HEADER TRANSFERASE 23-APR-07 2YX1 TITLE CRYSTAL STRUCTURE OF M.JANNASCHII TRNA M1G37 METHYLTRANSFERASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN MJ0883; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: 2.1.1.31; COMPND 5 SYNONYM: METHYL TRANSFERASE; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_TAXID: 2190; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET28C KEYWDS METHYL TRANSFERASE, TRNA MODIFICATION ENZYME, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.GOTO-ITO,T.ITO,R.ISHII,Y.BESSHO,S.YOKOYAMA REVDAT 5 30-OCT-24 2YX1 1 REMARK LINK REVDAT 4 13-JUL-11 2YX1 1 VERSN REVDAT 3 24-FEB-09 2YX1 1 VERSN REVDAT 2 05-AUG-08 2YX1 1 JRNL REVDAT 1 22-APR-08 2YX1 0 JRNL AUTH S.GOTO-ITO,T.ITO,R.ISHII,Y.MUTO,Y.BESSHO,S.YOKOYAMA JRNL TITL CRYSTAL STRUCTURE OF ARCHAEAL TRNA(M(1)G37)METHYLTRANSFERASE JRNL TITL 2 ATRM5. JRNL REF PROTEINS V. 72 1274 2008 JRNL REFN ISSN 0887-3585 JRNL PMID 18384044 JRNL DOI 10.1002/PROT.22019 REMARK 2 REMARK 2 RESOLUTION. 2.20 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1279276.810 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 36563 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) : 0.224 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1840 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4902 REMARK 3 BIN R VALUE (WORKING SET) : 0.2860 REMARK 3 BIN FREE R VALUE : 0.3240 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 260 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5168 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 64 REMARK 3 SOLVENT ATOMS : 253 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.44000 REMARK 3 B22 (A**2) : -7.38000 REMARK 3 B33 (A**2) : 3.95000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.89000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.29 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) : 0.37 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.33 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.890 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) : 4.410 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 5.650 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 6.540 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 8.090 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 49.64 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 : SFG_C2-ENDO.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 : SFG_C2-ENDO.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 2YX1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-APR-07. REMARK 100 THE DEPOSITION ID IS D_1000027241. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-NOV-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.50 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) : 0.97934, 0.97942, 0.96418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36694 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 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 (%) : 96.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.50400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M SODIUM CACODYLATE, 7.5% PEG 3350, REMARK 280 5% PEGMME 550, 0.02M HEPES PH 7.50, 0.002M ZINC SULFATE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 34.89500 REMARK 290 SMTRY3 2 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: 1090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -233.4 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 -1.000000 0.000000 0.000000 52.78446 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 34.89500 REMARK 350 BIOMT3 1 0.000000 0.000000 -1.000000 86.66139 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 MSE A 1 REMARK 465 LYS A 69 REMARK 465 ILE A 70 REMARK 465 ILE A 71 REMARK 465 LYS A 72 REMARK 465 LYS A 73 REMARK 465 SER A 138 REMARK 465 GLU A 139 REMARK 465 VAL A 140 REMARK 465 LYS A 141 REMARK 465 GLY A 142 REMARK 465 GLU A 143 REMARK 465 PHE A 144 REMARK 465 MSE B 1 REMARK 465 LYS B 69 REMARK 465 ILE B 70 REMARK 465 ILE B 71 REMARK 465 LYS B 72 REMARK 465 LYS B 73 REMARK 465 PRO B 74 REMARK 465 SER B 75 REMARK 465 SER B 81 REMARK 465 LYS B 82 REMARK 465 LYS B 83 REMARK 465 TYR B 84 REMARK 465 ARG B 85 REMARK 465 LYS B 86 REMARK 465 GLU B 87 REMARK 465 ILE B 88 REMARK 465 ASP B 89 REMARK 465 GLU B 90 REMARK 465 SER B 138 REMARK 465 GLU B 139 REMARK 465 VAL B 140 REMARK 465 LYS B 141 REMARK 465 GLY B 142 REMARK 465 GLU B 143 REMARK 465 PHE B 144 REMARK 465 ARG B 145 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 A 506 O HOH A 567 2.14 REMARK 500 O ASP B 110 N VAL B 112 2.17 REMARK 500 O HOH A 568 O HOH A 594 2.18 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 507 O HOH A 625 2755 2.07 REMARK 500 OE2 GLU B 64 O HOH A 604 2746 2.13 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 GLU A 111 N - CA - C ANGL. DEV. = -16.6 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 LYS A 63 134.93 -174.23 REMARK 500 SER A 75 -75.98 -175.03 REMARK 500 PHE A 76 -62.16 130.80 REMARK 500 LEU A 92 -49.27 -5.74 REMARK 500 GLU A 111 -15.39 173.24 REMARK 500 ASP A 113 166.97 -46.06 REMARK 500 ALA A 153 158.54 172.07 REMARK 500 LYS A 244 -52.94 -128.26 REMARK 500 SER A 250 167.08 175.68 REMARK 500 ASP A 295 -174.33 -172.61 REMARK 500 ALA A 321 170.78 178.43 REMARK 500 LEU B 65 -151.81 -143.05 REMARK 500 GLU B 67 -164.10 -100.40 REMARK 500 ARG B 77 -49.67 -15.63 REMARK 500 GLU B 78 -83.70 -58.38 REMARK 500 ILE B 79 -20.16 66.86 REMARK 500 LEU B 92 72.70 20.49 REMARK 500 ILE B 93 142.12 -173.39 REMARK 500 GLN B 107 74.92 -111.79 REMARK 500 SER B 109 135.53 -29.27 REMARK 500 ASP B 110 173.71 -46.10 REMARK 500 GLU B 111 71.26 -42.88 REMARK 500 VAL B 112 52.23 -149.21 REMARK 500 ASP B 113 -55.04 -146.62 REMARK 500 GLU B 114 170.52 141.59 REMARK 500 LYS B 115 25.01 -72.30 REMARK 500 ARG B 117 -17.82 -160.59 REMARK 500 ASN B 156 45.97 -101.93 REMARK 500 SER B 250 159.53 172.15 REMARK 500 MSE B 264 62.46 -119.32 REMARK 500 TYR B 320 -57.12 -123.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR B 37 0.07 SIDE CHAIN 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 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 227 ND1 REMARK 620 2 GLU A 230 OE1 108.5 REMARK 620 3 HOH A 632 O 96.0 121.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 303 O REMARK 620 2 CYS A 307 SG 111.3 REMARK 620 3 CYS A 309 SG 116.3 125.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 507 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE B 303 O REMARK 620 2 CYS B 307 SG 112.4 REMARK 620 3 CYS B 309 SG 118.6 124.7 REMARK 620 N 1 2 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SFG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SFG B 402 DBREF 2YX1 A 1 336 UNP Q58293 Y883_METJA 1 336 DBREF 2YX1 B 1 336 UNP Q58293 Y883_METJA 1 336 SEQRES 1 A 336 MSE PRO LEU CYS LEU LYS ILE ASN LYS LYS HIS GLY GLU SEQRES 2 A 336 GLN THR ARG ARG ILE LEU ILE GLU ASN ASN LEU LEU ASN SEQRES 3 A 336 LYS ASP TYR LYS ILE THR SER GLU GLY ASN TYR LEU TYR SEQRES 4 A 336 LEU PRO ILE LYS ASP VAL ASP GLU ASP ILE LEU LYS SER SEQRES 5 A 336 ILE LEU ASN ILE GLU PHE GLU LEU VAL ASP LYS GLU LEU SEQRES 6 A 336 GLU GLU LYS LYS ILE ILE LYS LYS PRO SER PHE ARG GLU SEQRES 7 A 336 ILE ILE SER LYS LYS TYR ARG LYS GLU ILE ASP GLU GLY SEQRES 8 A 336 LEU ILE SER LEU SER TYR ASP VAL VAL GLY ASP LEU VAL SEQRES 9 A 336 ILE LEU GLN ILE SER ASP GLU VAL ASP GLU LYS ILE ARG SEQRES 10 A 336 LYS GLU ILE GLY GLU LEU ALA TYR LYS LEU ILE PRO CYS SEQRES 11 A 336 LYS GLY VAL PHE ARG ARG LYS SER GLU VAL LYS GLY GLU SEQRES 12 A 336 PHE ARG VAL ARG GLU LEU GLU HIS LEU ALA GLY GLU ASN SEQRES 13 A 336 ARG THR LEU THR ILE HIS LYS GLU ASN GLY TYR ARG LEU SEQRES 14 A 336 TRP VAL ASP ILE ALA LYS VAL TYR PHE SER PRO ARG LEU SEQRES 15 A 336 GLY GLY GLU ARG ALA ARG ILE MSE LYS LYS VAL SER LEU SEQRES 16 A 336 ASN ASP VAL VAL VAL ASP MSE PHE ALA GLY VAL GLY PRO SEQRES 17 A 336 PHE SER ILE ALA CYS LYS ASN ALA LYS LYS ILE TYR ALA SEQRES 18 A 336 ILE ASP ILE ASN PRO HIS ALA ILE GLU LEU LEU LYS LYS SEQRES 19 A 336 ASN ILE LYS LEU ASN LYS LEU GLU HIS LYS ILE ILE PRO SEQRES 20 A 336 ILE LEU SER ASP VAL ARG GLU VAL ASP VAL LYS GLY ASN SEQRES 21 A 336 ARG VAL ILE MSE ASN LEU PRO LYS PHE ALA HIS LYS PHE SEQRES 22 A 336 ILE ASP LYS ALA LEU ASP ILE VAL GLU GLU GLY GLY VAL SEQRES 23 A 336 ILE HIS TYR TYR THR ILE GLY LYS ASP PHE ASP LYS ALA SEQRES 24 A 336 ILE LYS LEU PHE GLU LYS LYS CYS ASP CYS GLU VAL LEU SEQRES 25 A 336 GLU LYS ARG ILE VAL LYS SER TYR ALA PRO ARG GLU TYR SEQRES 26 A 336 ILE LEU ALA LEU ASP PHE LYS ILE ASN LYS LYS SEQRES 1 B 336 MSE PRO LEU CYS LEU LYS ILE ASN LYS LYS HIS GLY GLU SEQRES 2 B 336 GLN THR ARG ARG ILE LEU ILE GLU ASN ASN LEU LEU ASN SEQRES 3 B 336 LYS ASP TYR LYS ILE THR SER GLU GLY ASN TYR LEU TYR SEQRES 4 B 336 LEU PRO ILE LYS ASP VAL ASP GLU ASP ILE LEU LYS SER SEQRES 5 B 336 ILE LEU ASN ILE GLU PHE GLU LEU VAL ASP LYS GLU LEU SEQRES 6 B 336 GLU GLU LYS LYS ILE ILE LYS LYS PRO SER PHE ARG GLU SEQRES 7 B 336 ILE ILE SER LYS LYS TYR ARG LYS GLU ILE ASP GLU GLY SEQRES 8 B 336 LEU ILE SER LEU SER TYR ASP VAL VAL GLY ASP LEU VAL SEQRES 9 B 336 ILE LEU GLN ILE SER ASP GLU VAL ASP GLU LYS ILE ARG SEQRES 10 B 336 LYS GLU ILE GLY GLU LEU ALA TYR LYS LEU ILE PRO CYS SEQRES 11 B 336 LYS GLY VAL PHE ARG ARG LYS SER GLU VAL LYS GLY GLU SEQRES 12 B 336 PHE ARG VAL ARG GLU LEU GLU HIS LEU ALA GLY GLU ASN SEQRES 13 B 336 ARG THR LEU THR ILE HIS LYS GLU ASN GLY TYR ARG LEU SEQRES 14 B 336 TRP VAL ASP ILE ALA LYS VAL TYR PHE SER PRO ARG LEU SEQRES 15 B 336 GLY GLY GLU ARG ALA ARG ILE MSE LYS LYS VAL SER LEU SEQRES 16 B 336 ASN ASP VAL VAL VAL ASP MSE PHE ALA GLY VAL GLY PRO SEQRES 17 B 336 PHE SER ILE ALA CYS LYS ASN ALA LYS LYS ILE TYR ALA SEQRES 18 B 336 ILE ASP ILE ASN PRO HIS ALA ILE GLU LEU LEU LYS LYS SEQRES 19 B 336 ASN ILE LYS LEU ASN LYS LEU GLU HIS LYS ILE ILE PRO SEQRES 20 B 336 ILE LEU SER ASP VAL ARG GLU VAL ASP VAL LYS GLY ASN SEQRES 21 B 336 ARG VAL ILE MSE ASN LEU PRO LYS PHE ALA HIS LYS PHE SEQRES 22 B 336 ILE ASP LYS ALA LEU ASP ILE VAL GLU GLU GLY GLY VAL SEQRES 23 B 336 ILE HIS TYR TYR THR ILE GLY LYS ASP PHE ASP LYS ALA SEQRES 24 B 336 ILE LYS LEU PHE GLU LYS LYS CYS ASP CYS GLU VAL LEU SEQRES 25 B 336 GLU LYS ARG ILE VAL LYS SER TYR ALA PRO ARG GLU TYR SEQRES 26 B 336 ILE LEU ALA LEU ASP PHE LYS ILE ASN LYS LYS MODRES 2YX1 MSE A 190 MET SELENOMETHIONINE MODRES 2YX1 MSE A 202 MET SELENOMETHIONINE MODRES 2YX1 MSE A 264 MET SELENOMETHIONINE MODRES 2YX1 MSE B 190 MET SELENOMETHIONINE MODRES 2YX1 MSE B 202 MET SELENOMETHIONINE MODRES 2YX1 MSE B 264 MET SELENOMETHIONINE HET MSE A 190 8 HET MSE A 202 8 HET MSE A 264 8 HET MSE B 190 8 HET MSE B 202 8 HET MSE B 264 8 HET ZN A 501 1 HET ZN A 502 1 HET ZN A 503 1 HET ZN A 504 1 HET SFG A 401 27 HET ZN B 505 1 HET ZN B 506 1 HET ZN B 507 1 HET ZN B 508 1 HET ZN B 509 1 HET ZN B 510 1 HET SFG B 402 27 HETNAM MSE SELENOMETHIONINE HETNAM ZN ZINC ION HETNAM SFG SINEFUNGIN HETSYN SFG ADENOSYL-ORNITHINE FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 3 ZN 10(ZN 2+) FORMUL 7 SFG 2(C15 H23 N7 O5) FORMUL 15 HOH *253(H2 O) HELIX 1 1 HIS A 11 ASN A 22 1 12 HELIX 2 2 ASP A 46 LYS A 51 1 6 HELIX 3 3 PHE A 76 TYR A 84 1 9 HELIX 4 4 TYR A 84 ASP A 89 1 6 HELIX 5 5 ASP A 113 ILE A 128 1 16 HELIX 6 6 SER A 179 ARG A 181 5 3 HELIX 7 7 LEU A 182 VAL A 193 1 12 HELIX 8 8 GLY A 207 CYS A 213 1 7 HELIX 9 9 ASN A 225 ASN A 239 1 15 HELIX 10 10 ASP A 251 VAL A 255 5 5 HELIX 11 11 PHE A 269 LYS A 272 5 4 HELIX 12 12 PHE A 273 ILE A 280 1 8 HELIX 13 13 PHE A 296 CYS A 307 1 12 HELIX 14 14 HIS B 11 ASN B 22 1 12 HELIX 15 15 ASP B 46 LEU B 54 1 9 HELIX 16 16 ARG B 117 ILE B 128 1 12 HELIX 17 17 SER B 179 ARG B 181 5 3 HELIX 18 18 LEU B 182 LYS B 191 1 10 HELIX 19 19 GLY B 207 CYS B 213 1 7 HELIX 20 20 ASN B 225 ASN B 239 1 15 HELIX 21 21 ASP B 251 VAL B 255 5 5 HELIX 22 22 PHE B 269 LYS B 272 5 4 HELIX 23 23 PHE B 273 ILE B 280 1 8 HELIX 24 24 PHE B 296 CYS B 307 1 12 SHEET 1 A 4 THR A 32 GLU A 34 0 SHEET 2 A 4 TYR A 37 PRO A 41 -1 O TYR A 39 N THR A 32 SHEET 3 A 4 LEU A 3 ASN A 8 -1 N ILE A 7 O LEU A 38 SHEET 4 A 4 GLU A 59 ASP A 62 -1 O GLU A 59 N LYS A 6 SHEET 1 B 4 ASP A 98 VAL A 100 0 SHEET 2 B 4 LEU A 103 LEU A 106 -1 O LEU A 103 N VAL A 100 SHEET 3 B 4 GLY A 132 ARG A 136 1 O PHE A 134 N LEU A 106 SHEET 4 B 4 LEU A 149 GLY A 154 -1 O GLU A 150 N ARG A 135 SHEET 1 C 2 LEU A 159 GLU A 164 0 SHEET 2 C 2 TYR A 167 ASP A 172 -1 O VAL A 171 N THR A 160 SHEET 1 D 7 ILE A 245 LEU A 249 0 SHEET 2 D 7 LYS A 218 ASP A 223 1 N ILE A 219 O ILE A 246 SHEET 3 D 7 VAL A 198 ASP A 201 1 N ASP A 201 O TYR A 220 SHEET 4 D 7 GLY A 259 MSE A 264 1 O ARG A 261 N VAL A 200 SHEET 5 D 7 VAL A 281 GLY A 293 1 O VAL A 286 N ASN A 260 SHEET 6 D 7 GLU A 324 LYS A 335 -1 O ILE A 333 N GLY A 284 SHEET 7 D 7 ASP A 308 ALA A 321 -1 N GLU A 310 O LYS A 332 SHEET 1 E 4 THR B 32 GLU B 34 0 SHEET 2 E 4 TYR B 37 PRO B 41 -1 O TYR B 37 N GLU B 34 SHEET 3 E 4 LEU B 3 ASN B 8 -1 N ILE B 7 O LEU B 38 SHEET 4 E 4 GLU B 59 ASP B 62 -1 O VAL B 61 N CYS B 4 SHEET 1 F 4 ASP B 98 VAL B 100 0 SHEET 2 F 4 LEU B 103 LEU B 106 -1 O ILE B 105 N ASP B 98 SHEET 3 F 4 GLY B 132 ARG B 136 1 O PHE B 134 N VAL B 104 SHEET 4 F 4 LEU B 149 GLY B 154 -1 O LEU B 152 N VAL B 133 SHEET 1 G 2 LEU B 159 GLU B 164 0 SHEET 2 G 2 TYR B 167 ASP B 172 -1 O VAL B 171 N THR B 160 SHEET 1 H 7 ILE B 245 LEU B 249 0 SHEET 2 H 7 LYS B 218 ASP B 223 1 N ILE B 219 O ILE B 246 SHEET 3 H 7 VAL B 198 ASP B 201 1 N ASP B 201 O TYR B 220 SHEET 4 H 7 GLY B 259 MSE B 264 1 O ARG B 261 N VAL B 200 SHEET 5 H 7 VAL B 281 GLY B 293 1 O HIS B 288 N VAL B 262 SHEET 6 H 7 GLU B 324 LYS B 335 -1 O LEU B 327 N THR B 291 SHEET 7 H 7 ASP B 308 ALA B 321 -1 N GLU B 310 O LYS B 332 LINK C ILE A 189 N MSE A 190 1555 1555 1.32 LINK C MSE A 190 N LYS A 191 1555 1555 1.33 LINK C ASP A 201 N MSE A 202 1555 1555 1.33 LINK C MSE A 202 N PHE A 203 1555 1555 1.34 LINK C ILE A 263 N MSE A 264 1555 1555 1.33 LINK C MSE A 264 N ASN A 265 1555 1555 1.33 LINK C ILE B 189 N MSE B 190 1555 1555 1.32 LINK C MSE B 190 N LYS B 191 1555 1555 1.33 LINK C ASP B 201 N MSE B 202 1555 1555 1.33 LINK C MSE B 202 N PHE B 203 1555 1555 1.33 LINK C ILE B 263 N MSE B 264 1555 1555 1.34 LINK C MSE B 264 N ASN B 265 1555 1555 1.32 LINK ND1 HIS A 227 ZN ZN A 501 1555 1555 2.07 LINK OE1 GLU A 230 ZN ZN A 501 1555 1555 2.05 LINK ND1 HIS A 243 ZN ZN A 502 1555 1555 2.08 LINK O PHE A 303 ZN ZN A 503 1555 1555 2.16 LINK SG CYS A 307 ZN ZN A 503 1555 1555 2.41 LINK SG CYS A 309 ZN ZN A 503 1555 1555 2.48 LINK NE SFG A 401 ZN ZN A 504 1555 1555 2.19 LINK ZN ZN A 501 O HOH A 632 1555 1555 2.27 LINK ND1 HIS B 11 ZN ZN B 505 1555 1555 2.01 LINK OE1 GLU B 230 ZN ZN B 506 1555 1555 2.05 LINK O PHE B 303 ZN ZN B 507 1555 1555 2.14 LINK SG CYS B 307 ZN ZN B 507 1555 1555 2.57 LINK SG CYS B 309 ZN ZN B 507 1555 1555 2.42 LINK NE SFG B 402 ZN ZN B 508 1555 1555 2.39 SITE 1 AC1 3 HIS A 227 GLU A 230 HOH A 632 SITE 1 AC2 3 HIS A 243 HOH A 505 HOH A 625 SITE 1 AC3 3 PHE A 303 CYS A 307 CYS A 309 SITE 1 AC4 1 TYR A 177 SITE 1 AC5 3 LYS B 175 HIS B 227 GLU B 230 SITE 1 AC6 4 PHE B 303 GLU B 304 CYS B 307 CYS B 309 SITE 1 AC7 2 HIS B 271 LYS B 272 SITE 1 AC8 17 TYR A 177 ARG A 186 PHE A 203 ALA A 204 SITE 2 AC8 17 PRO A 208 PHE A 209 ASP A 223 ILE A 224 SITE 3 AC8 17 SER A 250 ASP A 251 ASN A 265 LEU A 266 SITE 4 AC8 17 HOH A 517 HOH A 531 HOH A 537 HOH A 581 SITE 5 AC8 17 HOH A 597 SITE 1 AC9 18 ARG B 186 PHE B 203 ALA B 204 GLY B 205 SITE 2 AC9 18 PRO B 208 PHE B 209 ASP B 223 ILE B 224 SITE 3 AC9 18 ASN B 225 SER B 250 ASP B 251 ASN B 265 SITE 4 AC9 18 LEU B 266 HOH B 515 HOH B 519 HOH B 529 SITE 5 AC9 18 HOH B 561 HOH B 603 CRYST1 62.000 69.790 87.150 90.00 96.07 90.00 P 1 21 1 4 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 0.016129 0.000000 0.001715 0.00000 SCALE2 0.000000 0.014329 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011539 0.00000