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- PDB-6gwv: Molybdenum storage protein without polymolybdate clusters and ATP -

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Basic information

Entry
Database: PDB / ID: 6gwv
TitleMolybdenum storage protein without polymolybdate clusters and ATP
Components
  • Molybdenum storage protein subunit alpha
  • Molybdenum storage protein subunit beta
KeywordsMETAL BINDING PROTEIN / Molybdenum storage protein / polyoxometalate clusters / cage / 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
ADENOSINE-5'-TRIPHOSPHATE / Molybdenum storage protein subunit beta / Molybdenum storage protein subunit alpha
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 26, 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 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
C: Molybdenum storage protein subunit beta
D: Molybdenum storage protein subunit alpha
E: Molybdenum storage protein subunit beta
F: Molybdenum storage protein subunit alpha
H: Molybdenum storage protein subunit beta
G: Molybdenum storage protein subunit alpha
I: Molybdenum storage protein subunit beta
J: Molybdenum storage protein subunit alpha
K: Molybdenum storage protein subunit beta
L: Molybdenum storage protein subunit alpha
N: Molybdenum storage protein subunit beta
M: Molybdenum storage protein subunit alpha
O: Molybdenum storage protein subunit beta
P: Molybdenum storage protein subunit alpha
Q: Molybdenum storage protein subunit beta
R: Molybdenum storage protein subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)519,44931
Polymers517,43818
Non-polymers2,01013
Water00
1
B: Molybdenum storage protein subunit beta
A: Molybdenum storage protein subunit alpha
C: Molybdenum storage protein subunit beta
D: Molybdenum storage protein subunit alpha
E: Molybdenum storage protein subunit beta
F: Molybdenum storage protein subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,37111
Polymers172,4796
Non-polymers8915
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28000 Å2
ΔGint-246 kcal/mol
Surface area49980 Å2
MethodPISA
2
H: Molybdenum storage protein subunit beta
G: Molybdenum storage protein subunit alpha
I: Molybdenum storage protein subunit beta
J: Molybdenum storage protein subunit alpha
K: Molybdenum storage protein subunit beta
L: Molybdenum storage protein subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,5767
Polymers172,4796
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25930 Å2
ΔGint-196 kcal/mol
Surface area52830 Å2
MethodPISA
3
N: Molybdenum storage protein subunit beta
M: Molybdenum storage protein subunit alpha
O: Molybdenum storage protein subunit beta
P: Molybdenum storage protein subunit alpha
Q: Molybdenum storage protein subunit beta
R: Molybdenum storage protein subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,50213
Polymers172,4796
Non-polymers1,0237
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28680 Å2
ΔGint-266 kcal/mol
Surface area49200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.710, 147.300, 192.320
Angle α, β, γ (deg.)90.00, 107.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Molybdenum storage protein subunit beta / MoSto subunit beta


Mass: 28247.582 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / Strain: DJ / 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.: 9 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / Strain: DJ / References: UniProt: P84308
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: 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
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

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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: 3.24 Å3/Da / Density % sol: 62.06 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 0.4 M ammonium sulfate, 20% PEG400, 10% isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 148308 / % possible obs: 92.2 % / Redundancy: 2.9 % / Rsym value: 0.139 / Net I/σ(I): 8.4
Reflection shellResolution: 2.8→2.9 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→47.794 Å / Cross valid method: FREE R-VALUE / σ(F): 2.11 / Phase error: 25.32
RfactorNum. reflection% reflection
Rfree0.2593 7689 5.18 %
Rwork0.2333 --
obs0.2413 148307 97.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→47.794 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34200 0 113 0 34313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00734978
X-RAY DIFFRACTIONf_angle_d1.08447667
X-RAY DIFFRACTIONf_dihedral_angle_d14.32121072
X-RAY DIFFRACTIONf_chiral_restr0.0615608
X-RAY DIFFRACTIONf_plane_restr0.0076258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.84840.33833890.32427100X-RAY DIFFRACTION93
2.8484-2.90010.32273940.30916989X-RAY DIFFRACTION93
2.9001-2.95590.35863660.30187064X-RAY DIFFRACTION93
2.9559-3.01620.32673770.28387026X-RAY DIFFRACTION93
3.0162-3.08180.31993360.28597152X-RAY DIFFRACTION94
3.0818-3.15340.32653850.27827063X-RAY DIFFRACTION93
3.1534-3.23220.28463660.26447073X-RAY DIFFRACTION93
3.2322-3.31960.27863680.26137047X-RAY DIFFRACTION93
3.3196-3.41720.28343840.25567023X-RAY DIFFRACTION92
3.4172-3.52740.26873690.24196994X-RAY DIFFRACTION92
3.5274-3.65340.25624150.23696980X-RAY DIFFRACTION92
3.6534-3.79960.24083590.23417021X-RAY DIFFRACTION92
3.7996-3.97230.24643740.22477028X-RAY DIFFRACTION92
3.9723-4.18150.26023760.21447049X-RAY DIFFRACTION92
4.1815-4.44320.23983830.20666824X-RAY DIFFRACTION90
4.4432-4.78560.21833730.19986960X-RAY DIFFRACTION91
4.7856-5.26610.24433630.20657048X-RAY DIFFRACTION92
5.2661-6.02570.24023750.22957074X-RAY DIFFRACTION93
6.0257-7.58220.26053420.22957097X-RAY DIFFRACTION93
7.5822-38.51040.27833710.25197182X-RAY DIFFRACTION92
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)
11.2768-0.041-0.15481.34-0.4380.8527-0.0150.28010.1116-0.23330.0343-0.1164-0.2871-0.1695-0.03420.53360.04050.11030.4909-0.03670.4345-84.895811.7059-25.7445
20.73050.10840.11671.17930.30691.03470.0482-0.12510.1742-0.1340.0372-0.28350.03790.1188-0.06320.3901-0.02830.07510.6673-0.06440.6393-49.5821-26.8171-16.7731
31.7328-0.4849-0.65030.22790.50421.91020.0214-0.0017-0.22920.0251-0.05480.10340.2218-0.04120.08820.432-0.06770.11550.4282-0.03430.5061-79.7024-27.8184-13.5399
41.50510.1382-0.24420.94120.31671.08220.0122-0.36310.08970.29280.01340.0245-0.1597-0.0063-0.01310.3430.01230.01870.30350.0380.13-73.893-71.6088-46.2345
51.0833-0.1479-0.24291.02110.17461.21380.0664-0.17010.19610.14890.107-0.1372-0.21460.226-0.16820.2193-0.06630.03360.2087-0.05330.1942-57.2901-57.4735-67.1731
60.3669-0.40240.05790.512-0.12830.746-0.0056-0.0756-0.31890.0630.0240.36880.278-0.3437-0.02430.2707-0.13870.03450.3681-0.00920.4792-99.955-88.2715-72.4467
71.3779-0.3025-0.15410.3158-0.03410.763-0.12430.0147-0.2460.00630.04310.13030.3843-0.0890.05410.2725-0.04010.05240.12410.00110.2796-70.595-95.7992-75.3395
81.6478-0.2118-0.22620.7232-0.01571.194-0.04210.01140.07240.04830.09860.1369-0.2175-0.355-0.04120.28240.1180.07050.25320.05480.2672-93.7242-48.1655-72.565
91.34040.1204-0.33540.6790.34830.86740.05620.34890.2257-0.1613-0.02230.184-0.1526-0.2436-0.02050.20050.0526-0.02150.25660.02550.2107-85.166-63.7973-97.3571
101.1746-0.1319-0.22140.8564-0.39360.6285-0.06990.02790.08890.10130.10310.22390.1257-0.2072-0.03980.2334-0.08640.07530.2572-0.04440.3574-37.6548-25.498-74.527
110.93420.4652-0.36650.4597-0.33821.0672-0.0679-0.1125-0.13170.0011-0.06720.08320.29490.06990.11210.22790.01780.07630.15690.03590.1975-7.4489-25.5924-77.687
120.8309-0.20490.16950.965-0.17291.03210.1347-0.04960.3498-0.0518-0.06110.357-0.2255-0.4232-0.06820.31030.11340.14160.3631-0.01970.6222-41.00714.8384-71.527
131.1290.2551-0.91971.02140.15171.02870.0110.29480.355-0.10110.0860.373-0.1186-0.3844-0.06890.18930.03280.00780.30350.09290.3422-29.0833.8063-97.1766
141.4648-0.105-0.49381.61720.08980.46240.048-0.44310.09640.4379-0.08810.0864-0.113-0.0080.04030.3897-0.0520.06210.4251-0.02890.1992-16.0242-5.3953-46.5888
151.0798-0.4496-0.70631.01760.03851.10810.1462-0.23760.25120.3359-0.0912-0.0135-0.33160.1701-0.06370.3287-0.09090.09890.2466-0.06450.276-3.255113.9977-66.2203
162.0546-0.64081.18661.0558-0.06290.76580.141-0.140.2938-0.2263-0.0615-0.38080.07750.4173-0.02370.51180.06680.21330.83020.08610.7255-47.081813.9321-20.5783
170.6317-0.19870.59340.693-0.19030.5211-0.0827-0.21980.11560.08940.1833-0.0982-0.08220.0434-0.08920.3660.0580.05130.77810.01360.3957-58.79632.73355.2437
180.6744-0.72450.06290.7862-0.13960.14620.10240.1368-0.0508-0.1229-0.1705-0.0672-0.0695-0.10870.06720.55720.03330.03240.8014-0.04990.5739-71.8193-7.6033-45.1389
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'J' and resid 33 through 276)
2X-RAY DIFFRACTION2(chain 'K' and resid 3 through 270)
3X-RAY DIFFRACTION3(chain 'L' and resid 33 through 276)
4X-RAY DIFFRACTION4(chain 'N' and resid 3 through 270)
5X-RAY DIFFRACTION5(chain 'M' and resid 33 through 276)
6X-RAY DIFFRACTION6(chain 'O' and resid 3 through 270)
7X-RAY DIFFRACTION7(chain 'P' and resid 33 through 276)
8X-RAY DIFFRACTION8(chain 'Q' and resid 3 through 270)
9X-RAY DIFFRACTION9(chain 'R' and resid 33 through 276)
10X-RAY DIFFRACTION10(chain 'B' and resid 3 through 270)
11X-RAY DIFFRACTION11(chain 'A' and resid 33 through 276)
12X-RAY DIFFRACTION12(chain 'C' and resid 3 through 270)
13X-RAY DIFFRACTION13(chain 'D' and resid 33 through 276)
14X-RAY DIFFRACTION14(chain 'E' and resid 3 through 270)
15X-RAY DIFFRACTION15(chain 'F' and resid 33 through 276)
16X-RAY DIFFRACTION16(chain 'H' and resid 3 through 270)
17X-RAY DIFFRACTION17(chain 'G' and resid 33 through 276)
18X-RAY DIFFRACTION18(chain 'I' and resid 3 through 270)

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