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- PDB-6h6w: Molybdenum storage protein- H156A -

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Basic information

Entry
Database: PDB / ID: 6h6w
TitleMolybdenum storage protein- H156A
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 / Acetylglutamate kinase-like / Carbamate kinase / Amino acid kinase family / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Molybdenum storage protein subunit beta / Chem-8M0 / ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / MOLYBDATE ION / MOLYBDENUM ATOM / Mo5 Cluster / Molybdenum storage protein subunit alpha
Similarity search - Component
Biological speciesAzotobacter vinelandii (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.0Dec 5, 2018Provider: repository / Type: Initial release

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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)61,92712
Polymers57,4262
Non-polymers4,50110
Water6,341352
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)185,78036
Polymers172,2786
Non-polymers13,50230
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 area33640 Å2
ΔGint-216 kcal/mol
Surface area44910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.270, 114.270, 234.140
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-304-

MOO

21A-426-

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 genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (unknown) / Gene: mosB, Avin_43210 / Production host: Escherichia coli BL21(DE3) (unknown) / References: UniProt: P84253
#2: Protein Molybdenum storage protein subunit alpha / Mo storage protein subunit alpha / MoSto subunit alpha


Mass: 29178.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (unknown) / Gene: mosA, Avin_43200 / Production host: Escherichia coli BL21(DE3) (unknown) / References: UniProt: P84308

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Non-polymers , 8 types, 362 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-FUQ / Mo5 Cluster


Mass: 899.844 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H20Mo5O25
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: 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.: 1 / Source method: obtained synthetically / Formula: Mo8O28
#8: Chemical ChemComp-MOO / MOLYBDATE ION / MOLYBDATE / Molybdate


Mass: 159.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: MoO4
#9: Chemical ChemComp-MO / MOLYBDENUM ATOM


Mass: 95.940 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mo
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 3.84 Å3/Da / Density % sol: 67.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M sodium citrate, pH 5.6, 1 M ammonium phosphate, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.738 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.738 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 144386 / % possible obs: 98.6 % / Redundancy: 3.2 % / Rsym value: 0.062 / Net I/σ(I): 12.6
Reflection shellResolution: 1.9→2 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: 4ndo
Resolution: 1.9→49.48 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.31 / Phase error: 20.77
RfactorNum. reflection% reflection
Rfree0.2031 7170 4.97 %
Rwork0.1758 --
obs0.1772 144293 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→49.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3795 0 172 350 4317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124113
X-RAY DIFFRACTIONf_angle_d1.9795786
X-RAY DIFFRACTIONf_dihedral_angle_d8.323283
X-RAY DIFFRACTIONf_chiral_restr0.075643
X-RAY DIFFRACTIONf_plane_restr0.007709
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8710.76682220.67023972X-RAY DIFFRACTION86
1.871-1.8930.67052410.62014222X-RAY DIFFRACTION92
1.893-1.91610.46692260.49334464X-RAY DIFFRACTION96
1.9161-1.94040.36611950.39444539X-RAY DIFFRACTION97
1.9404-1.96590.35852230.31794514X-RAY DIFFRACTION98
1.9659-1.99290.28992350.25974535X-RAY DIFFRACTION98
1.9929-2.02130.26152290.21934588X-RAY DIFFRACTION99
2.0213-2.05150.21572230.19984624X-RAY DIFFRACTION99
2.0515-2.08360.24852490.19294610X-RAY DIFFRACTION100
2.0836-2.11770.20352460.18464603X-RAY DIFFRACTION100
2.1177-2.15420.2472190.17514660X-RAY DIFFRACTION100
2.1542-2.19340.20952460.17164601X-RAY DIFFRACTION100
2.1934-2.23560.19432040.16934661X-RAY DIFFRACTION100
2.2356-2.28120.22012770.17414579X-RAY DIFFRACTION100
2.2812-2.33080.2112500.16724630X-RAY DIFFRACTION100
2.3308-2.3850.21671790.16064681X-RAY DIFFRACTION100
2.385-2.44470.19232540.1594601X-RAY DIFFRACTION100
2.4447-2.51080.2042670.16174595X-RAY DIFFRACTION100
2.5108-2.58470.18432180.15294643X-RAY DIFFRACTION100
2.5847-2.66810.16872540.14914602X-RAY DIFFRACTION100
2.6681-2.76340.1872480.16274629X-RAY DIFFRACTION100
2.7634-2.87410.18762490.16724651X-RAY DIFFRACTION100
2.8741-3.00490.21472510.1634621X-RAY DIFFRACTION100
3.0049-3.16320.17382310.16064613X-RAY DIFFRACTION100
3.1632-3.36140.19152740.15534615X-RAY DIFFRACTION100
3.3614-3.62090.15962410.14774606X-RAY DIFFRACTION100
3.6209-3.98510.18082500.14394626X-RAY DIFFRACTION100
3.9851-4.56140.15252600.134617X-RAY DIFFRACTION100
4.5614-5.74550.15372580.15174601X-RAY DIFFRACTION100
5.7455-49.4980.23862510.21754620X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
18.6357-0.64530.76967.8017-0.93538.5248-0.15750.5135-0.0728-0.63790.02761.0199-0.4058-0.84180.16040.30680.0885-0.07250.4866-0.03440.488619.678632.450822.5269
20.5853-0.09840.03820.46920.0290.6326-0.01660.1173-0.0363-0.1065-0.00120.01280.0842-0.04940.01860.2233-0.0233-0.01560.1846-0.03480.177451.466914.949917.9304
34.576-0.81173.12068.0982-3.75483.41690.0294-0.25680.51510.53360.1380.6639-0.8629-0.3614-0.13420.3540.0350.04210.2731-0.04670.312953.666425.399811.6404
41.6351-0.58140.80070.35880.37563.4378-0.05210.0101-0.06430.04570.01840.0560.0115-0.02770.03160.2258-0.0190.00370.1643-0.03650.228444.861513.730726.1901
52.4433-0.2528-0.95281.68070.95481.6132-0.128-0.1493-0.21790.0877-0.01940.17110.304-0.11080.13090.3366-0.0282-0.00290.245-0.03020.242943.73832.556811.5841
62.8288-2.13680.36962.6606-0.74511.77610.0019-0.0398-0.09680.08370.01170.1371-0.0012-0.11170.00210.1563-0.03120.01070.2029-0.0020.163337.080729.979447.551
70.2391-0.11650.21130.7748-0.12171.2130.01490.00210.0038-0.0453-0.00980.05480.0262-0.0644-0.00550.1462-0.00690.00870.187-0.00690.169437.676328.294636.8263
82.138-0.2865-0.38912.05490.65671.7588-0.0458-0.0005-0.23430.00760.03830.31390.2431-0.2934-0.01080.1688-0.0591-0.00130.23090.01940.20727.448717.777545.2552
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 3 through 14 )
2X-RAY DIFFRACTION2chain 'B' and (resid 15 through 121 )
3X-RAY DIFFRACTION3chain 'B' and (resid 122 through 147 )
4X-RAY DIFFRACTION4chain 'B' and (resid 148 through 180 )
5X-RAY DIFFRACTION5chain 'B' and (resid 181 through 270 )
6X-RAY DIFFRACTION6chain 'A' and (resid 33 through 68 )
7X-RAY DIFFRACTION7chain 'A' and (resid 69 through 204 )
8X-RAY DIFFRACTION8chain 'A' and (resid 205 through 276 )

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