.SHIROUZU,H.GROSJEAN, JRNL AUTH 2 Y.BESSHO,S.YOKOYAMA JRNL TITL CRYSTAL STRUCTURE OF TRNA N(2),N(2)-GUANOSINE JRNL TITL 2 DIMETHYLTRANSFERASE TRM1 FROM PYROCOCCUS HORIKOSHII JRNL REF J.MOL.BIOL. V. 383 871 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18789948 JRNL DOI 10.1016/J.JMB.2008.08.068 REMARK 2 REMARK 2 RESOLUTION. 2.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.91 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2085929.180 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 30136 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1494 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.82 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4258 REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE : 0.3010 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 243 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.019 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5877 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 72 REMARK 3 SOLVENT ATOMS : 272 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.67000 REMARK 3 B22 (A**2) : 8.00000 REMARK 3 B33 (A**2) : -13.67000 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.27 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.39 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.780 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 42.16 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : SAH.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : SAH.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2YTZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1000027131. 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 : 8.5 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) : 1.0 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 : 30188 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.650 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 7.110 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09500 REMARK 200 FOR THE DATA SET : 18.9800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.39200 REMARK 200 FOR SHELL : 3.620 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 2DUL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRISCL, 2M AMMONIUM SULFATE, PH REMARK 280 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 41.34200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 94.98000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 41.34200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 94.98000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: MONOMERIC 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -78.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 LEU A 331 REMARK 465 LYS A 332 REMARK 465 ILE A 333 REMARK 465 GLU A 334 REMARK 465 THR A 335 REMARK 465 ILE A 378 REMARK 465 MET B 1 REMARK 465 GLU B 2 REMARK 465 LYS B 17 REMARK 465 ALA B 18 REMARK 465 GLU B 19 REMARK 465 SER B 20 REMARK 465 ILE B 21 REMARK 465 TYR B 22 REMARK 465 LEU B 331 REMARK 465 LYS B 332 REMARK 465 ILE B 333 REMARK 465 ARG B 377 REMARK 465 ILE B 378 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 LYS B 10 CG CD CE NZ REMARK 470 LYS B 103 CG CD CE NZ 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 HOH B 1004 O HOH B 1094 2.10 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 TYR A 28 109.27 -163.69 REMARK 500 ALA A 57 -112.67 56.11 REMARK 500 LYS A 103 103.29 -54.43 REMARK 500 ARG A 130 51.71 37.64 REMARK 500 ASP A 166 47.25 -89.47 REMARK 500 HIS A 174 76.13 -116.48 REMARK 500 LYS A 223 137.20 -178.88 REMARK 500 LEU A 320 -169.57 63.89 REMARK 500 PHE A 321 -175.65 -171.40 REMARK 500 GLU B 8 -99.86 -80.29 REMARK 500 LYS B 10 33.40 -75.65 REMARK 500 TYR B 28 120.66 -170.93 REMARK 500 ALA B 57 -100.98 53.72 REMARK 500 PRO B 70 2.55 -69.21 REMARK 500 ASP B 78 146.74 -171.14 REMARK 500 SER B 102 118.06 -169.57 REMARK 500 ARG B 128 66.08 -101.85 REMARK 500 LYS B 223 131.90 -172.03 REMARK 500 ASP B 224 58.73 36.59 REMARK 500 THR B 256 -32.28 -131.20 REMARK 500 SER B 296 52.79 -100.07 REMARK 500 LEU B 320 -175.52 67.58 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 SO4 A 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1007 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAH A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAH B 1002 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2DUL RELATED DB: PDB REMARK 900 THE SAME PROTEIN BUT WITHOUT LIGAND REMARK 900 RELATED ID: 2EJT RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITH SAM REMARK 900 RELATED ID: 2EJU RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITH SAH IN THE CENTERED ORTHORHOMBIC CRYSTAL REMARK 900 LATTICE REMARK 900 RELATED ID: PHO001001829.5 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE RESIDUE WAS ENGINEERED FROM LEU TO MET AS INITIATING REMARK 999 METHIONINE. DBREF 2YTZ A 1 378 UNP O59493 TRM1_PYRHO 4 381 DBREF 2YTZ B 1 378 UNP O59493 TRM1_PYRHO 4 381 SEQADV 2YTZ MET A 1 UNP O59493 LEU 4 SEE REMARK 999 SEQADV 2YTZ MET B 1 UNP O59493 LEU 4 SEE REMARK 999 SEQRES 1 A 378 MET GLU LEU ILE GLU VAL GLN GLU GLY LYS ALA LYS ILE SEQRES 2 A 378 LEU ILE PRO LYS ALA GLU SER ILE TYR ASP SER PRO VAL SEQRES 3 A 378 PHE TYR ASN PRO ARG MET ALA LEU ASN ARG ASP ILE VAL SEQRES 4 A 378 VAL VAL LEU LEU ASN ILE LEU ASN PRO LYS ILE VAL LEU SEQRES 5 A 378 ASP ALA LEU SER ALA THR GLY ILE ARG GLY ILE ARG PHE SEQRES 6 A 378 ALA LEU GLU THR PRO ALA GLU GLU VAL TRP LEU ASN ASP SEQRES 7 A 378 ILE SER GLU ASP ALA TYR GLU LEU MET LYS ARG ASN VAL SEQRES 8 A 378 MET LEU ASN PHE ASP GLY GLU LEU ARG GLU SER LYS GLY SEQRES 9 A 378 ARG ALA ILE LEU LYS GLY GLU LYS THR ILE VAL ILE ASN SEQRES 10 A 378 HIS ASP ASP ALA ASN ARG LEU MET ALA GLU ARG HIS ARG SEQRES 11 A 378 TYR PHE HIS PHE ILE ASP LEU ASP PRO PHE GLY SER PRO SEQRES 12 A 378 MET GLU PHE LEU ASP THR ALA LEU ARG SER ALA LYS ARG SEQRES 13 A 378 ARG GLY ILE LEU GLY VAL THR ALA THR ASP GLY ALA PRO SEQRES 14 A 378 LEU CYS GLY ALA HIS PRO ARG ALA CYS LEU ARG LYS TYR SEQRES 15 A 378 LEU ALA VAL PRO LEU ARG GLY GLU LEU CYS HIS GLU VAL SEQRES 16 A 378 GLY THR ARG ILE LEU VAL GLY VAL ILE ALA ARG TYR ALA SEQRES 17 A 378 ALA LYS TYR ASP LEU GLY ILE ASP VAL ILE LEU ALA TYR SEQRES 18 A 378 TYR LYS ASP HIS TYR PHE ARG ALA PHE VAL LYS LEU LYS SEQRES 19 A 378 ASP GLY ALA ARG LYS GLY ASP GLU THR LEU GLU LYS LEU SEQRES 20 A 378 GLY TYR ILE TYR PHE ASP ASP LYS THR GLY LYS PHE GLU SEQRES 21 A 378 LEU GLU GLN GLY PHE LEU PRO THR ARG PRO ASN ALA TYR SEQRES 22 A 378 GLY PRO VAL TRP LEU GLY PRO LEU LYS ASP GLU LYS ILE SEQRES 23 A 378 VAL SER LYS MET VAL LYS GLU ALA GLU SER LEU SER LEU SEQRES 24 A 378 ALA ARG LYS LYS GLN ALA LEU LYS LEU LEU LYS MET ILE SEQRES 25 A 378 ASP GLN GLU LEU ASP ILE PRO LEU PHE TYR ASP THR HIS SEQRES 26 A 378 ALA ILE GLY ARG ARG LEU LYS ILE GLU THR LYS LYS VAL SEQRES 27 A 378 GLU GLU ILE ILE SER ALA LEU ARG GLU GLN GLY TYR GLU SEQRES 28 A 378 ALA THR ARG THR HIS PHE SER PRO THR GLY ILE LYS THR SEQRES 29 A 378 SER ALA PRO TYR GLU VAL PHE ILE GLU THR ILE LYS ARG SEQRES 30 A 378 ILE SEQRES 1 B 378 MET GLU LEU ILE GLU VAL GLN GLU GLY LYS ALA LYS ILE SEQRES 2 B 378 LEU ILE PRO LYS ALA GLU SER ILE TYR ASP SER PRO VAL SEQRES 3 B 378 PHE TYR ASN PRO ARG MET ALA LEU ASN ARG ASP ILE VAL SEQRES 4 B 378 VAL VAL LEU LEU ASN ILE LEU ASN PRO LYS ILE VAL LEU SEQRES 5 B 378 ASP ALA LEU SER ALA THR GLY ILE ARG GLY ILE ARG PHE SEQRES 6 B 378 ALA LEU GLU THR PRO ALA GLU GLU VAL TRP LEU ASN ASP SEQRES 7 B 378 ILE SER GLU ASP ALA TYR GLU LEU MET LYS ARG ASN VAL SEQRES 8 B 378 MET LEU ASN PHE ASP GLY GLU LEU ARG GLU SER LYS GLY SEQRES 9 B 378 ARG ALA ILE LEU LYS GLY GLU LYS THR ILE VAL ILE ASN SEQRES 10 B 378 HIS ASP ASP ALA ASN ARG LEU MET ALA GLU ARG HIS ARG SEQRES 11 B 378 TYR PHE HIS PHE ILE ASP LEU ASP PRO PHE GLY SER PRO SEQRES 12 B 378 MET GLU PHE LEU ASP THR ALA LEU ARG SER ALA LYS ARG SEQRES 13 B 378 ARG GLY ILE LEU GLY VAL THR ALA THR ASP GLY ALA PRO SEQRES 14 B 378 LEU CYS GLY ALA HIS PRO ARG ALA CYS LEU ARG LYS TYR SEQRES 15 B 378 LEU ALA VAL PRO LEU ARG GLY GLU LEU CYS HIS GLU VAL SEQRES 16 B 378 GLY THR ARG ILE LEU VAL GLY VAL ILE ALA ARG TYR ALA SEQRES 17 B 378 ALA LYS TYR ASP LEU GLY ILE ASP VAL ILE LEU ALA TYR SEQRES 18 B 378 TYR LYS ASP HIS TYR PHE ARG ALA PHE VAL LYS LEU LYS SEQRES 19 B 378 ASP GLY ALA ARG LYS GLY ASP GLU THR LEU GLU LYS LEU SEQRES 20 B 378 GLY TYR ILE TYR PHE ASP ASP LYS THR GLY LYS PHE GLU SEQRES 21 B 378 LEU GLU GLN GLY PHE LEU PRO THR ARG PRO ASN ALA TYR SEQRES 22 B 378 GLY PRO VAL TRP LEU GLY PRO LEU LYS ASP GLU LYS ILE SEQRES 23 B 378 VAL SER LYS MET VAL LYS GLU ALA GLU SER LEU SER LEU SEQRES 24 B 378 ALA ARG LYS LYS GLN ALA LEU LYS LEU LEU LYS MET ILE SEQRES 25 B 378 ASP GLN GLU LEU ASP ILE PRO LEU PHE TYR ASP THR HIS SEQRES 26 B 378 ALA ILE GLY ARG ARG LEU LYS ILE GLU THR LYS LYS VAL SEQRES 27 B 378 GLU GLU ILE ILE SER ALA LEU ARG GLU GLN GLY TYR GLU SEQRES 28 B 378 ALA THR ARG THR HIS PHE SER PRO THR GLY ILE LYS THR SEQRES 29 B 378 SER ALA PRO TYR GLU VAL PHE ILE GLU THR ILE LYS ARG SEQRES 30 B 378 ILE HET SO4 A1004 5 HET SO4 A1005 5 HET SO4 A1007 5 HET SAH A1001 26 HET SO4 B1003 5 HET SAH B1002 26 HETNAM SO4 SULFATE ION HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE FORMUL 3 SO4 4(O4 S 2-) FORMUL 6 SAH 2(C14 H20 N6 O5 S) FORMUL 9 HOH *272(H2 O) HELIX 1 1 ASN A 29 ARG A 31 5 3 HELIX 2 2 MET A 32 ASN A 47 1 16 HELIX 3 3 GLY A 59 THR A 69 1 11 HELIX 4 4 SER A 80 PHE A 95 1 16 HELIX 5 5 ASP A 120 ARG A 128 1 9 HELIX 6 6 PRO A 143 SER A 153 1 11 HELIX 7 7 ASP A 166 CYS A 171 1 6 HELIX 8 8 HIS A 174 LEU A 183 1 10 HELIX 9 9 LEU A 191 ALA A 209 1 19 HELIX 10 10 GLY A 236 GLU A 245 1 10 HELIX 11 11 ASP A 283 SER A 296 1 14 HELIX 12 12 ARG A 301 GLU A 315 1 15 HELIX 13 13 THR A 324 ARG A 330 1 7 HELIX 14 14 LYS A 337 GLN A 348 1 12 HELIX 15 15 PRO A 367 ARG A 377 1 11 HELIX 16 16 ASN B 29 ARG B 31 5 3 HELIX 17 17 MET B 32 ASN B 47 1 16 HELIX 18 18 GLY B 59 THR B 69 1 11 HELIX 19 19 SER B 80 LEU B 93 1 14 HELIX 20 20 ASP B 120 ARG B 128 1 9 HELIX 21 21 PRO B 143 SER B 153 1 11 HELIX 22 22 ASP B 166 CYS B 171 1 6 HELIX 23 23 HIS B 174 LEU B 183 1 10 HELIX 24 24 LEU B 191 LYS B 210 1 20 HELIX 25 25 GLY B 236 GLU B 245 1 10 HELIX 26 26 ASP B 283 SER B 296 1 14 HELIX 27 27 ARG B 301 GLU B 315 1 15 HELIX 28 28 THR B 324 ARG B 330 1 7 HELIX 29 29 LYS B 337 GLN B 348 1 12 HELIX 30 30 PRO B 367 LYS B 376 1 10 SHEET 1 A 2 LEU A 3 GLU A 8 0 SHEET 2 A 2 ALA A 11 PRO A 16 -1 O ILE A 15 N ILE A 4 SHEET 1 B 9 ARG A 100 SER A 102 0 SHEET 2 B 9 ARG A 105 LYS A 109 -1 O ILE A 107 N ARG A 100 SHEET 3 B 9 THR A 113 HIS A 118 -1 O ILE A 116 N ALA A 106 SHEET 4 B 9 GLU A 73 ASP A 78 1 N LEU A 76 O VAL A 115 SHEET 5 B 9 ILE A 50 ASP A 53 1 N ASP A 53 O TRP A 75 SHEET 6 B 9 PHE A 132 LEU A 137 1 O ASP A 136 N LEU A 52 SHEET 7 B 9 ALA A 154 ALA A 164 1 O GLY A 161 N LEU A 137 SHEET 8 B 9 TYR A 226 ASP A 235 -1 O ALA A 229 N VAL A 162 SHEET 9 B 9 LEU A 213 LYS A 223 -1 N TYR A 221 O ARG A 228 SHEET 1 C 3 PHE A 259 GLN A 263 0 SHEET 2 C 3 LEU A 247 PHE A 252 -1 N TYR A 251 O GLU A 260 SHEET 3 C 3 TYR A 273 TRP A 277 -1 O VAL A 276 N GLY A 248 SHEET 1 D 3 TYR A 322 ASP A 323 0 SHEET 2 D 3 SER A 358 THR A 364 -1 O ILE A 362 N TYR A 322 SHEET 3 D 3 ALA A 352 THR A 355 -1 N THR A 353 O LYS A 363 SHEET 1 E 2 ILE B 4 GLN B 7 0 SHEET 2 E 2 LYS B 12 ILE B 15 -1 O ILE B 15 N ILE B 4 SHEET 1 F 9 ARG B 100 SER B 102 0 SHEET 2 F 9 ARG B 105 LEU B 108 -1 O ARG B 105 N SER B 102 SHEET 3 F 9 THR B 113 HIS B 118 -1 O ILE B 116 N ALA B 106 SHEET 4 F 9 GLU B 73 ASP B 78 1 N LEU B 76 O ASN B 117 SHEET 5 F 9 ILE B 50 ASP B 53 1 N VAL B 51 O GLU B 73 SHEET 6 F 9 PHE B 132 LEU B 137 1 O HIS B 133 N ILE B 50 SHEET 7 F 9 ALA B 154 ALA B 164 1 O LYS B 155 N PHE B 132 SHEET 8 F 9 TYR B 226 ASP B 235 -1 O ALA B 229 N VAL B 162 SHEET 9 F 9 LEU B 213 LYS B 223 -1 N ILE B 218 O PHE B 230 SHEET 1 G 3 PHE B 259 GLN B 263 0 SHEET 2 G 3 LEU B 247 PHE B 252 -1 N TYR B 251 O GLU B 260 SHEET 3 G 3 TYR B 273 TRP B 277 -1 O VAL B 276 N GLY B 248 SHEET 1 H 3 TYR B 322 ASP B 323 0 SHEET 2 H 3 SER B 358 THR B 364 -1 O ILE B 362 N TYR B 322 SHEET 3 H 3 ALA B 352 THR B 355 -1 N THR B 353 O LYS B 363 CISPEP 1 GLY A 274 PRO A 275 0 0.09 CISPEP 2 GLY B 274 PRO B 275 0 0.26 SITE 1 AC1 4 HIS A 129 ARG A 130 ARG A 156 HOH B1071 SITE 1 AC2 4 HIS A 174 PRO A 175 ARG A 176 ALA A 177 SITE 1 AC3 5 LYS A 337 VAL A 338 GLU A 339 ARG A 354 SITE 2 AC3 5 HOH A1162 SITE 1 AC4 22 ARG A 36 LEU A 55 ALA A 57 ILE A 60 SITE 2 AC4 22 ARG A 61 ASN A 77 ASP A 78 ILE A 79 SITE 3 AC4 22 SER A 80 ASP A 119 ASP A 120 ALA A 121 SITE 4 AC4 22 ASP A 138 PHE A 140 PHE A 146 GLN A 348 SITE 5 AC4 22 HOH A1009 HOH A1012 HOH A1030 HOH A1043 SITE 6 AC4 22 HOH A1095 HOH A1100 SITE 1 AC5 5 HIS B 174 PRO B 175 ARG B 176 ALA B 177 SITE 2 AC5 5 HOH B1046 SITE 1 AC6 19 PHE B 27 ARG B 36 LEU B 55 ALA B 57 SITE 2 AC6 19 ILE B 60 ARG B 61 ASP B 78 ILE B 79 SITE 3 AC6 19 SER B 80 ASP B 119 ASP B 120 ALA B 121 SITE 4 AC6 19 ASP B 138 PHE B 140 PHE B 146 HOH B1013 SITE 5 AC6 19 HOH B1030 HOH B1037 HOH B1116 CRYST1 82.684 189.960 66.894 90.00 90.00 90.00 P 21 21 2 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 0.012094 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005264 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014949 0.00000