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- PDB-4f6t: The crystal structure of the molybdenum storage protein (MoSto) f... -

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Basic information

Entry
Database: PDB / ID: 4f6t
TitleThe crystal structure of the molybdenum storage protein (MoSto) from Azotobacter vinelandii loaded with various polyoxometalates
Components(Molybdenum storage protein subunit ...) x 2
KeywordsMETAL BINDING PROTEIN / molybdenum storage / ATP hydrolyzation / hexamer / polyoxometalate / POM / Rossmanfold like / ATP Hydrolysis / Molybdate
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 / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Molybdenum storage protein subunit beta / MO(6)-O(26) Cluster / Chem-8M0 / PHOSPHATE ION / MOLYBDENUM ATOM / ADENOSINE-5'-TRIPHOSPHATE / Molybdenum storage protein subunit alpha
Similarity search - Component
Biological speciesAzotobacter vinelandii (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKowalewski, B. / Poppe, J. / Schneider, K. / Demmer, U. / Warkentin, E. / Ermler, U.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Nature's Polyoxometalate Chemistry: X-ray Structure of the Mo Storage Protein Loaded with Discrete Polynuclear Mo-O Clusters.
Authors: Kowalewski, B. / Poppe, J. / Demmer, U. / Warkentin, E. / Dierks, T. / Ermler, U. / Schneider, K.
History
DepositionMay 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Non-polymer description

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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)58,78912
Polymers54,0012
Non-polymers4,78810
Water9,440524
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)176,36636
Polymers162,0046
Non-polymers14,36330
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 area25380 Å2
ΔGint-180 kcal/mol
Surface area48720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.740, 115.740, 233.620
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-519-

HOH

21A-646-

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 / Mo storage protein subunit beta / MoSto subunit beta


Mass: 28176.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (unknown) / Strain: ATCC 13705 / References: UniProt: P84253
#2: Protein Molybdenum storage protein subunit alpha / Mo storage protein subunit alpha / MoSto subunit alpha


Mass: 25824.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (unknown) / Strain: ATCC 13705 / References: UniProt: P84308

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Non-polymers , 7 types, 534 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-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 / Phosphate


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-6M0 / MO(6)-O(26) Cluster


Mass: 1007.751 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H16Mo6O26
#8: Chemical ChemComp-MO / MOLYBDENUM ATOM


Mass: 95.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mo
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 524 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsAUTHOR STATES THAT SINGLE MOLYBDENUM ATOMS FORM A MO3 CLUSTER WITH THE SYMMETRY RELATED SUBUNITS.

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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

Crystal
IDDensity Matthews3/Da)Density % sol (%)
14.1870.59
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, hanging drop5.6NH4H2PO4, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
2832vapor diffusion, sitting drop5.6NH4H2PO4, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 283K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X10SA11.008
SYNCHROTRONESRF ID2921.71
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDMar 3, 2009
ADSC QUANTUM 315r2CCDJun 28, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SiSINGLE WAVELENGTHMx-ray1
2SiSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.0081
21.711
ReflectionResolution: 1.6→46 Å / Num. all: 121767 / Num. obs: 109553 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 22.705 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 13.45
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.6-1.70.5483.6147364118531,259.4
1.7-1.90.3636.05118419262981,292.5
1.9-2.20.17411.02114068247821,296.6
2.2-2.60.09616.2280798181151,298.2
2.6-3.10.06520.6950356115231,298.2
3.1-3.80.04924.873256176461,297.8
3.8-4.50.04128.051533236521,297.3
4.5-60.03929.311371232351,296.8
6-80.03431.88582414171,296.7
8-120.0333.4627767271,292.1
12-46.0580.03129.9610553051,278.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
EDNAdata collection
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OGX
Resolution: 1.6→46 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.1714 / WRfactor Rwork: 0.1388 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.9154 / SU B: 2.201 / SU ML: 0.034 / SU R Cruickshank DPI: 0.0638 / SU Rfree: 0.0615 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.064 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1733 5467 5 %RANDOM
Rwork0.1394 ---
all0.1421 121767 --
obs0.1421 109551 89.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 169.52 Å2 / Biso mean: 22.3128 Å2 / Biso min: 4.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.05 Å20 Å2
2---0.09 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.6→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3800 0 172 524 4496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0224168
X-RAY DIFFRACTIONr_angle_refined_deg5.82.4475855
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1855548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.96522.611157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89415659
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.841538
X-RAY DIFFRACTIONr_chiral_restr0.3220.2666
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213065
X-RAY DIFFRACTIONr_mcbond_it2.6681.52603
X-RAY DIFFRACTIONr_mcangle_it3.92724194
X-RAY DIFFRACTIONr_scbond_it5.72731565
X-RAY DIFFRACTIONr_scangle_it8.0054.51594
X-RAY DIFFRACTIONr_rigid_bond_restr3.04734168
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 243 -
Rwork0.21 4430 -
all-4673 -
obs--52.87 %

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