HEADER TRANSPORT 17-JUN-97 1WOD TITLE CRYSTAL STRUCTURE OF MODA, A MOLYBDATE PROTEIN, COMPLEXED WITH TITLE 2 TUNGSTATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MODA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-DOMAIN, C-DOMAIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 CELLULAR_LOCATION: PERIPLASM KEYWDS MOLYBDATE TRANSPORT PROTEIN, MOLYBDATE, TUNGSTATE, PERIPLASMIC, KEYWDS 2 TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR Y.HU,S.RECH,R.P.GUNSALUS,D.C.REES REVDAT 3 14-FEB-24 1WOD 1 REMARK REVDAT 2 24-FEB-09 1WOD 1 VERSN REVDAT 1 17-DEC-97 1WOD 0 JRNL AUTH Y.HU,S.RECH,R.P.GUNSALUS,D.C.REES JRNL TITL CRYSTAL STRUCTURE OF THE MOLYBDATE BINDING PROTEIN MODA. JRNL REF NAT.STRUCT.BIOL. V. 4 703 1997 JRNL REFN ISSN 1072-8368 JRNL PMID 9302996 JRNL DOI 10.1038/NSB0997-703 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.RECH,C.WOLIN,R.P.GUNSALUS REMARK 1 TITL PROPERTIES OF THE PERIPLASMIC MODA MOLYBDATE-BINDING PROTEIN REMARK 1 TITL 2 OF ESCHERICHIA COLI REMARK 1 REF J.BIOL.CHEM. V. 271 2557 1996 REMARK 1 REFN ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 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) (%) : 93.8 REMARK 3 NUMBER OF REFLECTIONS : 30630 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.83 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2304 REMARK 3 BIN R VALUE (WORKING SET) : 0.3830 REMARK 3 BIN FREE R VALUE : 0.4040 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1743 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 69 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.570 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.360 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1WOD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000177217. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : AUG-96 REMARK 200 TEMPERATURE (KELVIN) : 300 REMARK 200 PH : 4.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30630 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 61.2 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.26300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: SOLOMON, X-PLOR 3.851 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 27.5% PEG 8000, 0.1M SODIUM ACETATE, REMARK 280 PH 4.7, AND 2MM SODIUM TUNGSTATE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.34667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.17333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 27.17333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 54.34667 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 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 ASP A 1 REMARK 465 GLU A 2 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 LEU A 54 CA - CB - CG ANGL. DEV. = 14.6 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 ALA A 37 -178.01 -173.47 REMARK 500 LYS A 103 59.49 -116.63 REMARK 500 HIS A 122 -19.70 -155.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: TUN REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: TUNGSTATE BINDING SITE. REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE WO4 A 234 DBREF 1WOD A 1 233 UNP P37329 MODA_ECOLI 25 257 SEQRES 1 A 233 ASP GLU GLY LYS ILE THR VAL PHE ALA ALA ALA SER LEU SEQRES 2 A 233 THR ASN ALA MET GLN ASP ILE ALA THR GLN PHE LYS LYS SEQRES 3 A 233 GLU LYS GLY VAL ASP VAL VAL SER SER PHE ALA SER SER SEQRES 4 A 233 SER THR LEU ALA ARG GLN ILE GLU ALA GLY ALA PRO ALA SEQRES 5 A 233 ASP LEU PHE ILE SER ALA ASP GLN LYS TRP MET ASP TYR SEQRES 6 A 233 ALA VAL ASP LYS LYS ALA ILE ASP THR ALA THR ARG GLN SEQRES 7 A 233 THR LEU LEU GLY ASN SER LEU VAL VAL VAL ALA PRO LYS SEQRES 8 A 233 ALA SER VAL GLN LYS ASP PHE THR ILE ASP SER LYS THR SEQRES 9 A 233 ASN TRP THR SER LEU LEU ASN GLY GLY ARG LEU ALA VAL SEQRES 10 A 233 GLY ASP PRO GLU HIS VAL PRO ALA GLY ILE TYR ALA LYS SEQRES 11 A 233 GLU ALA LEU GLN LYS LEU GLY ALA TRP ASP THR LEU SER SEQRES 12 A 233 PRO LYS LEU ALA PRO ALA GLU ASP VAL ARG GLY ALA LEU SEQRES 13 A 233 ALA LEU VAL GLU ARG ASN GLU ALA PRO LEU GLY ILE VAL SEQRES 14 A 233 TYR GLY SER ASP ALA VAL ALA SER LYS GLY VAL LYS VAL SEQRES 15 A 233 VAL ALA THR PHE PRO GLU ASP SER HIS LYS LYS VAL GLU SEQRES 16 A 233 TYR PRO VAL ALA VAL VAL GLU GLY HIS ASN ASN ALA THR SEQRES 17 A 233 VAL LYS ALA PHE TYR ASP TYR LEU LYS GLY PRO GLN ALA SEQRES 18 A 233 ALA GLU ILE PHE LYS ARG TYR GLY PHE THR ILE LYS HET WO4 A 234 5 HETNAM WO4 TUNGSTATE(VI)ION FORMUL 2 WO4 O4 W 2- FORMUL 3 HOH *69(H2 O) HELIX 1 1 ALA A 11 LYS A 28 5 18 HELIX 2 2 SER A 39 ALA A 48 1 10 HELIX 3 3 GLN A 60 ASP A 68 1 9 HELIX 4 4 THR A 74 THR A 76 5 3 HELIX 5 5 TRP A 106 LEU A 110 1 5 HELIX 6 6 PRO A 124 LYS A 135 1 12 HELIX 7 7 TRP A 139 LYS A 145 1 7 HELIX 8 8 VAL A 152 GLU A 160 1 9 HELIX 9 9 GLY A 171 ALA A 176 1 6 HELIX 10 10 GLU A 188 SER A 190 5 3 HELIX 11 11 ALA A 207 LYS A 217 1 11 HELIX 12 12 PRO A 219 ARG A 227 1 9 SHEET 1 A 5 ASP A 31 ALA A 37 0 SHEET 2 A 5 LYS A 4 ALA A 10 1 N ILE A 5 O ASP A 31 SHEET 3 A 5 LEU A 54 ILE A 56 1 N LEU A 54 O PHE A 8 SHEET 4 A 5 GLU A 195 VAL A 200 -1 N ALA A 199 O PHE A 55 SHEET 5 A 5 GLN A 78 GLY A 82 -1 N LEU A 81 O TYR A 196 SHEET 1 B 3 GLY A 167 TYR A 170 0 SHEET 2 B 3 LEU A 85 PRO A 90 -1 N VAL A 88 O GLY A 167 SHEET 3 B 3 VAL A 180 THR A 185 -1 N ALA A 184 O VAL A 87 SHEET 1 C 2 LEU A 115 GLY A 118 0 SHEET 2 C 2 LEU A 146 ALA A 149 1 N ALA A 147 O LEU A 115 SITE 1 TUN 5 SER A 12 SER A 39 ALA A 125 VAL A 152 SITE 2 TUN 5 TYR A 170 SITE 1 AC1 11 ALA A 10 ALA A 11 SER A 12 SER A 39 SITE 2 AC1 11 ALA A 58 VAL A 123 PRO A 124 ALA A 125 SITE 3 AC1 11 ASP A 151 VAL A 152 TYR A 170 CRYST1 82.590 82.590 81.520 90.00 90.00 120.00 P 32 2 1 6 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 0.012108 0.006991 0.000000 0.00000 SCALE2 0.000000 0.013981 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012267 0.00000