HEADER TRANSFERASE 29-JUN-09 3I2V TITLE CRYSTAL STRUCTURE OF HUMAN MOCS3 RHODANESE-LIKE DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADENYLYLTRANSFERASE AND SULFURTRANSFERASE MOCS3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RHODANESE-LIKE DOMAIN, RESIDUES 335-460; COMPND 5 SYNONYM: MOLYBDENUM COFACTOR SYNTHESIS PROTEIN 3, MOLYBDOPTERIN COMPND 6 SYNTHASE SULFURYLASE, MPT SYNTHASE SULFURYLASE, ADENYLYLTRANSFERASE COMPND 7 MOCS3, SULFURTRANSFERASE MOCS3; COMPND 8 EC: 2.7.7.-, 2.8.1.-; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MOCS3, MOCS3_HUMAN, UBA4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28ALIC KEYWDS RHODANESE, SULFURTRANSFERASE, MOCS3, UBA4, STRUCTURAL GENOMICS, KEYWDS 2 UBIQUITIN BIOLOGY, STRUCTURAL GENOMICS CONSORTIUM, SGC, ATP-BINDING, KEYWDS 3 CYTOPLASM, MOLYBDENUM COFACTOR BIOSYNTHESIS, MULTIFUNCTIONAL ENZYME, KEYWDS 4 NUCLEOTIDE-BINDING, TRANSFERASE, TRNA PROCESSING EXPDTA X-RAY DIFFRACTION AUTHOR J.P.BACIK,J.R.WALKER,L.LOPEZ,Y.LI,J.WEIGELT,C.BOUNTRA,C.H.ARROWSMITH, AUTHOR 2 A.M.EDWARDS,A.BOCHKAREV,S.DHE-PAGANON,STRUCTURAL GENOMICS CONSORTIUM AUTHOR 3 (SGC) REVDAT 2 09-OCT-24 3I2V 1 SEQADV LINK REVDAT 1 21-JUL-09 3I2V 0 JRNL AUTH J.P.BACIK,J.R.WALKER,L.LOPEZ,Y.LI,J.WEIGELT,C.BOUNTRA, JRNL AUTH 2 C.H.ARROWSMITH,A.M.EDWARDS,A.BOCHKAREV,S.DHE-PAGANON JRNL TITL CRYSTAL STRUCTURE OF THE HUMAN MOCS3 RHODANESE-LIKE DOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 29228 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 1457 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 24.2624 - 2.6919 0.97 2913 163 0.1712 0.1977 REMARK 3 2 2.6919 - 2.1371 1.00 2919 168 0.1535 0.2108 REMARK 3 3 2.1371 - 1.8671 0.99 2904 156 0.1452 0.1843 REMARK 3 4 1.8671 - 1.6964 0.99 2906 164 0.1418 0.1994 REMARK 3 5 1.6964 - 1.5748 0.98 2831 154 0.1304 0.1754 REMARK 3 6 1.5748 - 1.4820 0.98 2895 129 0.1252 0.2094 REMARK 3 7 1.4820 - 1.4078 0.97 2826 135 0.1325 0.2038 REMARK 3 8 1.4078 - 1.3465 0.97 2834 157 0.1310 0.2028 REMARK 3 9 1.3465 - 1.2947 0.93 2704 130 0.1777 0.2282 REMARK 3 10 1.2947 - 1.2500 0.71 2039 101 0.2761 0.3358 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.37 REMARK 3 B_SOL : 60.26 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.780 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.61 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.35400 REMARK 3 B22 (A**2) : -0.38400 REMARK 3 B33 (A**2) : 0.73800 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.33000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.015 1004 REMARK 3 ANGLE : 1.593 1369 REMARK 3 CHIRALITY : 0.108 162 REMARK 3 PLANARITY : 0.010 175 REMARK 3 DIHEDRAL : 15.521 375 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: INITIAL DATASET USED TO LOCATE SEMET REMARK 3 COLLECTED AT 0.96426 A REMARK 4 REMARK 4 3I2V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000053894. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0720 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30819 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 24.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.7 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 33.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 66.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.61700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.830 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5, 21% PEG3350, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 15.95550 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 GLN A 67 REMARK 465 GLU A 68 REMARK 465 GLY A 69 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 A 42 CG CD CE NZ REMARK 470 ARG A 46 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 89 CG CD CE NZ DBREF 3I2V A 1 126 UNP O95396 MOCS3_HUMAN 335 460 SEQADV 3I2V SER A 0 UNP O95396 EXPRESSION TAG SEQRES 1 A 127 SER ARG VAL SER VAL THR ASP TYR LYS ARG LEU LEU ASP SEQRES 2 A 127 SER GLY ALA PHE HIS LEU LEU LEU ASP VAL ARG PRO GLN SEQRES 3 A 127 VAL GLU VAL ASP ILE CYS ARG LEU PRO HIS ALA LEU HIS SEQRES 4 A 127 ILE PRO LEU LYS HIS LEU GLU ARG ARG ASP ALA GLU SER SEQRES 5 A 127 LEU LYS LEU LEU LYS GLU ALA ILE TRP GLU GLU LYS GLN SEQRES 6 A 127 GLY THR GLN GLU GLY ALA ALA VAL PRO ILE TYR VAL ILE SEQRES 7 A 127 CYS LYS LEU GLY ASN ASP SER GLN LYS ALA VAL LYS ILE SEQRES 8 A 127 LEU GLN SER LEU SER ALA ALA GLN GLU LEU ASP PRO LEU SEQRES 9 A 127 THR VAL ARG ASP VAL VAL GLY GLY LEU MSE ALA TRP ALA SEQRES 10 A 127 ALA LYS ILE ASP GLY THR PHE PRO GLN TYR MODRES 3I2V MSE A 113 MET SELENOMETHIONINE HET MSE A 113 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE C5 H11 N O2 SE FORMUL 2 HOH *186(H2 O) HELIX 1 1 SER A 3 GLY A 14 1 12 HELIX 2 2 PRO A 24 CYS A 31 1 8 HELIX 3 3 PRO A 40 ARG A 46 1 7 HELIX 4 4 ASP A 48 GLN A 64 1 17 HELIX 5 5 ASN A 82 ALA A 97 1 16 HELIX 6 6 GLY A 110 ILE A 119 1 10 SHEET 1 A 5 ARG A 1 VAL A 2 0 SHEET 2 A 5 LEU A 103 VAL A 108 1 O ASP A 107 N VAL A 2 SHEET 3 A 5 VAL A 72 ILE A 77 1 N ILE A 74 O THR A 104 SHEET 4 A 5 LEU A 18 ASP A 21 1 N LEU A 20 O TYR A 75 SHEET 5 A 5 LEU A 37 HIS A 38 1 O LEU A 37 N LEU A 19 LINK C LEU A 112 N MSE A 113 1555 1555 1.32 LINK C MSE A 113 N ALA A 114 1555 1555 1.35 CRYST1 36.817 31.911 50.640 90.00 110.16 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 0.027161 0.000000 0.009972 0.00000 SCALE2 0.000000 0.031337 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021036 0.00000