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- PDB-1fr3: THE HIGH RESOLUTION STRUCTURE OF A MOLYBDATE BINDING PROTEIN FROM... -

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Basic information

Entry
Database: PDB / ID: 1fr3
TitleTHE HIGH RESOLUTION STRUCTURE OF A MOLYBDATE BINDING PROTEIN FROM SPOROMUSA OVATA
ComponentsMOLYBDATE/TUNGSTATE BINDING PROTEIN
KeywordsMETAL BINDING PROTEIN / molybdate / tungstate / molybdate homeostasis
Function / homology
Function and homology information


molybdate ion transport
Similarity search - Function
Molybdenum-pterin binding domain / Transport-associated OB, type 1 / TOBE domain / Molybdate/tungstate binding, C-terminal / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
TUNGSTATE(VI)ION / Metal binding protein
Similarity search - Component
Biological speciesSporomusa ovata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsWagner, U.G. / Stupperich, E. / Kratky, C.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Structure of the molybdate/tungstate binding protein mop from Sporomusa ovata.
Authors: Wagner, U.G. / Stupperich, E. / Kratky, C.
History
DepositionSep 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MOLYBDATE/TUNGSTATE BINDING PROTEIN
B: MOLYBDATE/TUNGSTATE BINDING PROTEIN
C: MOLYBDATE/TUNGSTATE BINDING PROTEIN
D: MOLYBDATE/TUNGSTATE BINDING PROTEIN
E: MOLYBDATE/TUNGSTATE BINDING PROTEIN
F: MOLYBDATE/TUNGSTATE BINDING PROTEIN
G: MOLYBDATE/TUNGSTATE BINDING PROTEIN
H: MOLYBDATE/TUNGSTATE BINDING PROTEIN
I: MOLYBDATE/TUNGSTATE BINDING PROTEIN
J: MOLYBDATE/TUNGSTATE BINDING PROTEIN
K: MOLYBDATE/TUNGSTATE BINDING PROTEIN
L: MOLYBDATE/TUNGSTATE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,37228
Polymers86,40712
Non-polymers3,96516
Water6,846380
1
A: MOLYBDATE/TUNGSTATE BINDING PROTEIN
B: MOLYBDATE/TUNGSTATE BINDING PROTEIN
C: MOLYBDATE/TUNGSTATE BINDING PROTEIN
D: MOLYBDATE/TUNGSTATE BINDING PROTEIN
E: MOLYBDATE/TUNGSTATE BINDING PROTEIN
F: MOLYBDATE/TUNGSTATE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,18614
Polymers43,2036
Non-polymers1,9838
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21000 Å2
ΔGint-139 kcal/mol
Surface area12830 Å2
MethodPISA
2
G: MOLYBDATE/TUNGSTATE BINDING PROTEIN
H: MOLYBDATE/TUNGSTATE BINDING PROTEIN
I: MOLYBDATE/TUNGSTATE BINDING PROTEIN
J: MOLYBDATE/TUNGSTATE BINDING PROTEIN
K: MOLYBDATE/TUNGSTATE BINDING PROTEIN
L: MOLYBDATE/TUNGSTATE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,18614
Polymers43,2036
Non-polymers1,9838
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20940 Å2
ΔGint-133 kcal/mol
Surface area12970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.724, 138.328, 110.368
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a hexamer formed by chain A,B,C,D,E,F and symmetry related by one triad and three diads

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Components

#1: Protein
MOLYBDATE/TUNGSTATE BINDING PROTEIN / MOP


Mass: 7200.582 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Sporomusa ovata (bacteria) / References: UniProt: Q7SIF7
#2: Chemical
ChemComp-WO4 / TUNGSTATE(VI)ION


Mass: 247.838 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: WO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.24 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Temperature: 22 ℃ / Details: Wagner, U.G., (1994) J.Mol. Biol., 236, 388.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
215 %(w/v)PEG80001drop
30.05 MTris-HCl1drop
40.001 mM1dropMoO4
50.001 mM1dropWO4
630 %(w/v)PEG80001reservoir
70.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 9, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. all: 131014 / Num. obs: 129178 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 7.9 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 4.2
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.282 / Num. unique all: 6126 / % possible all: 92.3

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Processing

Software
NameClassification
CNSrefinement
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 1.5→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.198 6639 random
Rwork0.185 --
all-129320 -
obs-129320 -
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6000 0 80 380 6460
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.006
X-RAY DIFFRACTIONp_angle_d1.6

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