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- PDB-6h73: Molybdenum storage protein - recombinantly produced and loaded wi... -

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Basic information

Entry
Database: PDB / ID: 6h73
TitleMolybdenum storage protein - recombinantly produced and loaded with molybdate under in vitro conditions
Components(Molybdenum storage protein subunit ...) x 2
KeywordsMETAL BINDING PROTEIN / polyoxometalate cluster assembly / 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 / Amino acid kinase family / Acetylglutamate kinase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Mo5 Cluster / Mo6 cluster / 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: 2.3 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
DepositionJul 30, 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)60,98312
Polymers57,4932
Non-polymers3,49010
Water1,56787
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)182,95036
Polymers172,4796
Non-polymers10,47030
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 area36650 Å2
ΔGint-312 kcal/mol
Surface area46160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.190, 115.190, 233.060
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-305-

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 , 7 types, 97 molecules

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


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


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-FUQ / Mo5 Cluster


Mass: 899.844 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H20Mo5O25
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-GUH / Mo6 cluster


Mass: 1011.783 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H20Mo6O26
#8: Chemical ChemComp-MOO / MOLYBDATE ION / MOLYBDATE / Molybdate


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


Mass: 18.015 Da / Num. of mol.: 87 / 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: 3.88 Å3/Da / Density % sol: 68.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M sodium citrate, pH 5.6, 1 M ammonium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.618 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.618 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 76855 / % possible obs: 100 % / Redundancy: 10.2 % / CC1/2: 0.992 / Rsym value: 0.195 / Net I/σ(I): 9
Reflection shellResolution: 2.3→2.4 Å / CC1/2: 0.634 / Rsym value: 1.708

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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: 2.3→42.23 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2325 3765 4.9 %
Rwork0.2113 --
obs0.2124 76845 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→42.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3809 0 152 85 4046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034054
X-RAY DIFFRACTIONf_angle_d1.8245614
X-RAY DIFFRACTIONf_dihedral_angle_d15.1822389
X-RAY DIFFRACTIONf_chiral_restr0.045633
X-RAY DIFFRACTIONf_plane_restr0.004702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32910.30531210.30072710X-RAY DIFFRACTION100
2.3291-2.35980.33521290.28622726X-RAY DIFFRACTION100
2.3598-2.39210.30791460.27722688X-RAY DIFFRACTION100
2.3921-2.42630.30361560.27942687X-RAY DIFFRACTION100
2.4263-2.46250.27871350.28312722X-RAY DIFFRACTION100
2.4625-2.50090.3132950.27412772X-RAY DIFFRACTION100
2.5009-2.54190.33741230.26642696X-RAY DIFFRACTION100
2.5419-2.58580.27731560.26222665X-RAY DIFFRACTION100
2.5858-2.63280.2981420.24832711X-RAY DIFFRACTION100
2.6328-2.68340.29611770.24422696X-RAY DIFFRACTION100
2.6834-2.73820.31171410.24672714X-RAY DIFFRACTION100
2.7382-2.79770.22251490.2342685X-RAY DIFFRACTION100
2.7977-2.86280.24461260.23092701X-RAY DIFFRACTION100
2.8628-2.93430.32641660.23192672X-RAY DIFFRACTION100
2.9343-3.01370.23231370.21732702X-RAY DIFFRACTION100
3.0137-3.10230.23651630.20262713X-RAY DIFFRACTION100
3.1023-3.20240.24361060.20592755X-RAY DIFFRACTION100
3.2024-3.31680.2381300.20062684X-RAY DIFFRACTION100
3.3168-3.44960.18141490.19182713X-RAY DIFFRACTION100
3.4496-3.60650.16521240.18192728X-RAY DIFFRACTION100
3.6065-3.79650.21651460.17432685X-RAY DIFFRACTION100
3.7965-4.03420.20321470.17352713X-RAY DIFFRACTION100
4.0342-4.34540.18311530.17332675X-RAY DIFFRACTION100
4.3454-4.78220.18861630.17362693X-RAY DIFFRACTION100
4.7822-5.47290.2171410.18842719X-RAY DIFFRACTION100
5.4729-6.89040.24371410.23432701X-RAY DIFFRACTION100
6.8904-42.23660.25111030.23652754X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.2756-1.4403-2.52892.05480.61234.3273-0.00450.1608-0.1326-0.05470.12981.2164-0.2757-1.2376-0.01120.46660.0114-0.0260.5743-0.02040.618120.60428.411923.742
20.67190.17530.31480.802-0.04320.9857-0.04050.1337-0.0676-0.1204-0.02510.02930.0333-0.04910.0680.34770.01540.00310.2839-0.04260.251955.759413.265817.1344
33.7831-4.6771-2.57617.23690.54686.40060.1219-0.11660.36270.0231-0.04020.1983-0.66070.5066-0.07670.443-0.05650.00080.3448-0.09050.384858.97524.843311.8441
41.06650.1327-0.63571.14271.02831.8845-0.00360.0306-0.15950.0657-0.0340.07040.29470.03360.03870.36880.0216-0.01920.34-0.02290.327446.16218.54117.1018
54.3461-1.176-1.97692.48881.65382.7697-0.1815-0.0941-0.20030.0866-0.01950.21310.2988-0.24530.22690.3962-0.0203-0.00650.3299-0.05150.303243.47875.821410.9894
63.2984-2.62410.42223.1025-0.27391.7093-0.023-0.1743-0.05520.10740.03840.1933-0.0102-0.15870.00140.2431-0.0410.02850.315800.198837.590429.264947.1625
7-0.035-0.14040.06410.3767-0.13310.82790.00470.0299-0.0033-0.0841-0.00880.04370.0419-0.1035-0.00160.3167-0.00690.00660.3498-0.02040.268238.706628.515336.7433
84.3629-1.1604-0.62563.55950.71892.7827-0.08560.3074-0.2567-0.1244-0.06560.60340.1159-0.5510.14910.3806-0.1145-0.01890.5195-0.050.411124.446916.793739.8296
92.71961.1093-0.61791.42321.75854.81020.0167-0.1272-0.2090.4936-0.01430.16660.4968-0.18440.04110.3184-0.0238-0.00250.40190.00980.319129.990921.041851.4393
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 3 through 28 )
2X-RAY DIFFRACTION2chain 'B' and (resid 29 through 117 )
3X-RAY DIFFRACTION3chain 'B' and (resid 118 through 132 )
4X-RAY DIFFRACTION4chain 'B' and (resid 133 through 219 )
5X-RAY DIFFRACTION5chain 'B' and (resid 220 through 270 )
6X-RAY DIFFRACTION6chain 'A' and (resid 32 through 68 )
7X-RAY DIFFRACTION7chain 'A' and (resid 69 through 200 )
8X-RAY DIFFRACTION8chain 'A' and (resid 201 through 243 )
9X-RAY DIFFRACTION9chain 'A' and (resid 244 through 276 )

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