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- PDB-1amf: CRYSTAL STRUCTURE OF MODA, A MOLYBDATE TRANSPORT PROTEIN, COMPLEX... -

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Basic information

Entry
Database: PDB / ID: 1amf
TitleCRYSTAL STRUCTURE OF MODA, A MOLYBDATE TRANSPORT PROTEIN, COMPLEXED WITH MOLYBDATE
ComponentsMOLYBDATE TRANSPORT PROTEIN MODA
KeywordsBINDING PROTEIN / MOLYBDATE TRANSPORT PROTEIN / MOLYBDATE / 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
MOLYBDATE 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 13, 1997Processing site: BNL
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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 / 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: MOLYBDATE TRANSPORT PROTEIN MODA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1082
Polymers24,9481
Non-polymers1601
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.570, 82.570, 81.510
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 MOLYBDATE TRANSPORT PROTEIN MODA


Mass: 24948.264 Da / Num. of mol.: 1 / Fragment: N-DOMAIN, C-DOMAIN / Source method: isolated from a natural source
Details: MOLYBDATE ANION IS SEQUESTERED BETWEEN N-AND C-DOMAINS
Source: (natural) Escherichia coli (E. coli) / Cellular location: PERIPLASMICPeriplasm / References: UniProt: P37329
#2: Chemical ChemComp-MOO / MOLYBDATE ION / MOLYBDATE / Molybdate


Mass: 159.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: MoO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 61.73 %
Crystal growpH: 4.7
Details: PROTEIN WAS CRYSTALLIZED FROM 27.5% PEG 8000, 0.1M SODIUM ACETATE, PH 4.7, AND 2MM SODIUM MOLYBDATE
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 mM1reservoiror Na2WO4Na2MoO4
427.5 %PEG80001reservoir
50.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Aug 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 30575 / % possible obs: 93.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 24.9 Å2 / Rsym value: 0.055 / Net I/σ(I): 21
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.244 / % possible all: 60.8
Reflection
*PLUS
Num. measured all: 112116 / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
% possible obs: 60.8 % / Rmerge(I) obs: 0.244

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Processing

Software
NameVersionClassification
SOLOMONphasing
X-PLOR4model building
X-PLOR4refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR4phasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.75→30 Å
RfactorNum. reflection% reflectionSelection details
Rfree0.203 -5 %RANDOM
Rwork0.161 ---
obs0.161 30575 93.2 %-
Displacement parametersBiso mean: 28.6 Å2
Refinement stepCycle: LAST / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1743 0 5 76 1824
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_d23.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.39
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 4 / 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_deg23.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.39

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