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- PDB-7zr4: Molybdenum storage protein loaded with polyoxotungstates in the i... -

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Basic information

Entry
Database: PDB / ID: 7zr4
TitleMolybdenum storage protein loaded with polyoxotungstates in the in vivo-like state
Components(Molybdenum storage protein subunit ...) x 2
KeywordsMETAL BINDING PROTEIN / molybdenum storage / polyoxotungstates / 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 / Amino acid kinase family / Acetylglutamate kinase-like superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / 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 / Resolution: 1.701 Å
AuthorsErmler, U. / Aziz, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
Alexander von Humboldt Foundation 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 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 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)61,18112
Polymers57,4932
Non-polymers3,68810
Water5,405300
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)183,54236
Polymers172,4796
Non-polymers11,06330
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 area40980 Å2
ΔGint-268 kcal/mol
Surface area45490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.670, 115.670, 234.490
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

21A-303-

UNL

31A-305-

UNL

41A-305-

UNL

51A-305-

UNL

61B-304-

UNL

71B-304-

UNL

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

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Non-polymers , 5 types, 310 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: 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
#5: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Mass: 435.585 Da / Num. of mol.: 6 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 300 / 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

CrystalDensity Matthews: 3.94 Å3/Da / Density % sol: 68.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M NaAc, pH 4.6, 1.1 M NH4H2 citrate, 10% glycerol

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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: Jul 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.214 Å / Relative weight: 1
ReflectionResolution: 1.7→46.492 Å / Num. obs: 191044 / % possible obs: 98.9 % / Redundancy: 3.2 % / CC1/2: 0.99 / Rsym value: 0.052 / Net I/σ(I): 10.5
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
1.7-1.82.8931.3370.928631930406298410.4651.65298.1
1.8-22.7850.5092.1612169244093436970.850.62999.1
2-2.32.9730.1915.5212011740603404030.9690.23599.5
2.3-2.72.8440.08810.318377429768294600.9910.10899
2.7-3.33.6250.05419.177790421793214910.9970.06298.6
3.3-4.34.7480.03932.646833014466143910.9980.04499.5
4.3-64.4270.03138.2332756754773990.9990.03698
6-84.9670.02944.8912641255325450.9990.03399.7
8-124.6750.02648.586068130812980.9990.0399.2
12-46.4924.0130.02745.9120835625190.9980.03292.3

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Processing

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

4ndo


Resolution: 1.701→46.492 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0.96 / Phase error: 29.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2403 9469 4.96 %
Rwork0.2178 181308 -
obs0.2189 190777 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 323.51 Å2 / Biso mean: 42.4539 Å2 / Biso min: 20.62 Å2
Refinement stepCycle: final / Resolution: 1.701→46.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3812 0 154 303 4269
Biso mean--109.7 47.1 -
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 (%)
1.701-1.72030.42152710.419602398
1.7203-1.74060.43543110.4094602699
1.7406-1.76180.41553220.4018606099
1.7618-1.78410.38023040.3814608899
1.7841-1.80760.37323350.371602999
1.8076-1.83230.38823090.3538608099
1.8323-1.85850.37443180.3416603499
1.8585-1.88630.3333040.3287603999
1.8863-1.91570.30723100.3171603999
1.9157-1.94720.31173420.299596198
1.9472-1.98070.30343250.2661601799
1.9807-2.01670.29463100.2617606299
2.0167-2.05550.26663100.2525608299
2.0555-2.09750.26623090.2505608799
2.0975-2.14310.26893210.2317608999
2.1431-2.1930.24083620.218596299
2.193-2.24780.24583090.2126607799
2.2478-2.30860.24633360.2188608199
2.3086-2.37650.22093020.208604499
2.3765-2.45320.22323400.2156604999
2.4532-2.54090.26643690.2255600099
2.5409-2.64260.22563200.2143600898
2.6426-2.76290.23093130.2237599898
2.7629-2.90850.25793310.217596198
2.9085-3.09070.25932690.2071607999
3.0907-3.32930.2083290.2038605399
3.3293-3.66420.1993060.1784608099
3.6642-4.19410.17392670.162613899
4.1941-5.28290.19453210.1568603799
5.2829-46.4920.25142940.2431602598
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)
11.0567-0.23610.4860.5351-0.33033.60620.0359-0.0741-0.0778-0.00630.04370.13120.0479-0.2139-0.04750.1513-0.0360.00130.1568-0.0040.217136.844830.384741.9407
2-0.0055-0.04590.10681.12220.24221.26830.02030.04750.0362-0.0664-0.0033-0.1793-0.03820.1751-0.04660.2072-0.00810.01610.2497-0.00040.259442.124327.937337.4461
33.5331-0.7635-0.54513.61331.4023.3443-0.06470.0976-0.28710.00430.0030.56090.2737-0.5580.00960.2024-0.06730.02190.30250.03010.280226.119519.506544.6955
45.29120.0325-4.84718.72870.8667.9184-0.00920.70850.1571-0.4371-0.0030.9915-0.5338-1.6411-0.00310.30790.0344-0.0570.493-0.01570.378720.978528.859124.2614
50.7134-0.2020.06350.48380.35920.94110.05450.1411-0.0783-0.1297-0.00950.00140.0940.0962-0.0320.2622-0.02720.0010.2128-0.02560.251454.859312.818815.1421
60.47440.6259-1.2590.8413-1.7614.0460.0545-0.02180.10450.07560.06530.0856-0.4294-0.2514-0.11880.31610.0180.00130.2512-0.03920.268156.725720.470216.5731
71.0305-0.075-0.08040.65370.77242.8382-0.06060.0177-0.0862-0.0423-0.02040.08410.0805-0.05850.06810.2424-0.01710.01150.1702-0.02770.261345.830311.364620.8596
88.7281.592-0.80286.5932.55259.1042-0.1316-0.1882-1.27560.3673-0.1370.07591.24860.43090.28190.4092-0.01850.08120.26370.00950.318545.2576-7.036112.2439
94.0021-1.504-2.24641.95851.22612.8392-0.1717-0.0846-0.28440.0458-0.02230.23820.3217-0.18760.20490.3149-0.0348-0.01770.214-0.0490.279142.86364.887811.6046
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 97 )A31 - 97
2X-RAY DIFFRACTION2chain 'A' and (resid 98 through 190 )A98 - 190
3X-RAY DIFFRACTION3chain 'A' and (resid 191 through 276 )A191 - 276
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 28 )B3 - 28
5X-RAY DIFFRACTION5chain 'B' and (resid 29 through 95 )B29 - 95
6X-RAY DIFFRACTION6chain 'B' and (resid 96 through 152 )B96 - 152
7X-RAY DIFFRACTION7chain 'B' and (resid 153 through 194 )B153 - 194
8X-RAY DIFFRACTION8chain 'B' and (resid 195 through 213 )B195 - 213
9X-RAY DIFFRACTION9chain 'B' and (resid 214 through 270 )B214 - 270

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