HEADER BINDING PROTEIN 14-AUG-97 1ATG TITLE AZOTOBACTER VINELANDII PERIPLASMIC MOLYBDATE-BINDING PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PERIPLASMIC MOLYBDATE-BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MODA SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AZOTOBACTER VINELANDII; SOURCE 3 ORGANISM_TAXID: 354; SOURCE 4 STRAIN: RP2; SOURCE 5 CELLULAR_LOCATION: PERIPLASM KEYWDS MOLYBDATE, TUNGSTATE, BINDING PROTEIN, PERIPLASM, ABC TRANSPORTER EXPDTA X-RAY DIFFRACTION AUTHOR D.M.LAWSON,R.N.PAU,C.E.M.WILLIAMS,L.A.MITCHENALL REVDAT 3 07-FEB-24 1ATG 1 REMARK REVDAT 2 24-FEB-09 1ATG 1 VERSN REVDAT 1 14-OCT-98 1ATG 0 JRNL AUTH D.M.LAWSON,C.E.WILLIAMS,L.A.MITCHENALL,R.N.PAU JRNL TITL LIGAND SIZE IS A MAJOR DETERMINANT OF SPECIFICITY IN JRNL TITL 2 PERIPLASMIC OXYANION-BINDING PROTEINS: THE 1.2 A RESOLUTION JRNL TITL 3 CRYSTAL STRUCTURE OF AZOTOBACTER VINELANDII MODA. JRNL REF STRUCTURE V. 6 1529 1998 JRNL REFN ISSN 0969-2126 JRNL PMID 9862806 JRNL DOI 10.1016/S0969-2126(98)00151-8 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.M.LAWSON,C.E.M.WILLIAMS,D.J.WHITE,A.P.CHOAY, REMARK 1 AUTH 2 L.A.MITCHENALL,R.N.PAU REMARK 1 TITL PROTEIN LIGANDS FOR MOLYBDATE. SPECIFICITY AND CHARGE REMARK 1 TITL 2 STABILISATION AT THE ANION-BINDING SITES OF PERIPLASMIC AND REMARK 1 TITL 3 INTRACELLULAR MOLYBDATE-BINDING PROTEINS OF AZOTOBACTER REMARK 1 TITL 4 VINELANDII REMARK 1 REF J.CHEM.SOC.,DALTON TRANS. 3981 1997 REMARK 1 REFN ISSN 0300-9246 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 74061 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) : NULL REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3730 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1721 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 355 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.007 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.020 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.026 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.225 ; 0.030 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.080 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.165 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.246 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : 0.148 ; 0.300 REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 4.000 ; 7.000 REMARK 3 STAGGERED (DEGREES) : 13.800; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 23.700; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.164 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.627 ; 2.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.304 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.171 ; 4.500 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: LUZZATI ESD BASED ON TEST REFLECTIONS REMARK 3 ONLY. PLANE RESTRAINT RMS BASED ON NON-AROMATIC PLANAR GROUPS REMARK 3 ONLY. REMARK 4 REMARK 4 1ATG 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_1000171236. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : SEP-96 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0-7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9116 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 74061 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.16100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SINGLE ISOMORPHOUS REMARK 200 REPLACEMENT WITH ANOMALOUS SCATTERING REMARK 200 SOFTWARE USED: CCP4 (MLPHARE, DM, OTHERS) REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HANGING DROP VAPOUR DIFFUSION WITH REMARK 280 PROTEIN CONCENTRATION IN THE RANGE 10-15 MG/ML IN 10MM TRIS-HCL REMARK 280 PH 7.0. 1 OR 2 MICROLITER DROPS OF THE LATTER WERE MIXED WITH AN REMARK 280 EQUAL VOLUME OF 11-14% (W/V) PEG 4000 AND 0.4M AMMONIUM SULFATE REMARK 280 IN 0.1M ACETATE BUFFER AT PH 4.0, AND THEN EQUILIBRATED AGAINST REMARK 280 THIS SOLUTION AT 18 DEG C. CRYOPROTECTED USING THE SAME SOLUTION REMARK 280 CONTAINING 25% (V/V) ETHYLENE GLYCOL., VAPOR DIFFUSION - HANGING REMARK 280 DROP, TEMPERATURE 291K, VAPOR DIFFUSION, HANGING DROP 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 44.40100 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 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 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 2 CG CD OE1 OE2 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 649 O HOH A 650 2.14 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 ARG A 106 -74.59 -96.01 REMARK 500 ALA A 174 11.40 93.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: MOB REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: ANION-BINDING POCKET LOCATED AT THE INTERFACE REMARK 800 BETWEEN THE 2 DOMAINS OF THE PROTEIN. BINDS BOTH MOLYBDATE AND REMARK 800 TUNGSTATE. REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE WO4 A 250 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 451 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 402 DBREF 1ATG A 2 232 UNP Q7SIH2 Q7SIH2_AZOVI 1 231 SEQRES 1 A 231 GLU LEU LYS VAL VAL THR ALA THR ASN PHE LEU GLY THR SEQRES 2 A 231 LEU GLU GLN LEU ALA GLY GLN PHE ALA LYS GLN THR GLY SEQRES 3 A 231 HIS ALA VAL VAL ILE SER SER GLY SER SER GLY PRO VAL SEQRES 4 A 231 TYR ALA GLN ILE VAL ASN GLY ALA PRO TYR ASN VAL PHE SEQRES 5 A 231 PHE SER ALA ASP GLU LYS SER PRO GLU LYS LEU ASP ASN SEQRES 6 A 231 GLN GLY PHE ALA LEU PRO GLY SER ARG PHE THR TYR ALA SEQRES 7 A 231 ILE GLY LYS LEU VAL LEU TRP SER ALA LYS PRO GLY LEU SEQRES 8 A 231 VAL ASP ASN GLN GLY LYS VAL LEU ALA GLY ASN GLY TRP SEQRES 9 A 231 ARG HIS ILE ALA ILE SER ASN PRO GLN ILE ALA PRO TYR SEQRES 10 A 231 GLY LEU ALA GLY THR GLN VAL LEU THR HIS LEU GLY LEU SEQRES 11 A 231 LEU ASP LYS LEU THR ALA GLN GLU ARG ILE VAL GLU ALA SEQRES 12 A 231 ASN SER VAL GLY GLN ALA HIS SER GLN THR ALA SER GLY SEQRES 13 A 231 ALA ALA ASP LEU GLY PHE VAL ALA LEU ALA GLN ILE ILE SEQRES 14 A 231 GLN ALA ALA ALA LYS ILE PRO GLY SER HIS TRP PHE PRO SEQRES 15 A 231 PRO ALA ASN TYR TYR GLU PRO ILE VAL GLN GLN ALA VAL SEQRES 16 A 231 ILE THR LYS SER THR ALA GLU LYS ALA ASN ALA GLU GLN SEQRES 17 A 231 PHE MET SER TRP MET LYS GLY PRO LYS ALA VAL ALA ILE SEQRES 18 A 231 ILE LYS ALA ALA GLY TYR VAL LEU PRO GLN HET WO4 A 250 5 HET ACT A 301 4 HET SO4 A 451 5 HET EDO A 401 4 HET EDO A 402 4 HETNAM WO4 TUNGSTATE(VI)ION HETNAM ACT ACETATE ION HETNAM SO4 SULFATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 WO4 O4 W 2- FORMUL 3 ACT C2 H3 O2 1- FORMUL 4 SO4 O4 S 2- FORMUL 5 EDO 2(C2 H6 O2) FORMUL 7 HOH *355(H2 O) HELIX 1 1 THR A 9 THR A 26 5 18 HELIX 2 2 SER A 37 VAL A 45 1 9 HELIX 3 3 LYS A 59 ASN A 66 1 8 HELIX 4 4 LYS A 98 ALA A 101 5 4 HELIX 5 5 PRO A 117 LEU A 129 1 13 HELIX 6 6 LEU A 132 ALA A 137 1 6 HELIX 7 7 VAL A 147 ALA A 155 1 9 HELIX 8 8 LEU A 166 GLN A 168 5 3 HELIX 9 9 LYS A 204 LYS A 215 1 12 HELIX 10 10 PRO A 217 ALA A 225 1 9 SHEET 1 A 5 VAL A 30 GLY A 35 0 SHEET 2 A 5 LEU A 3 ALA A 8 1 N LEU A 3 O VAL A 31 SHEET 3 A 5 VAL A 52 PHE A 54 1 N VAL A 52 O VAL A 6 SHEET 4 A 5 VAL A 192 ILE A 197 -1 N VAL A 196 O PHE A 53 SHEET 5 A 5 PHE A 76 ILE A 80 -1 N ALA A 79 O GLN A 193 SHEET 1 B 3 GLY A 162 ALA A 165 0 SHEET 2 B 3 LEU A 83 SER A 87 -1 N TRP A 86 O GLY A 162 SHEET 3 B 3 SER A 179 TRP A 181 -1 N TRP A 181 O LEU A 85 SHEET 1 C 2 ILE A 108 SER A 111 0 SHEET 2 C 2 ILE A 141 ALA A 144 1 N VAL A 142 O ILE A 108 SITE 1 MOB 5 THR A 9 ASN A 10 SER A 37 TYR A 118 SITE 2 MOB 5 VAL A 147 SITE 1 AC1 11 ALA A 8 THR A 9 ASN A 10 SER A 36 SITE 2 AC1 11 SER A 37 ALA A 56 ALA A 116 PRO A 117 SITE 3 AC1 11 TYR A 118 SER A 146 VAL A 147 SITE 1 AC2 7 ARG A 106 HIS A 107 GLY A 157 ALA A 158 SITE 2 AC2 7 ALA A 159 ASP A 160 GLU A 189 SITE 1 AC3 6 ARG A 75 GLN A 149 SER A 152 GLN A 153 SITE 2 AC3 6 GLN A 194 HOH A 702 SITE 1 AC4 5 GLN A 17 ILE A 170 GLN A 171 ALA A 225 SITE 2 AC4 5 HOH A 700 SITE 1 AC5 3 SER A 34 GLN A 43 TYR A 50 CRYST1 32.934 88.802 41.746 90.00 93.55 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 0.030364 0.000000 0.001884 0.00000 SCALE2 0.000000 0.011261 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024000 0.00000