HEADER TRANSFERASE 14-JUL-09 3A4T TITLE CRYSTAL STRUCTURE OF ATRM4 FROM M.JANNASCHII WITH SINEFUNGIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE METHYLTRANSFERASE MJ0026; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.1.1.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_COMMON: METHANOCOCCUS JANNASCHII; SOURCE 4 ORGANISM_TAXID: 2190; SOURCE 5 GENE: MJ0026; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS TRNA, M5C, ROSSMANN FOLD, STRUCTURAL GENOMICS, RSGI, RIKEN STRUCTURAL KEYWDS 2 GENOMICS/PROTEOMICS INITIATIVE, METHYLTRANSFERASE, S-ADENOSYL-L- KEYWDS 3 METHIONINE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.HIRANO,M.KURATANI,S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS AUTHOR 2 INITIATIVE (RSGI) REVDAT 3 01-NOV-23 3A4T 1 REMARK REVDAT 2 01-DEC-10 3A4T 1 JRNL REVDAT 1 30-JUN-10 3A4T 0 JRNL AUTH M.KURATANI,M.HIRANO,S.GOTO-ITO,Y.ITOH,Y.HIKIDA,M.NISHIMOTO, JRNL AUTH 2 S.SEKINE,Y.BESSHO,T.ITO,H.GROSJEAN,S.YOKOYAMA JRNL TITL CRYSTAL STRUCTURE OF METHANOCALDOCOCCUS JANNASCHII TRM4 JRNL TITL 2 COMPLEXED WITH SINEFUNGIN. JRNL REF J.MOL.BIOL. V. 401 323 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 20600111 JRNL DOI 10.1016/J.JMB.2010.06.046 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.45 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 23309 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 + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1248 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1700 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.2050 REMARK 3 BIN FREE R VALUE SET COUNT : 118 REMARK 3 BIN FREE R VALUE : 0.3190 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4111 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 54 REMARK 3 SOLVENT ATOMS : 167 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.65 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.361 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.270 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.180 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.269 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.887 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4237 ; 0.027 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5702 ; 2.284 ; 2.015 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 507 ; 8.712 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 174 ;36.500 ;25.057 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 849 ;20.052 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;21.199 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 656 ; 0.154 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3034 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2080 ; 0.228 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2864 ; 0.313 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 220 ; 0.178 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 58 ; 0.241 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 11 ; 0.357 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2672 ; 1.163 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4177 ; 1.843 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1815 ; 3.386 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1525 ; 5.029 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3A4T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000028811. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24668 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 42.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 1.0 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.02200 REMARK 200 R SYM (I) : 0.02400 REMARK 200 FOR THE DATA SET : 19.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.04 REMARK 200 R MERGE FOR SHELL (I) : 0.56400 REMARK 200 R SYM FOR SHELL (I) : 0.62700 REMARK 200 FOR SHELL : 0.488 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: PDB ENTRY 3A1X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM TRIS-HCL BUFFER (PH 7.4) , 200MM REMARK 280 MGCL2 ,25% PEG 3350, 10MM CYTIDINE, 3MM SINEFUNGIN, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 85.12950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.04850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 85.12950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.04850 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 276 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 1 REMARK 465 MET A 2 REMARK 465 ILE A 3 REMARK 465 VAL A 4 REMARK 465 TYR A 5 REMARK 465 LYS A 6 REMARK 465 GLY A 7 REMARK 465 GLU A 8 REMARK 465 ILE A 171 REMARK 465 LYS A 172 REMARK 465 ASP A 173 REMARK 465 LYS A 174 REMARK 465 ASN A 175 REMARK 465 ARG A 176 REMARK 465 ASN A 177 REMARK 465 VAL A 178 REMARK 465 MET B 1 REMARK 465 MET B 2 REMARK 465 ILE B 3 REMARK 465 VAL B 4 REMARK 465 TYR B 5 REMARK 465 LYS B 6 REMARK 465 GLY B 7 REMARK 465 GLU B 8 REMARK 465 LYS B 9 REMARK 465 ILE B 170 REMARK 465 ILE B 171 REMARK 465 LYS B 172 REMARK 465 ASP B 173 REMARK 465 LYS B 174 REMARK 465 ASN B 175 REMARK 465 ARG B 176 REMARK 465 ASN B 177 REMARK 465 VAL B 178 REMARK 465 SER B 179 REMARK 465 GLU B 180 REMARK 465 GLU B 181 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 335 O HOH A 343 1.99 REMARK 500 OD2 ASP B 199 O HOH B 371 2.13 REMARK 500 O HOH A 277 O HOH B 350 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 342 O HOH A 342 2554 2.16 REMARK 500 O HOH A 344 O HOH B 370 1545 2.17 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 B 184 N LYS B 184 CA 0.123 REMARK 500 GLU B 215 CD GLU B 215 OE2 0.142 REMARK 500 LYS B 249 CD LYS B 249 CE 0.214 REMARK 500 LYS B 249 CE LYS B 249 NZ 0.161 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 ARG A 120 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 120 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG B 14 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ILE B 183 CB - CA - C ANGL. DEV. = 16.9 DEGREES REMARK 500 LEU B 201 CA - CB - CG ANGL. DEV. = 15.4 DEGREES REMARK 500 LEU B 235 CA - CB - CG ANGL. DEV. = 18.1 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 38 163.66 -40.43 REMARK 500 ASP A 204 2.29 83.65 REMARK 500 CYS A 212 38.95 -86.01 REMARK 500 ASN A 219 -103.89 -123.92 REMARK 500 ILE B 183 -73.78 45.86 REMARK 500 TYR B 185 59.22 -100.08 REMARK 500 ASP B 204 -0.46 68.40 REMARK 500 CYS B 212 39.66 -91.37 REMARK 500 ASN B 219 -94.17 -125.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASP B 182 ILE B 183 61.61 REMARK 500 ILE B 183 LYS B 184 149.68 REMARK 500 LYS B 184 TYR B 185 58.94 REMARK 500 TYR B 185 CYS B 186 133.94 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 SFG A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SFG B 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: MJA001000026.2 RELATED DB: TARGETDB DBREF 3A4T A 1 274 UNP Q60343 Y026_METJA 1 274 DBREF 3A4T B 1 274 UNP Q60343 Y026_METJA 1 274 SEQRES 1 A 274 MET MET ILE VAL TYR LYS GLY GLU LYS MET GLN PHE ILE SEQRES 2 A 274 ARG VAL ASN THR LEU LYS ILE ASN PRO GLU VAL LEU LYS SEQRES 3 A 274 LYS ARG LEU GLU ASN LYS GLY VAL VAL LEU GLU LYS THR SEQRES 4 A 274 PHE LEU ASP TYR ALA PHE GLU VAL LYS LYS SER PRO PHE SEQRES 5 A 274 SER ILE GLY SER THR PRO GLU TYR LEU PHE GLY TYR TYR SEQRES 6 A 274 MET PRO GLN SER ILE SER SER MET ILE PRO PRO ILE VAL SEQRES 7 A 274 LEU ASN PRO ARG GLU ASP ASP PHE ILE LEU ASP MET CYS SEQRES 8 A 274 ALA ALA PRO GLY GLY LYS THR THR HIS LEU ALA GLN LEU SEQRES 9 A 274 MET LYS ASN LYS GLY THR ILE VAL ALA VAL GLU ILE SER SEQRES 10 A 274 LYS THR ARG THR LYS ALA LEU LYS SER ASN ILE ASN ARG SEQRES 11 A 274 MET GLY VAL LEU ASN THR ILE ILE ILE ASN ALA ASP MET SEQRES 12 A 274 ARG LYS TYR LYS ASP TYR LEU LEU LYS ASN GLU ILE PHE SEQRES 13 A 274 PHE ASP LYS ILE LEU LEU ASP ALA PRO CYS SER GLY ASN SEQRES 14 A 274 ILE ILE LYS ASP LYS ASN ARG ASN VAL SER GLU GLU ASP SEQRES 15 A 274 ILE LYS TYR CYS SER LEU ARG GLN LYS GLU LEU ILE ASP SEQRES 16 A 274 ILE GLY ILE ASP LEU LEU LYS LYS ASP GLY GLU LEU VAL SEQRES 17 A 274 TYR SER THR CYS SER MET GLU VAL GLU GLU ASN GLU GLU SEQRES 18 A 274 VAL ILE LYS TYR ILE LEU GLN LYS ARG ASN ASP VAL GLU SEQRES 19 A 274 LEU ILE ILE ILE LYS ALA ASN GLU PHE LYS GLY ILE ASN SEQRES 20 A 274 ILE LYS GLU GLY TYR ILE LYS GLY THR LEU ARG VAL PHE SEQRES 21 A 274 PRO PRO ASN GLU PRO PHE PHE ILE ALA LYS LEU ARG LYS SEQRES 22 A 274 ILE SEQRES 1 B 274 MET MET ILE VAL TYR LYS GLY GLU LYS MET GLN PHE ILE SEQRES 2 B 274 ARG VAL ASN THR LEU LYS ILE ASN PRO GLU VAL LEU LYS SEQRES 3 B 274 LYS ARG LEU GLU ASN LYS GLY VAL VAL LEU GLU LYS THR SEQRES 4 B 274 PHE LEU ASP TYR ALA PHE GLU VAL LYS LYS SER PRO PHE SEQRES 5 B 274 SER ILE GLY SER THR PRO GLU TYR LEU PHE GLY TYR TYR SEQRES 6 B 274 MET PRO GLN SER ILE SER SER MET ILE PRO PRO ILE VAL SEQRES 7 B 274 LEU ASN PRO ARG GLU ASP ASP PHE ILE LEU ASP MET CYS SEQRES 8 B 274 ALA ALA PRO GLY GLY LYS THR THR HIS LEU ALA GLN LEU SEQRES 9 B 274 MET LYS ASN LYS GLY THR ILE VAL ALA VAL GLU ILE SER SEQRES 10 B 274 LYS THR ARG THR LYS ALA LEU LYS SER ASN ILE ASN ARG SEQRES 11 B 274 MET GLY VAL LEU ASN THR ILE ILE ILE ASN ALA ASP MET SEQRES 12 B 274 ARG LYS TYR LYS ASP TYR LEU LEU LYS ASN GLU ILE PHE SEQRES 13 B 274 PHE ASP LYS ILE LEU LEU ASP ALA PRO CYS SER GLY ASN SEQRES 14 B 274 ILE ILE LYS ASP LYS ASN ARG ASN VAL SER GLU GLU ASP SEQRES 15 B 274 ILE LYS TYR CYS SER LEU ARG GLN LYS GLU LEU ILE ASP SEQRES 16 B 274 ILE GLY ILE ASP LEU LEU LYS LYS ASP GLY GLU LEU VAL SEQRES 17 B 274 TYR SER THR CYS SER MET GLU VAL GLU GLU ASN GLU GLU SEQRES 18 B 274 VAL ILE LYS TYR ILE LEU GLN LYS ARG ASN ASP VAL GLU SEQRES 19 B 274 LEU ILE ILE ILE LYS ALA ASN GLU PHE LYS GLY ILE ASN SEQRES 20 B 274 ILE LYS GLU GLY TYR ILE LYS GLY THR LEU ARG VAL PHE SEQRES 21 B 274 PRO PRO ASN GLU PRO PHE PHE ILE ALA LYS LEU ARG LYS SEQRES 22 B 274 ILE HET SFG A 500 27 HET SFG B 501 27 HETNAM SFG SINEFUNGIN HETSYN SFG ADENOSYL-ORNITHINE FORMUL 3 SFG 2(C15 H23 N7 O5) FORMUL 5 HOH *167(H2 O) HELIX 1 1 ASN A 21 LYS A 32 1 12 HELIX 2 2 THR A 57 PHE A 62 1 6 HELIX 3 3 SER A 69 SER A 72 5 4 HELIX 4 4 MET A 73 ASN A 80 1 8 HELIX 5 5 GLY A 95 MET A 105 1 11 HELIX 6 6 SER A 117 MET A 131 1 15 HELIX 7 7 ASP A 142 ASN A 153 1 12 HELIX 8 8 CYS A 166 ILE A 170 5 5 HELIX 9 9 SER A 179 LEU A 200 1 22 HELIX 10 10 GLU A 215 GLU A 218 5 4 HELIX 11 11 ASN A 219 ARG A 230 1 12 HELIX 12 12 ASN B 21 ASN B 31 1 11 HELIX 13 13 SER B 53 SER B 56 5 4 HELIX 14 14 THR B 57 PHE B 62 1 6 HELIX 15 15 ILE B 70 SER B 72 5 3 HELIX 16 16 MET B 73 ASN B 80 1 8 HELIX 17 17 GLY B 95 MET B 105 1 11 HELIX 18 18 SER B 117 GLY B 132 1 16 HELIX 19 19 ASP B 142 ASN B 153 1 12 HELIX 20 20 TYR B 185 LEU B 200 1 16 HELIX 21 21 ASN B 219 ARG B 230 1 12 HELIX 22 22 LYS B 239 PHE B 243 5 5 SHEET 1 A 4 VAL A 35 GLU A 37 0 SHEET 2 A 4 ALA A 44 LYS A 49 -1 O GLU A 46 N GLU A 37 SHEET 3 A 4 GLN A 11 VAL A 15 -1 N GLN A 11 O VAL A 47 SHEET 4 A 4 TYR A 65 PRO A 67 -1 O MET A 66 N ARG A 14 SHEET 1 B 7 THR A 136 ASN A 140 0 SHEET 2 B 7 THR A 110 GLU A 115 1 N ALA A 113 O ILE A 139 SHEET 3 B 7 PHE A 86 ASP A 89 1 N ASP A 89 O VAL A 112 SHEET 4 B 7 PHE A 157 ASP A 163 1 O LEU A 161 N LEU A 88 SHEET 5 B 7 LEU A 201 THR A 211 1 O VAL A 208 N LEU A 162 SHEET 6 B 7 PHE A 266 LYS A 273 -1 O LEU A 271 N LEU A 207 SHEET 7 B 7 VAL A 233 ILE A 236 -1 N ILE A 236 O LYS A 270 SHEET 1 C 8 THR A 136 ASN A 140 0 SHEET 2 C 8 THR A 110 GLU A 115 1 N ALA A 113 O ILE A 139 SHEET 3 C 8 PHE A 86 ASP A 89 1 N ASP A 89 O VAL A 112 SHEET 4 C 8 PHE A 157 ASP A 163 1 O LEU A 161 N LEU A 88 SHEET 5 C 8 LEU A 201 THR A 211 1 O VAL A 208 N LEU A 162 SHEET 6 C 8 PHE A 266 LYS A 273 -1 O LEU A 271 N LEU A 207 SHEET 7 C 8 LEU A 257 VAL A 259 -1 N VAL A 259 O PHE A 266 SHEET 8 C 8 ILE A 248 GLU A 250 -1 N LYS A 249 O ARG A 258 SHEET 1 D 4 VAL B 35 GLU B 37 0 SHEET 2 D 4 ALA B 44 LYS B 49 -1 O LYS B 49 N VAL B 35 SHEET 3 D 4 GLN B 11 VAL B 15 -1 N GLN B 11 O VAL B 47 SHEET 4 D 4 TYR B 65 PRO B 67 -1 O MET B 66 N ARG B 14 SHEET 1 E 7 THR B 136 ASN B 140 0 SHEET 2 E 7 THR B 110 GLU B 115 1 N ILE B 111 O ILE B 137 SHEET 3 E 7 PHE B 86 ASP B 89 1 N ILE B 87 O THR B 110 SHEET 4 E 7 PHE B 157 ALA B 164 1 O LEU B 161 N LEU B 88 SHEET 5 E 7 LEU B 201 THR B 211 1 O VAL B 208 N LEU B 162 SHEET 6 E 7 PHE B 266 LYS B 273 -1 O LEU B 271 N LEU B 207 SHEET 7 E 7 VAL B 233 ILE B 236 -1 N ILE B 236 O LYS B 270 SHEET 1 F 8 THR B 136 ASN B 140 0 SHEET 2 F 8 THR B 110 GLU B 115 1 N ILE B 111 O ILE B 137 SHEET 3 F 8 PHE B 86 ASP B 89 1 N ILE B 87 O THR B 110 SHEET 4 F 8 PHE B 157 ALA B 164 1 O LEU B 161 N LEU B 88 SHEET 5 F 8 LEU B 201 THR B 211 1 O VAL B 208 N LEU B 162 SHEET 6 F 8 PHE B 266 LYS B 273 -1 O LEU B 271 N LEU B 207 SHEET 7 F 8 LEU B 257 VAL B 259 -1 N LEU B 257 O ILE B 268 SHEET 8 F 8 ILE B 248 GLU B 250 -1 N LYS B 249 O ARG B 258 SSBOND 1 CYS A 166 CYS A 212 1555 1555 2.10 SSBOND 2 CYS B 166 CYS B 212 1555 1555 2.10 CISPEP 1 ALA A 93 PRO A 94 0 4.77 CISPEP 2 PRO A 261 PRO A 262 0 14.12 CISPEP 3 ALA B 93 PRO B 94 0 1.23 CISPEP 4 PRO B 261 PRO B 262 0 7.44 SITE 1 AC1 19 MET A 90 CYS A 91 ALA A 92 ALA A 93 SITE 2 AC1 19 PRO A 94 GLY A 95 GLY A 96 LYS A 97 SITE 3 AC1 19 GLU A 115 ILE A 116 ARG A 120 ALA A 141 SITE 4 AC1 19 ASP A 142 MET A 143 ASP A 163 PRO A 165 SITE 5 AC1 19 ASN A 169 ARG A 189 HOH A 295 SITE 1 AC2 17 MET B 90 CYS B 91 ALA B 92 ALA B 93 SITE 2 AC2 17 PRO B 94 GLY B 95 GLY B 96 LYS B 97 SITE 3 AC2 17 GLU B 115 ILE B 116 ARG B 120 ASP B 142 SITE 4 AC2 17 MET B 143 ASP B 163 PRO B 165 ARG B 189 SITE 5 AC2 17 HOH B 290 CRYST1 170.259 40.097 85.951 90.00 110.84 90.00 C 1 2 1 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 0.005873 0.000000 0.002236 0.00000 SCALE2 0.000000 0.024940 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012449 0.00000