HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 22-FEB-08 3CBN TITLE CRYSTAL STRUCTURE OF A CONSERVED PROTEIN (MTH639) FROM TITLE 2 METHANOBACTERIUM THERMOAUTOTROPHICUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: CONSERVED PROTEIN MTH639; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 22-161; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOTHERMOBACTER THERMAUTOTROPHICUS; SOURCE 3 ORGANISM_TAXID: 187420; SOURCE 4 STRAIN: DELTA H; SOURCE 5 GENE: MTH639; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-CODON+RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: BC-PSGX3(BC) KEYWDS RP-A, 10241D, PSI-II, NYSGXRC, STRUCTURAL GENOMICS, PROTEIN STRUCTURE KEYWDS 2 INITIATIVE, NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS, KEYWDS 3 UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR L.SATYANARAYANA,S.ESWARAMOORTHY,S.K.BURLEY,S.SWAMINATHAN,NEW YORK SGX AUTHOR 2 RESEARCH CENTER FOR STRUCTURAL GENOMICS (NYSGXRC) REVDAT 4 03-FEB-21 3CBN 1 AUTHOR JRNL SEQADV LINK REVDAT 3 13-JUL-11 3CBN 1 VERSN REVDAT 2 24-FEB-09 3CBN 1 VERSN REVDAT 1 04-MAR-08 3CBN 0 JRNL AUTH L.SATYANARAYANA,S.ESWARAMOORTHY,S.K.BURLEY,S.SWAMINATHAN JRNL TITL CRYSTAL STRUCTURE OF A CONSERVED PROTEIN (MTH639) FROM JRNL TITL 2 METHANOBACTERIUM THERMOAUTOTROPHICUM. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.63 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) : 1.63 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 14122 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) : 0.213 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 574 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.63 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.73 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2440 REMARK 3 BIN FREE R VALUE : 0.2770 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 91 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.029 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1136 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 126 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.11300 REMARK 3 B22 (A**2) : -0.94000 REMARK 3 B33 (A**2) : 1.05200 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.41500 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.11 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) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.13 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 1.400 REMARK 3 BOND ANGLES (DEGREES) : 0.005 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.760 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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 : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESIDUES LISTED AS MISSING IN REMARK REMARK 3 465 ARE DUE TO LACK OF ELECTRON DENSITY. RESIDUES WITH MISSING REMARK 3 ATOMS LISTED IN REMARK 470 ARE DUE TO LACK OF ELECTRON DENSITY REMARK 3 FOR SIDE CHAINS AND MODELED AS ALANINES. REMARK 4 REMARK 4 3CBN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-FEB-08. REMARK 100 THE DEPOSITION ID IS D_1000046580. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9790 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14179 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.630 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 34.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.63 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.10700 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: SAD REMARK 200 SOFTWARE USED: SHELXD, SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 28.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20%(W/V) PEG 3350, 0.1M BIS-TRIS REMARK 280 BUFFER PH 5.5. 3%(W/V) 6-AMINOHEXANOIC ACID, VAPOR DIFFUSION, REMARK 280 SITTING 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 31.58100 REMARK 290 SMTRY3 2 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 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 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 19 REMARK 465 SER A 20 REMARK 465 SER A 83 REMARK 465 HIS A 166 REMARK 465 HIS A 167 REMARK 465 HIS A 168 REMARK 465 HIS A 169 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 GLU A 54 CG CD OE1 OE2 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 ASP A 57 1.51 -69.43 REMARK 500 LEU A 109 56.17 39.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NYSGXRC-10241D RELATED DB: TARGETDB DBREF 3CBN A 22 161 UNP O26735 O26735_METTH 22 161 SEQADV 3CBN MSE A 19 UNP O26735 EXPRESSION TAG SEQADV 3CBN SER A 20 UNP O26735 EXPRESSION TAG SEQADV 3CBN LEU A 21 UNP O26735 EXPRESSION TAG SEQADV 3CBN GLU A 162 UNP O26735 EXPRESSION TAG SEQADV 3CBN GLY A 163 UNP O26735 EXPRESSION TAG SEQADV 3CBN HIS A 164 UNP O26735 EXPRESSION TAG SEQADV 3CBN HIS A 165 UNP O26735 EXPRESSION TAG SEQADV 3CBN HIS A 166 UNP O26735 EXPRESSION TAG SEQADV 3CBN HIS A 167 UNP O26735 EXPRESSION TAG SEQADV 3CBN HIS A 168 UNP O26735 EXPRESSION TAG SEQADV 3CBN HIS A 169 UNP O26735 EXPRESSION TAG SEQRES 1 A 151 MSE SER LEU GLY VAL LEU ARG TYR THR LEU ARG ALA ARG SEQRES 2 A 151 GLY HIS PRO ASN VAL THR ALA GLY HIS ARG THR THR PHE SEQRES 3 A 151 GLU VAL THR VAL ASP PRO GLU ILE GLY GLU THR ALA ASP SEQRES 4 A 151 CYS ILE ILE GLY VAL SER SER SER ASP SER ILE SER THR SEQRES 5 A 151 LEU PRO ASP GLU MSE LYS ARG ALA ILE ALA ARG GLU SER SEQRES 6 A 151 SER LEU VAL ARG VAL ILE LEU ARG THR GLU ASN GLY TYR SEQRES 7 A 151 ASP GLU ILE ARG GLY TYR GLY HIS PRO GLU LEU THR LEU SEQRES 8 A 151 ASP HIS PRO THR ASP ILE VAL CYS ARG LYS SER ASP TYR SEQRES 9 A 151 ILE CYS SER ARG THR LEU MSE ILE ARG ALA ASP LYS ALA SEQRES 10 A 151 ALA PHE ASP LEU ASP GLU ASN LEU VAL ARG ASP LEU ARG SEQRES 11 A 151 LYS GLY ARG GLU LEU LYS VAL GLU ILE ILE VAL GLU TYR SEQRES 12 A 151 GLU GLY HIS HIS HIS HIS HIS HIS MODRES 3CBN MSE A 75 MET SELENOMETHIONINE MODRES 3CBN MSE A 129 MET SELENOMETHIONINE HET MSE A 75 8 HET MSE A 129 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 2 HOH *126(H2 O) HELIX 1 1 SER A 67 LEU A 71 5 5 HELIX 2 2 PRO A 72 ALA A 80 1 9 HELIX 3 3 ALA A 135 LEU A 139 5 5 HELIX 4 4 ASP A 140 LYS A 149 1 10 SHEET 1 A 4 GLY A 22 ARG A 31 0 SHEET 2 A 4 GLU A 152 TYR A 161 -1 O LEU A 153 N ALA A 30 SHEET 3 A 4 LEU A 85 ARG A 91 -1 N ARG A 87 O ILE A 158 SHEET 4 A 4 TYR A 96 TYR A 102 -1 O GLY A 101 N VAL A 86 SHEET 1 B 4 ILE A 59 GLY A 61 0 SHEET 2 B 4 THR A 43 THR A 47 1 N GLU A 45 O ILE A 60 SHEET 3 B 4 ASP A 114 ARG A 118 -1 O CYS A 117 N PHE A 44 SHEET 4 B 4 THR A 127 MSE A 129 1 O LEU A 128 N VAL A 116 LINK C GLU A 74 N MSE A 75 1555 1555 1.33 LINK C MSE A 75 N LYS A 76 1555 1555 1.33 LINK C LEU A 128 N MSE A 129 1555 1555 1.33 LINK C MSE A 129 N ILE A 130 1555 1555 1.33 CRYST1 31.559 63.162 32.182 90.00 112.33 90.00 P 1 21 1 2 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 0.031687 0.000000 0.013015 0.00000 SCALE2 0.000000 0.015832 0.000000 0.00000 SCALE3 0.000000 0.000000 0.033592 0.00000