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- PDB-7zqq: Molybdenum storage protein - LB131H -

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Basic information

Entry
Database: PDB / ID: 7zqq
TitleMolybdenum storage protein - LB131H
Components(Molybdenum storage protein subunit ...) x 2
KeywordsMETAL BINDING PROTEIN / polyoxotungstate / metal storage / Keggin ion
Function / homology
Function and homology information


nutrient reservoir activity / molybdenum ion binding / cytoplasm
Similarity search - Function
Molybdenum storage protein subunit alpha/beta / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / Amino acid kinase family
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / Unknown ligand / Molybdenum storage protein subunit beta / Molybdenum storage protein subunit alpha
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsErmler, U. / Aziz, I.
Funding support Germany, 2items
OrganizationGrant numberCountry
Alexander von Humboldt Foundation Germany
Max Planck Society Germany
CitationJournal: J Inorg Biochem / Year: 2022
Title: The molybdenum storage protein forms and deposits distinct polynuclear tungsten oxygen aggregates.
Authors: Iram Aziz / Susann Kaltwasser / Kanwal Kayastha / Radhika Khera / Janet Vonck / Ulrich Ermler /
Abstract: Some N-fixing bacteria store Mo to maintain the formation of the vital FeMo-cofactor dependent nitrogenase under Mo depleting conditions. The Mo storage protein (MoSto), developed for this purpose, ...Some N-fixing bacteria store Mo to maintain the formation of the vital FeMo-cofactor dependent nitrogenase under Mo depleting conditions. The Mo storage protein (MoSto), developed for this purpose, has the unique capability to compactly deposit molybdate as polyoxometalate (POM) clusters in a (αβ) hexameric cage; the same occurs with the physicochemically related tungstate. To explore the structural diversity of W-based POM clusters, MoSto loaded under different conditions with tungstate and two site-specifically modified MoSto variants were structurally characterized by X-ray crystallography or single-particle cryo-EM. The MoSto cage contains five major locations for POM clusters occupied among others by heptanuclear, Keggin ion and even Dawson-like species also found in bulk solvent under defined conditions. We found both lacunary derivatives of these archetypical POM clusters with missing WO units at positions exposed to bulk solvent and expanded derivatives with additional WO units next to protecting polypeptide segments or other POM clusters. The cryo-EM map, unexpectedly, reveals a POM cluster in the cage center anchored to the wall by a WO linker. Interestingly, distinct POM cluster structures can originate from identical, highly occupied core fragments of three to seven WO units that partly correspond to those found in MoSto loaded with molybdate. These core fragments are firmly bound to the complementary protein template in contrast to the more variable, less occupied residual parts of the visible POM clusters. Due to their higher stability, W-based POM clusters are, on average, larger and more diverse than their Mo-based counterparts.
History
DepositionMay 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Molybdenum storage protein subunit alpha
B: Molybdenum storage protein subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,82415
Polymers57,5182
Non-polymers3,30513
Water5,999333
1
A: Molybdenum storage protein subunit alpha
B: Molybdenum storage protein subunit beta
hetero molecules

A: Molybdenum storage protein subunit alpha
B: Molybdenum storage protein subunit beta
hetero molecules

A: Molybdenum storage protein subunit alpha
B: Molybdenum storage protein subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,47145
Polymers172,5546
Non-polymers9,91639
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 area41270 Å2
ΔGint-315 kcal/mol
Surface area46110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.040, 115.040, 234.410
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-303-

UNL

21B-303-

UNL

31A-430-

HOH

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Components

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Molybdenum storage protein subunit ... , 2 types, 2 molecules AB

#1: 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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P84308
#2: Protein Molybdenum storage protein subunit beta / MoSto subunit beta


Mass: 28272.570 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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P84253

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Non-polymers , 6 types, 346 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Mass: 324.400 Da / Num. of mol.: 6 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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 growTemperature: 293 K / Method: vapor diffusion / pH: 5.6 / Details: 0.1 M sodium citrate, pH 5.6, 0.7 M NH4H2PO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.214 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.214 Å / Relative weight: 1
ReflectionResolution: 1.75→45.845 Å / Num. obs: 173868 / % possible obs: 99.3 % / Redundancy: 3.449 % / Biso Wilson estimate: 32.12 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.104 / Rrim(I) all: 0.123 / Χ2: 1.993 / Net I/σ(I): 7.96 / Num. measured all: 599725 / Scaling rejects: 5815
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.75-1.853.310.9391.878855426881267550.6571.11699.5
1.85-2.053.5430.4463.7213825739255390240.910.52499.4
2.05-2.43.3720.1787.0213705341052406470.9730.21199
2.4-2.93.5210.10110.9610299529374292510.9860.11999.6
2.9-3.43.5730.0814.085198814599145500.9870.09499.7
3.4-4.23.3690.07315.553748811197111260.9870.08699.4
4.2-63.4310.07316.2528419834582830.9860.08799.3
6-83.7040.07616.929267251525020.9860.08999.5
8-123.3830.07616.464256129212580.9830.09197.4
12-45.8453.0680.07315.8714485584720.9810.08984.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ndo

4ndo


Resolution: 1.75→45.845 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.11 / Phase error: 22.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2201 8619 4.96 %
Rwork0.2065 165208 -
obs0.2072 173827 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 996.88 Å2 / Biso mean: 34.1146 Å2 / Biso min: 13.12 Å2
Refinement stepCycle: final / Resolution: 1.75→45.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3815 0 122 337 4274
Biso mean--131.81 39.58 -
Num. residues----514
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.75-1.76990.35132320.33275596100
1.7699-1.79070.2872860.3207551599
1.7907-1.81260.30712940.3055549299
1.8126-1.83550.32312920.29655477100
1.8355-1.85970.31052540.28155572100
1.8597-1.88520.2652720.2716557199
1.8852-1.91210.24633180.2539547199
1.9121-1.94060.24922890.2453548499
1.9406-1.9710.2363050.2414547899
1.971-2.00330.25592790.2331551099
2.0033-2.03780.22553010.2284550599
2.0378-2.07490.2563370.2217544699
2.0749-2.11480.21842430.2143551599
2.1148-2.15790.22892780.2058556299
2.1579-2.20490.21792720.2042550299
2.2049-2.25610.20093050.2022547399
2.2561-2.31260.21922920.1961546399
2.3126-2.37510.21242990.1936543299
2.3751-2.4450.19612830.2012554999
2.445-2.52390.22253280.2122544099
2.5239-2.61410.21933010.20575514100
2.6141-2.71870.21523070.21595520100
2.7187-2.84250.22692600.21245533100
2.8425-2.99230.24443150.2125504100
2.9923-3.17970.20872980.20175543100
3.1797-3.42520.23582740.19715525100
3.4252-3.76970.17852810.1663553699
3.7697-4.31480.18062870.1596550399
4.3148-5.43480.16372830.1631550999
5.4348-45.8450.27112540.2452546898
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)
15.4711-1.7020.66950.59960.38684.8162-0.2034-0.1507-0.49960.25810.17360.14480.47560.14950.0110.1837-0.03560.03260.16240.01820.195944.198817.364947.5364
20.48380.09990.73930.41180.16313.23270.0004-0.00050.0021-0.00340.01710.0672-0.0208-0.0707-0.01780.15260.00780.00070.17180.00070.172635.91734.988438.5746
37.5757-3.81791.25943.54991.74443.71340.28720.4618-0.3245-0.3375-0.1727-0.19860.07620.3811-0.0920.2671-0.02810.03910.30080.02130.297551.158529.463442.4913
40.5788-0.21440.90820.61380.09372.6585-0.010.0422-0.0069-0.1160.03460.03910.05860.0811-0.02710.1778-0.01960.01040.1975-0.00770.178338.771723.103536.1602
52.4941-0.7961-0.32.83380.8571.8818-0.07080.0461-0.2603-0.04580.02690.44080.2426-0.368-0.01320.1599-0.0760.01310.25180.02190.21326.122419.095344.7538
66.2510.4847-2.38978.74091.44977.23040.05870.34010.357-0.3633-0.04880.9384-0.4352-1.2547-0.03580.18880.0115-0.07350.4752-0.00970.353120.596928.652124.266
73.5142-2.2153-0.45621.85990.29690.89760.06220.2027-0.0358-0.2079-0.0520.00840.0613-0.0047-0.01910.2615-0.0363-0.01860.1896-0.0520.177454.398813.81749.0378
80.6767-0.23990.15111.1624-1.23282.12550.03360.0882-0.0618-0.1275-0.050.0510.2765-0.0388-0.02850.236-0.00930.00050.1707-0.0430.182855.521510.531424.7274
90.50320.9781-1.01662.4474-3.82426.7990.0971-0.0380.06790.09320.07220.1438-0.40960-0.21940.2606-0.0157-0.01020.1756-0.04140.216457.975819.954917.6849
101.1328-0.5223-0.67690.5374-0.87656.34110.014-0.0136-0.081-0.1288-0.07340.02540.00930.13610.01560.2262-0.012-0.01160.1494-0.04440.206347.062616.004521.996
113.3189-1.1591-1.5093.26931.37772.0154-0.2111-0.189-0.33020.1690.04090.21330.373-0.10350.1580.3189-0.0278-0.0140.2145-0.0330.197243.93552.485411.59
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 47 )A31 - 47
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 123 )A48 - 123
3X-RAY DIFFRACTION3chain 'A' and (resid 124 through 143 )A124 - 143
4X-RAY DIFFRACTION4chain 'A' and (resid 144 through 190 )A144 - 190
5X-RAY DIFFRACTION5chain 'A' and (resid 191 through 276 )A191 - 276
6X-RAY DIFFRACTION6chain 'B' and (resid 3 through 28 )B3 - 28
7X-RAY DIFFRACTION7chain 'B' and (resid 29 through 68 )B29 - 68
8X-RAY DIFFRACTION8chain 'B' and (resid 69 through 95 )B69 - 95
9X-RAY DIFFRACTION9chain 'B' and (resid 96 through 137 )B96 - 137
10X-RAY DIFFRACTION10chain 'B' and (resid 138 through 180 )B138 - 180
11X-RAY DIFFRACTION11chain 'B' and (resid 181 through 270 )B181 - 270

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