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- PDB-6h8h: Molybdenum storage protein - in a recombinant and in vivo-like form -

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Basic information

Entry
Database: PDB / ID: 6h8h
TitleMolybdenum storage protein - in a recombinant and in vivo-like form
Components(Molybdenum storage protein subunit ...) x 2
KeywordsMETAL BINDING PROTEIN / polyoxomolybdate cluster / molybdenum storage protein / bionanolab
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
Chem-8M0 / ADENOSINE-5'-TRIPHOSPHATE / Mo5 Cluster / Mo14O47 cluster / bis(mu2-oxo)-octaoxo-dimolybdenum (VI) / MOLYBDATE ION / 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: 1.901 Å
AuthorsErmler, U. / Bruenle, S.
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
DepositionAug 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_CC_half / _reflns.pdbx_Rsym_value ..._reflns.pdbx_CC_half / _reflns.pdbx_Rsym_value / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rsym_value
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)64,17012
Polymers57,4932
Non-polymers6,67610
Water4,450247
1
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)192,50936
Polymers172,4796
Non-polymers20,02930
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 area33210 Å2
ΔGint-274 kcal/mol
Surface area47810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.100, 117.100, 235.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11B-303-

GX2

21B-303-

GX2

31B-303-

GX2

41B-303-

GX2

51A-304-

MOO

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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 (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 (bacteria) / Gene: mosA, Avin_43200 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P84308

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Non-polymers , 9 types, 257 molecules

#3: Chemical ChemComp-8M0 / bis(mu4-oxo)-tetrakis(mu3-oxo)-hexakis(mu2-oxo)-hexadecaoxo-octamolybdenum (VI) / Octamolybdate [Mo(VI)8O28]8-


Mass: 1215.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mo8O28
#4: Chemical ChemComp-FUQ / Mo5 Cluster


Mass: 899.844 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H20Mo5O25
#5: Chemical ChemComp-GX2 / Mo14O47 cluster


Mass: 2112.267 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H17Mo14O47
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: 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
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-MOO / MOLYBDATE ION / MOLYBDATE


Mass: 159.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: MoO4
#10: Chemical ChemComp-M27 / bis(mu2-oxo)-octaoxo-dimolybdenum (VI) / dimolybdate [Mo(VI)2O10]8-


Mass: 351.874 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mo2O10
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 4.06 Å3/Da / Density % sol: 69.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1 M sodium citrate, 1 M NH4H2PO4, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 141946 / % possible obs: 99.3 % / Redundancy: 6.9 % / CC1/2: 0.997 / Rsym value: 0.1 / Net I/σ(I): 11.5
Reflection shellResolution: 1.9→2 Å / CC1/2: 0.735 / Rsym value: 1.276

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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: 4NDO

4ndo


Resolution: 1.901→46.942 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.07 / Phase error: 22.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.221 7159 5.06 %
Rwork0.206 --
obs0.2068 141489 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.901→46.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3800 0 183 245 4228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064122
X-RAY DIFFRACTIONf_angle_d2.5085851
X-RAY DIFFRACTIONf_dihedral_angle_d14.2782430
X-RAY DIFFRACTIONf_chiral_restr0.044634
X-RAY DIFFRACTIONf_plane_restr0.004705
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9011-1.92270.33982520.34644363X-RAY DIFFRACTION97
1.9227-1.94530.34232250.31924527X-RAY DIFFRACTION100
1.9453-1.9690.30622420.29324462X-RAY DIFFRACTION100
1.969-1.9940.28182550.28354497X-RAY DIFFRACTION100
1.994-2.02020.26812360.27764499X-RAY DIFFRACTION100
2.0202-2.04790.28622280.26664522X-RAY DIFFRACTION100
2.0479-2.07710.28782710.2634409X-RAY DIFFRACTION100
2.0771-2.10810.26742290.24384526X-RAY DIFFRACTION100
2.1081-2.14110.26432470.22924484X-RAY DIFFRACTION100
2.1411-2.17620.23782490.22194503X-RAY DIFFRACTION100
2.1762-2.21370.23222380.21394512X-RAY DIFFRACTION100
2.2137-2.25390.20522370.20844476X-RAY DIFFRACTION100
2.2539-2.29730.22832640.20824447X-RAY DIFFRACTION100
2.2973-2.34420.21892660.20664501X-RAY DIFFRACTION100
2.3442-2.39520.2112600.19384446X-RAY DIFFRACTION100
2.3952-2.45090.21572300.20854490X-RAY DIFFRACTION100
2.4509-2.51220.22372210.21644517X-RAY DIFFRACTION100
2.5122-2.58010.27392360.20844498X-RAY DIFFRACTION100
2.5801-2.6560.21772200.19274527X-RAY DIFFRACTION100
2.656-2.74170.21722490.20714475X-RAY DIFFRACTION100
2.7417-2.83970.21372260.20374483X-RAY DIFFRACTION100
2.8397-2.95340.25072420.20774470X-RAY DIFFRACTION100
2.9534-3.08780.22892580.20574477X-RAY DIFFRACTION100
3.0878-3.25050.22632420.21424469X-RAY DIFFRACTION99
3.2505-3.45410.23892320.20284470X-RAY DIFFRACTION99
3.4541-3.72070.1812350.18114437X-RAY DIFFRACTION99
3.7207-4.09490.20042210.17144494X-RAY DIFFRACTION99
4.0949-4.6870.15681980.15854510X-RAY DIFFRACTION99
4.687-5.90330.17912400.17844398X-RAY DIFFRACTION98
5.9033-46.95590.24982100.24824441X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 42.543 Å / Origin y: 19.9155 Å / Origin z: 28.1741 Å
111213212223313233
T0.1983 Å2-0.0376 Å2-0.0285 Å2-0.1866 Å20.0003 Å2--0.217 Å2
L0.8477 °2-0.5378 °2-0.652 °2-0.8845 °20.7986 °2--1.9743 °2
S-0.0104 Å °0.1307 Å °-0.1342 Å °-0.0979 Å °-0.042 Å °0.1454 Å °0.1056 Å °-0.2116 Å °0.0456 Å °
Refinement TLS groupSelection details: all

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