PDB Short entry for 1DUS HEADER STRUCTURAL GENOMICS 18-JAN-00 1DUS TITLE MJ0882-A HYPOTHETICAL PROTEIN FROM M. JANNASCHII COMPND MOL_ID: 1; COMPND 2 MOLECULE: MJ0882; COMPND 3 CHAIN: A; COMPND 4 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 KEYWDS HYPOTHETICAL PROTEIN, METHANOCOCCUS JANNASCHII, STRUCTURAL KEYWDS 2 GENOMICS, BSGC STRUCTURE FUNDED BY NIH, PROTEIN STRUCTURE KEYWDS 3 INITIATIVE, PSI, BERKELEY STRUCTURAL GENOMICS CENTER EXPDTA X-RAY DIFFRACTION AUTHOR L.HUNG,L.HUANG,R.KIM,S.H.KIM,BERKELEY STRUCTURAL GENOMICS AUTHOR 2 CENTER (BSGC) REVDAT 5 24-FEB-09 1DUS 1 VERSN REVDAT 4 29-MAR-05 1DUS 1 JRNL REVDAT 3 25-JAN-05 1DUS 1 AUTHOR KEYWDS REMARK REVDAT 2 24-AUG-04 1DUS 1 KEYWDS REMARK REVDAT 1 19-JUL-00 1DUS 0 JRNL AUTH L.HUANG,L.HUNG,M.ODELL,H.YOKOTA,R.KIM,S.H.KIM JRNL TITL STRUCTURE-BASED EXPERIMENTAL CONFIRMATION OF JRNL TITL 2 BIOCHEMICAL FUNCTION TO A METHYLTRANSFERASE, JRNL TITL 3 MJ0882, FROM HYPERTHERMOPHILE METHANOCOCCUS JRNL TITL 4 JANNASCHII JRNL REF J.STRUCT.FUNCT.GENOM. V. 2 121 2002 JRNL REFN ISSN 1345-711X JRNL PMID 12836702 JRNL DOI 10.1023/A:1021279113558 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 543599.170 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 16370 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) : 0.188 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1609 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2270 REMARK 3 BIN R VALUE (WORKING SET) : 0.1730 REMARK 3 BIN FREE R VALUE : 0.2310 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 253 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.015 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1534 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 163 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.90000 REMARK 3 B22 (A**2) : -0.15000 REMARK 3 B33 (A**2) : -1.76000 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) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : 0.03 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) : 0.23 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.06 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.70 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.92 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) : 2.430 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.200 ; 2.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.350 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.010 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.39 REMARK 3 BSOL : 50.36 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 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DUS COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JAN-00. REMARK 100 THE RCSB ID CODE IS RCSB010388. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JUL-98 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.13 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) : 0.9797 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23819 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 8.00 REMARK 200 R MERGE FOR SHELL (I) : 0.32000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.75 M AMMONIUM SULFATE, 0.1 M MES, REMARK 280 PH 5.13, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K 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 34.67000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.39000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.67000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.39000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 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 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 462 LIES ON A SPECIAL POSITION. 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 401 O HOH A 507 3545 2.07 REMARK 500 OE1 GLU A 137 O HOH A 405 2665 2.13 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 LEU A 114 -122.95 54.27 REMARK 500 THR A 162 -174.09 -33.04 REMARK 500 LYS A 163 -136.17 72.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: BSGCAIR30382 RELATED DB: TARGETDB DBREF 1DUS A 4 197 UNP Q58292 Y882_METJA 4 197 SEQADV 1DUS MSE A 82 UNP Q58292 MET 82 MODIFIED RESIDUE SEQADV 1DUS MSE A 173 UNP Q58292 MET 173 MODIFIED RESIDUE SEQRES 1 A 194 PHE SER GLU LYS PRO THR THR LYS SER ASP VAL LYS ILE SEQRES 2 A 194 VAL GLU ASP ILE LEU ARG GLY LYS LYS LEU LYS PHE LYS SEQRES 3 A 194 THR ASP SER GLY VAL PHE SER TYR GLY LYS VAL ASP LYS SEQRES 4 A 194 GLY THR LYS ILE LEU VAL GLU ASN VAL VAL VAL ASP LYS SEQRES 5 A 194 ASP ASP ASP ILE LEU ASP LEU GLY CYS GLY TYR GLY VAL SEQRES 6 A 194 ILE GLY ILE ALA LEU ALA ASP GLU VAL LYS SER THR THR SEQRES 7 A 194 MSE ALA ASP ILE ASN ARG ARG ALA ILE LYS LEU ALA LYS SEQRES 8 A 194 GLU ASN ILE LYS LEU ASN ASN LEU ASP ASN TYR ASP ILE SEQRES 9 A 194 ARG VAL VAL HIS SER ASP LEU TYR GLU ASN VAL LYS ASP SEQRES 10 A 194 ARG LYS TYR ASN LYS ILE ILE THR ASN PRO PRO ILE ARG SEQRES 11 A 194 ALA GLY LYS GLU VAL LEU HIS ARG ILE ILE GLU GLU GLY SEQRES 12 A 194 LYS GLU LEU LEU LYS ASP ASN GLY GLU ILE TRP VAL VAL SEQRES 13 A 194 ILE GLN THR LYS GLN GLY ALA LYS SER LEU ALA LYS TYR SEQRES 14 A 194 MSE LYS ASP VAL PHE GLY ASN VAL GLU THR VAL THR ILE SEQRES 15 A 194 LYS GLY GLY TYR ARG VAL LEU LYS SER LYS LYS LEU MODRES 1DUS MSE A 82 MET SELENOMETHIONINE MODRES 1DUS MSE A 173 MET SELENOMETHIONINE HET MSE A 82 8 HET MSE A 173 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 2 HOH *163(H2 O) HELIX 1 1 ASP A 41 VAL A 51 1 11 HELIX 2 2 GLY A 67 ALA A 74 1 8 HELIX 3 3 ASP A 75 VAL A 77 5 3 HELIX 4 4 ASN A 86 ASN A 100 1 15 HELIX 5 5 GLY A 135 LEU A 149 1 15 HELIX 6 6 LYS A 163 GLY A 178 1 16 SHEET 1 A 2 VAL A 14 LEU A 21 0 SHEET 2 A 2 LYS A 24 ASP A 31 -1 N LYS A 24 O LEU A 21 SHEET 1 B 7 ILE A 107 HIS A 111 0 SHEET 2 B 7 SER A 79 ASP A 84 1 O THR A 80 N ARG A 108 SHEET 3 B 7 ASP A 58 LEU A 62 1 N ILE A 59 O SER A 79 SHEET 4 B 7 TYR A 123 THR A 128 1 N ASN A 124 O ASP A 58 SHEET 5 B 7 LEU A 150 GLN A 161 1 N LYS A 151 O TYR A 123 SHEET 6 B 7 TYR A 189 LYS A 195 -1 N ARG A 190 O ILE A 160 SHEET 7 B 7 GLU A 181 LYS A 186 -1 O GLU A 181 N LYS A 193 LINK C THR A 81 N MSE A 82 1555 1555 1.34 LINK C MSE A 82 N ALA A 83 1555 1555 1.32 LINK C TYR A 172 N MSE A 173 1555 1555 1.33 LINK C MSE A 173 N LYS A 174 1555 1555 1.33 CRYST1 69.340 36.780 68.340 90.00 90.00 90.00 P 21 21 2 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 0.014422 0.000000 0.000000 0.00000 SCALE2 0.000000 0.027189 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014633 0.00000