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- PDB-1wod: CRYSTAL STRUCTURE OF MODA, A MOLYBDATE PROTEIN, COMPLEXED WITH TU... -

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Basic information

Entry
Database: PDB / ID: 1wod
TitleCRYSTAL STRUCTURE OF MODA, A MOLYBDATE PROTEIN, COMPLEXED WITH TUNGSTATE
ComponentsMODA
KeywordsTRANSPORT / MOLYBDATE TRANSPORT PROTEIN / MOLYBDATE / TUNGSTATE / PERIPLASMIC
Function / homology
Function and homology information


response to chromate / tungstate ion transport / ABC-type molybdate transporter activity / molybdate ion binding / tungstate binding / molybdate ion transport / molybdenum ion binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / membrane
Similarity search - Function
Molybdate ABC transporter, substrate-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TUNGSTATE(VI)ION / Molybdate-binding protein ModA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 1.75 Å
AuthorsHu, Y. / Rech, S. / Gunsalus, R.P. / Rees, D.C.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: Crystal structure of the molybdate binding protein ModA.
Authors: Hu, Y. / Rech, S. / Gunsalus, R.P. / Rees, D.C.
#1: Journal: J.Biol.Chem. / Year: 1996
Title: Properties of the Periplasmic Moda Molybdate-Binding Protein of Escherichia Coli
Authors: Rech, S. / Wolin, C. / Gunsalus, R.P.
History
DepositionJun 17, 1997Processing site: BNL
Revision 1.0Dec 17, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: MODA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1962
Polymers24,9481
Non-polymers2481
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.590, 82.590, 81.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein MODA


Mass: 24948.264 Da / Num. of mol.: 1 / Fragment: N-DOMAIN, C-DOMAIN / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Cellular location: PERIPLASM / References: UniProt: P37329
#2: Chemical ChemComp-WO4 / TUNGSTATE(VI)ION


Mass: 247.838 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: WO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 3.1 Å3/Da / Density % sol: 61.75 %
Crystal growpH: 4.7
Details: 27.5% PEG 8000, 0.1M SODIUM ACETATE, PH 4.7, AND 2MM SODIUM TUNGSTATE
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
250 mMTris-HCl1drop
32.2 mM1reservoiror Na2WO4Na2MoO4
427.5 %PEG80001reservoir
50.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Aug 1, 1996 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→40 Å / Num. obs: 30630 / % possible obs: 93.8 % / Redundancy: 4.1 % / Biso Wilson estimate: 24.7 Å2 / Rsym value: 0.065 / Net I/σ(I): 21
Reflection shellResolution: 1.75→1.83 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2 / Rsym value: 0.263 / % possible all: 61.2
Reflection
*PLUS
Num. measured all: 124197 / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 61.2 % / Rmerge(I) obs: 26.3

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Processing

Software
NameVersionClassification
SOLOMONphasing
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.75→40 Å
RfactorNum. reflection% reflectionSelection details
Rfree0.187 -5 %RANDOM
Rwork0.163 ---
obs0.163 30630 93.8 %-
Displacement parametersBiso mean: 28.7 Å2
Refinement stepCycle: LAST / Resolution: 1.75→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1743 0 5 69 1817
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.57
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.36
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.75→1.83 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.404 -5 %
Rwork0.383 2304 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.36
LS refinement shell
*PLUS
Rfactor obs: 0.383

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