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- PDB-1h9m: Two crystal structures of the cytoplasmic molybdate-binding prote... -

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Basic information

Entry
Database: PDB / ID: 1h9m
TitleTwo crystal structures of the cytoplasmic molybdate-binding protein ModG suggest a novel cooperative binding mechanism and provide insights into ligand-binding specificity. PEG-grown form with molybdate bound
ComponentsMOLYBDENUM-BINDING-PROTEIN
KeywordsBINDING PROTEIN / MOLYBDATE HOMEOSTASIS
Function / homology
Function and homology information


molybdate ion transport / protein-containing complex
Similarity search - Function
Mop domain profile. / 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
MOLYBDATE ION / Potential molybdenum-pterin-binding-protein
Similarity search - Component
Biological speciesAZOTOBACTER VINELANDII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
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
B: MOLYBDENUM-BINDING-PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,58910
Polymers29,3102
Non-polymers1,2808
Water1,42379
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)45,88415
Polymers43,9653
Non-polymers1,91912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
MethodPQS
2
B: MOLYBDENUM-BINDING-PROTEIN
hetero molecules

B: MOLYBDENUM-BINDING-PROTEIN
hetero molecules

B: MOLYBDENUM-BINDING-PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,88415
Polymers43,9653
Non-polymers1,91912
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)81.960, 81.960, 93.417
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-1142-

MOO

21A-1142-

MOO

31A-1143-

MOO

41A-1143-

MOO

51B-1142-

MOO

61B-1142-

MOO

71B-1143-

MOO

81B-1143-

MOO

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.50232, 0.86468, -0.00062), (0.86468, 0.50232, 0.00259), (0.00255, 0.00076, -1)
Vector: 0.11845, -0.19583, 93.3504)
DetailsBIOMOLECULE

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Components

#1: Protein MOLYBDENUM-BINDING-PROTEIN / MODG


Mass: 14654.964 Da / Num. of mol.: 2
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-MOO / MOLYBDATE ION / MOLYBDATE / Molybdate


Mass: 159.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: MoO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 41 %
Crystal growMethod: vapor diffusion / pH: 7.5
Details: VAPOUR DIFFUSION. 20% PEG 4000, 5% ISOPROPANOL IN 100MM HEPES PH7.5 WITH 2MM NA2MOO4., pH 7.50
Crystal grow
*PLUS
Method: vapor diffusion / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 %(w/v)PEG40001reservoir
25 %(v/v)isopropanol1reservoir
3100 mMHEPES1reservoirpH7.5
42 mM1reservoirNa2MoO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.65→41 Å / Num. obs: 28231 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 12.4 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 41.7
Reflection shellResolution: 1.65→1.68 Å / Rmerge(I) obs: 0.107 / Mean I/σ(I) obs: 8.8 / % possible all: 100
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H9J

1h9j


Resolution: 1.65→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.108
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1385 5 %RANDOM
Rwork0.191 ---
obs-28231 98.7 %-
Displacement parametersBiso mean: 27 Å2
Refinement stepCycle: LAST / Resolution: 1.65→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1954 0 32 79 2065
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0260.02
X-RAY DIFFRACTIONp_angle_d0.0380.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0430.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it4.433
X-RAY DIFFRACTIONp_mcangle_it3.9675
X-RAY DIFFRACTIONp_scbond_it4.9956
X-RAY DIFFRACTIONp_scangle_it6.9188
X-RAY DIFFRACTIONp_plane_restr0.02330.03
X-RAY DIFFRACTIONp_chiral_restr0.1620.15
X-RAY DIFFRACTIONp_singtor_nbd0.180.3
X-RAY DIFFRACTIONp_multtor_nbd0.2650.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1310.3
X-RAY DIFFRACTIONp_planar_tor4.47
X-RAY DIFFRACTIONp_staggered_tor14.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor51.720
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS

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