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- PDB-6guj: Molybdenum storage protein with two occupied ATP binding sites -

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Basic information

Entry
Database: PDB / ID: 6guj
TitleMolybdenum storage protein with two occupied ATP binding sites
Components(Molybdenum storage protein subunit ...) x 2
KeywordsMETAL BINDING PROTEIN / Molybdenum storage / polyoxomolybdate clusters / 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
Chem-8M0 / ADENOSINE-5'-TRIPHOSPHATE / MOLYBDENUM ATOM / MOLYBDATE 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: 2.102 Å
AuthorsErmler, U. / Poppe, J. / Bruenle, S.
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

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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)61,79415
Polymers57,4932
Non-polymers4,30113
Water6,053336
1
B: Molybdenum storage protein subunit beta
A: Molybdenum storage protein subunit alpha
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)370,76690
Polymers344,95912
Non-polymers25,80778
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
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
11B-305-

MO

21A-307-

MO

31A-415-

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 , 6 types, 349 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-MO / MOLYBDENUM ATOM


Mass: 95.940 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mo
#6: Chemical ChemComp-MG / MAGNESIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 336 / 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: 3.9 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: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2012
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 53819 / % possible obs: 99.2 % / Redundancy: 4.4 % / Rsym value: 0.1 / Net I/σ(I): 13.7
Reflection shellResolution: 2.1→2.2 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: 2.102→48.771 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.42
RfactorNum. reflection% reflection
Rfree0.2137 2732 5.08 %
Rwork0.1787 --
obs0.1804 53814 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.102→48.771 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3809 0 144 336 4289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064123
X-RAY DIFFRACTIONf_angle_d1.2625808
X-RAY DIFFRACTIONf_dihedral_angle_d8.1523326
X-RAY DIFFRACTIONf_chiral_restr0.053646
X-RAY DIFFRACTIONf_plane_restr0.005715
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1016-2.13790.39331170.27912515X-RAY DIFFRACTION99
2.1379-2.17670.28711560.24062503X-RAY DIFFRACTION100
2.1767-2.21860.30241370.22892509X-RAY DIFFRACTION100
2.2186-2.26390.25221350.2212508X-RAY DIFFRACTION100
2.2639-2.31310.28171510.21362508X-RAY DIFFRACTION100
2.3131-2.36690.20981150.2032533X-RAY DIFFRACTION100
2.3669-2.42610.25731360.19392528X-RAY DIFFRACTION100
2.4261-2.49170.22371460.20122520X-RAY DIFFRACTION100
2.4917-2.5650.23031390.19062553X-RAY DIFFRACTION100
2.565-2.64780.21941300.17982513X-RAY DIFFRACTION99
2.6478-2.74240.22221300.18532560X-RAY DIFFRACTION99
2.7424-2.85220.21111310.17622528X-RAY DIFFRACTION99
2.8522-2.9820.21091370.16832552X-RAY DIFFRACTION99
2.982-3.13920.17751410.16662546X-RAY DIFFRACTION100
3.1392-3.33590.18551210.16262574X-RAY DIFFRACTION99
3.3359-3.59330.17391370.15252582X-RAY DIFFRACTION99
3.5933-3.95480.17841270.14332586X-RAY DIFFRACTION99
3.9548-4.52670.17211570.13462561X-RAY DIFFRACTION98
4.5267-5.70180.19551580.15932622X-RAY DIFFRACTION99
5.7018-48.78420.24631310.21462781X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 41.3166 Å / Origin y: 19.1953 Å / Origin z: 28.3767 Å
111213212223313233
T0.1759 Å2-0.0203 Å2-0.0167 Å2-0.1803 Å2-0.0144 Å2--0.1897 Å2
L0.3106 °2-0.1172 °2-0.1657 °2-0.4402 °20.2241 °2--0.8078 °2
S0.0002 Å °0.0613 Å °-0.072 Å °-0.0782 Å °-0.0272 Å °0.0755 Å °0.0957 Å °-0.1615 Å °0.0348 Å °
Refinement TLS groupSelection details: all

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