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- PDB-6gwb: Molybdenum storage protein without polyoxomolybdate clusters -

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Basic information

Entry
Database: PDB / ID: 6gwb
TitleMolybdenum storage protein without polyoxomolybdate clusters
Components(Molybdenum storage protein subunit ...) x 2
KeywordsMETAL BINDING PROTEIN / molybdate storage / polyoxometalate binding / ATP
Function / homology
Function and homology information


nutrient reservoir activity / molybdenum ion binding / cytoplasm
Similarity search - Function
Molybdenum storage protein subunit alpha/beta / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / Amino acid kinase family / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / Molybdenum storage protein subunit beta / Molybdenum storage protein subunit alpha
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsErmler, U.
CitationJournal: J. Inorg. Biochem. / Year: 2018
Title: The molybdenum storage protein - A bionanolab for creating experimentally alterable polyoxomolybdate clusters.
Authors: Brunle, S. / Poppe, J. / Hail, R. / Demmer, U. / Ermler, U.
History
DepositionJun 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Molybdenum storage protein subunit beta
A: Molybdenum storage protein subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,63011
Polymers57,4932
Non-polymers1,1379
Water6,107339
1
B: Molybdenum storage protein subunit beta
A: Molybdenum storage protein subunit alpha
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)351,78066
Polymers344,95912
Non-polymers6,82154
Water21612
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
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
2
B: Molybdenum storage protein subunit beta
A: Molybdenum storage protein subunit alpha
hetero molecules

B: Molybdenum storage protein subunit beta
A: Molybdenum storage protein subunit alpha
hetero molecules

B: Molybdenum storage protein subunit beta
A: Molybdenum storage protein subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,89033
Polymers172,4796
Non-polymers3,41027
Water1086
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
Buried area33860 Å2
ΔGint-378 kcal/mol
Surface area48220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.400, 115.400, 234.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

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Molybdenum storage protein subunit ... , 2 types, 2 molecules BA

#1: Protein Molybdenum storage protein subunit beta / MoSto subunit beta


Mass: 28247.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (strain DJ / ATCC BAA-1303) (bacteria)
Gene: mosB, Avin_43210 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P84253
#2: Protein Molybdenum storage protein subunit alpha / Mo storage protein subunit alpha / MoSto subunit alpha


Mass: 29245.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (strain DJ / ATCC BAA-1303) (bacteria)
Gene: mosA, Avin_43200 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P84308

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Non-polymers , 5 types, 348 molecules

#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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

Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 5.6
Details: 0.1 M sodium citrate, 1 M ammonium phosphate, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 73302 / % possible obs: 98.7 % / Redundancy: 4.2 % / Rsym value: 0.071 / Net I/σ(I): 12.9
Reflection shellResolution: 1.7→1.8 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F6T

4f6t


Resolution: 1.9→46.422 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.186 3565 4.93 %
Rwork0.1621 --
obs0.1633 72286 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→46.422 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3809 0 65 337 4211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.023986
X-RAY DIFFRACTIONf_angle_d1.5045444
X-RAY DIFFRACTIONf_dihedral_angle_d7.5033257
X-RAY DIFFRACTIONf_chiral_restr0.114634
X-RAY DIFFRACTIONf_plane_restr0.009707
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8998-1.92580.29361280.22952754X-RAY DIFFRACTION99
1.9258-1.95340.23131220.22312726X-RAY DIFFRACTION99
1.9534-1.98250.25761500.20082708X-RAY DIFFRACTION99
1.9825-2.01350.22141180.19532725X-RAY DIFFRACTION99
2.0135-2.04650.18261340.18372707X-RAY DIFFRACTION99
2.0465-2.08180.21391550.17992715X-RAY DIFFRACTION99
2.0818-2.11970.24241470.17872681X-RAY DIFFRACTION99
2.1197-2.16040.19941430.16682677X-RAY DIFFRACTION97
2.1604-2.20450.1751210.16282682X-RAY DIFFRACTION98
2.2045-2.25250.2131540.15672744X-RAY DIFFRACTION99
2.2525-2.30480.19511460.15722730X-RAY DIFFRACTION100
2.3048-2.36250.19241430.15452738X-RAY DIFFRACTION99
2.3625-2.42640.18481230.15552744X-RAY DIFFRACTION99
2.4264-2.49770.20711510.16512753X-RAY DIFFRACTION99
2.4977-2.57840.19541440.15922724X-RAY DIFFRACTION99
2.5784-2.67050.17531430.16182753X-RAY DIFFRACTION99
2.6705-2.77740.19221520.16412735X-RAY DIFFRACTION99
2.7774-2.90380.21341390.16552746X-RAY DIFFRACTION98
2.9038-3.05690.1771630.16092693X-RAY DIFFRACTION97
3.0569-3.24830.18891470.16182720X-RAY DIFFRACTION97
3.2483-3.49910.18811410.1592802X-RAY DIFFRACTION99
3.4991-3.8510.15311580.14472777X-RAY DIFFRACTION98
3.851-4.40790.15031310.13582819X-RAY DIFFRACTION99
4.4079-5.55210.1611590.14682851X-RAY DIFFRACTION98
5.5521-46.43620.1871530.18233017X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 41.2679 Å / Origin y: 18.86 Å / Origin z: 28.4962 Å
111213212223313233
T0.1615 Å2-0.0222 Å2-0.0097 Å2-0.1548 Å2-0.0077 Å2--0.1841 Å2
L0.3439 °2-0.1156 °2-0.1684 °2-0.4402 °20.2529 °2--0.8814 °2
S-0.0158 Å °0.0447 Å °-0.0991 Å °-0.0443 Å °-0.0206 Å °0.1126 Å °0.1049 Å °-0.1419 Å °0.0456 Å °
Refinement TLS groupSelection details: all

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