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- PDB-6gu5: Mosto containing the core POM clusters -

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Basic information

Entry
Database: PDB / ID: 6gu5
TitleMosto containing the core POM clusters
Components(Molybdenum storage protein subunit ...) x 2
KeywordsMETAL BINDING PROTEIN / Molybdenum storage / polyoxometalate clusters / ATP binding
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 / MOLYBDATE ION / PHOSPHATE ION / Molybdenum storage protein subunit beta / Molybdenum storage protein subunit alpha
Similarity search - Component
Biological speciesAzotobacter vinelandii DJ (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsErmler, U. / Poppe, J. / Bruenle, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
Germany
CitationJournal: FEBS J. / Year: 2018
Title: The Molybdenum Storage Protein: A soluble ATP hydrolysis-dependent molybdate pump.
Authors: Poppe, J. / Brunle, S. / Hail, R. / Wiesemann, K. / Schneider, K. / Ermler, U.
History
DepositionJun 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 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
Revision 1.3Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact / struct_conn

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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)61,1938
Polymers57,4932
Non-polymers3,7006
Water6,774376
1
B: Molybdenum storage protein subunit beta
A: Molybdenum storage protein subunit alpha
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)367,16148
Polymers344,95912
Non-polymers22,20236
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)183,58024
Polymers172,4796
Non-polymers11,10118
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 area32790 Å2
ΔGint-212 kcal/mol
Surface area47230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.150, 115.150, 234.500
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
11A-409-

HOH

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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 natural source / Source: (natural) Azotobacter vinelandii DJ (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 natural source / Source: (natural) Azotobacter vinelandii DJ (bacteria) / References: UniProt: P84308

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Non-polymers , 5 types, 382 molecules

#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: 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
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-MOO / MOLYBDATE ION / MOLYBDATE


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


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 3.9 Å3/Da / Density % sol: 68.49 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 4.6
Details: 0.1 M sodium acetate, 1.1 M ammonium citrate, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 1, 2012
RadiationMonochromator: Si (111) / Protocol: 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: 72069 / % possible obs: 98.8 % / Redundancy: 4.1 % / Rsym value: 0.09 / Net I/σ(I): 12.5
Reflection shellResolution: 1.9→2 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4f6t

4f6t


Resolution: 1.9→41.078 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.95
RfactorNum. reflection% reflection
Rfree0.1917 3629 5.04 %
Rwork0.1712 --
obs0.1722 72066 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→41.078 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3809 0 142 376 4327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0194116
X-RAY DIFFRACTIONf_angle_d1.6885790
X-RAY DIFFRACTIONf_dihedral_angle_d14.8582468
X-RAY DIFFRACTIONf_chiral_restr0.101639
X-RAY DIFFRACTIONf_plane_restr0.009714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9250.29531290.2772599X-RAY DIFFRACTION99
1.925-1.95130.31591360.25592616X-RAY DIFFRACTION99
1.9513-1.97920.24961220.24052588X-RAY DIFFRACTION99
1.9792-2.00880.23661350.23912587X-RAY DIFFRACTION99
2.0088-2.04010.27481640.22112575X-RAY DIFFRACTION99
2.0401-2.07360.25181320.21452618X-RAY DIFFRACTION99
2.0736-2.10930.22891350.21072592X-RAY DIFFRACTION99
2.1093-2.14770.22431310.19892606X-RAY DIFFRACTION99
2.1477-2.1890.23631500.18662578X-RAY DIFFRACTION99
2.189-2.23370.23151270.17732611X-RAY DIFFRACTION99
2.2337-2.28230.1891470.17692557X-RAY DIFFRACTION98
2.2823-2.33530.20621330.17452579X-RAY DIFFRACTION98
2.3353-2.39370.20331440.15912598X-RAY DIFFRACTION99
2.3937-2.45840.20061410.16412601X-RAY DIFFRACTION99
2.4584-2.53080.16821340.16422616X-RAY DIFFRACTION99
2.5308-2.61250.20361500.15662626X-RAY DIFFRACTION99
2.6125-2.70580.17791620.15782571X-RAY DIFFRACTION99
2.7058-2.81410.18021180.1632648X-RAY DIFFRACTION99
2.8141-2.94220.20741370.16292642X-RAY DIFFRACTION99
2.9422-3.09720.17291310.15692651X-RAY DIFFRACTION99
3.0972-3.29120.17831240.15732663X-RAY DIFFRACTION98
3.2912-3.54520.17451490.14992646X-RAY DIFFRACTION99
3.5452-3.90170.15871690.14482674X-RAY DIFFRACTION99
3.9017-4.46570.15221430.13512713X-RAY DIFFRACTION99
4.4657-5.6240.16861430.16052760X-RAY DIFFRACTION99
5.624-41.08750.19941430.20382922X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 41.3635 Å / Origin y: 19.0449 Å / Origin z: 28.4616 Å
111213212223313233
T0.1454 Å2-0.0379 Å2-0.0174 Å2-0.1349 Å2-0.0088 Å2--0.1673 Å2
L0.5086 °2-0.3292 °2-0.4114 °2-0.6014 °20.5522 °2--1.5912 °2
S-0.0143 Å °0.072 Å °-0.1083 Å °-0.0603 Å °-0.0362 Å °0.1173 Å °0.1436 Å °-0.2129 Å °0.0452 Å °
Refinement TLS groupSelection details: all

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