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- PDB-1h9k: Two crystal structures of the cytoplasmic molybdate-binding prote... -

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Basic information

Entry
Database: PDB / ID: 1h9k
TitleTwo crystal structures of the cytoplasmic molybdate-binding protein ModG suggest a novel cooperative binding mechanism and provide insights into ligand-binding specificity. Phosphate-grown form with tungstate and phosphate bound
ComponentsMOLYBDENUM-BINDING-PROTEIN
KeywordsBINDING PROTEIN / MOLYBDATE HOMEOSTASIS
Function / homology
Function and homology information


molybdate ion transport / protein-containing complex
Similarity search - Function
Molybdenum-pterin binding domain / Mop domain profile. / 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
PHOSPHATE ION / TUNGSTATE(VI)ION / Potential molybdenum-pterin-binding-protein
Similarity search - Component
Biological speciesAZOTOBACTER VINELANDII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsDelarbre, L. / Stevenson, C.E.M. / White, D.J. / Mitchenall, L.A. / Pau, R.N. / Lawson, D.M.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Two Crystal Structures of the Cytoplasmic Molybdate-Binding Protein Modg Suggest a Novel Cooperative Binding Mechanism and Provide Insights Into Ligand-Binding Specificity
Authors: Delarbre, L. / Stevenson, C.E.M. / White, D.J. / Mitchenall, L.A. / Pau, R.N. / Lawson, D.M.
History
DepositionMar 13, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MOLYBDENUM-BINDING-PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3415
Polymers14,6551
Non-polymers6864
Water1,09961
1
A: MOLYBDENUM-BINDING-PROTEIN
hetero molecules

A: MOLYBDENUM-BINDING-PROTEIN
hetero molecules

A: MOLYBDENUM-BINDING-PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,02215
Polymers43,9653
Non-polymers2,05712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.685, 50.685, 79.112
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-1142-

WO4

21A-1142-

WO4

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Components

#1: Protein MOLYBDENUM-BINDING-PROTEIN / MODG


Mass: 14654.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AZOTOBACTER VINELANDII (bacteria) / Strain: E162 / Cellular location: CYTOPLASM / Gene: MODG / Gene (production host): MODG / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q44529
#2: Chemical ChemComp-WO4 / TUNGSTATE(VI)ION


Mass: 247.838 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: WO4
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 1.34 Å3/Da / Density % sol: 40 %
Crystal growMethod: vapor diffusion / pH: 8.5
Details: VAPOUR DIFFUSION. 75% SATURATED KH2PO4 IN 100MM TRIS-HCL PH8.5 WITH 2MM NA2WO4., pH 8.50
Crystal grow
*PLUS
Method: vapor diffusion / pH: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
175 %sat1reservoirKH2PO4
2100 mMTris-HCl1reservoirpH8.5
32 mM1reservoirNa2WO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.947
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.947 Å / Relative weight: 1
ReflectionResolution: 1.8→44 Å / Num. obs: 10860 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 5.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 2.7 / % possible all: 95.6
Reflection shell
*PLUS
% possible obs: 95.6 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.133
RfactorNum. reflection% reflectionSelection details
Rfree0.227 538 5 %RANDOM
Rwork0.186 ---
obs-10860 98.9 %-
Displacement parametersBiso mean: 19 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms994 0 18 61 1073
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0340.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.040.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.5793
X-RAY DIFFRACTIONp_mcangle_it3.8095
X-RAY DIFFRACTIONp_scbond_it5.0986
X-RAY DIFFRACTIONp_scangle_it7.0678
X-RAY DIFFRACTIONp_plane_restr0.02130.03
X-RAY DIFFRACTIONp_chiral_restr0.1340.15
X-RAY DIFFRACTIONp_singtor_nbd0.1770.3
X-RAY DIFFRACTIONp_multtor_nbd0.2710.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.150.3
X-RAY DIFFRACTIONp_planar_tor3.67
X-RAY DIFFRACTIONp_staggered_tor13.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor46.520
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19 Å2

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