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- PDB-7zse: Molybdenum storage protein in complex with polyoxotungstates in t... -

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Basic information

Entry
Database: PDB / ID: 7zse
TitleMolybdenum storage protein in complex with polyoxotungstates in the in-vitro state
Components(Molybdenum storage protein subunit ...) x 2
KeywordsMETAL BINDING PROTEIN / Molybdenum storage protein / polyoxotungstate clusters
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 / PHOSPHATE ION / Unknown ligand / Molybdenum storage protein subunit beta / Molybdenum storage protein subunit alpha
Similarity search - Component
Biological speciesAzotobacter vinelandii (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)61,43518
Polymers57,4932
Non-polymers3,94216
Water6,161342
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)184,30654
Polymers172,4796
Non-polymers11,82648
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 area40510 Å2
ΔGint-288 kcal/mol
Surface area46940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.390, 115.390, 234.340
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-304-

UNL

31A-310-

UNL

41A-310-

UNL

51B-302-

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 (unknown) / Gene: mosA, Avin_43200
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (unknown)
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 (unknown) / Gene: mosB, Avin_43210
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (unknown)
References: UniProt: P84253

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Non-polymers , 5 types, 358 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: 280.387 Da / Num. of mol.: 9 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 342 / 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
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: 1.213 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.213 Å / Relative weight: 1
ReflectionResolution: 1.4→45.961 Å / Num. obs: 343224 / % possible obs: 99.8 % / Redundancy: 8.326 % / Biso Wilson estimate: 29.681 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.082 / Χ2: 0.913 / Net I/σ(I): 14.16 / Num. measured all: 2857837 / Scaling rejects: 32053
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
1.4-1.57.7913.0510.9149676364273637600.4233.2799.2
1.5-1.78.241.1712.7772076787514874760.8551.25100
1.7-28.70.338.8464461174100740940.9870.352100
2-2.58.3330.09422.8347957657552575510.9980.1100
2.5-3.28.7610.05137.7927687231602316020.9990.054100
3.2-4.37.9870.03946.3213529216939169380.9990.042100
4.3-69.0590.0453.0667941750175000.9990.042100
6-89.1720.0453.0523224253525320.9990.04399.9
8-127.5240.03847.259541130312680.9980.04197.3
12-45.9616.4610.04142.4132505605030.9940.04689.8

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NDO
Resolution: 1.4→45.961 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.09 / Phase error: 26.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2122 17006 4.96 %
Rwork0.2 326114 -
obs0.2006 343120 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 409.7 Å2 / Biso mean: 34.9302 Å2 / Biso min: 13.08 Å2
Refinement stepCycle: final / Resolution: 1.4→45.961 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3777 0 182 344 4303
Biso mean--71.17 38.54 -
Num. residues----507
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.41590.45075460.4282103961094296
1.4159-1.43250.39925420.40091092311465100
1.4325-1.450.3736090.38181085011459100
1.45-1.46840.36085710.37081089711468100
1.4684-1.48770.36665450.34651088411429100
1.4877-1.50810.33715640.32711086211426100
1.5081-1.52960.33235970.31231081811415100
1.5296-1.55240.2925130.29991097211485100
1.5524-1.57670.29565340.29051094811482100
1.5767-1.60260.33285850.2921092411509100
1.6026-1.63020.28755180.2771083811356100
1.6302-1.65980.28496560.26581081611472100
1.6598-1.69180.28985860.26271088011466100
1.6918-1.72630.2586140.24721084311457100
1.7263-1.76380.25775430.23751090911452100
1.7638-1.80490.23685870.21831089311480100
1.8049-1.850.24985790.22171083011409100
1.85-1.90.23825420.21051091411456100
1.9-1.95590.22895940.1991089411488100
1.9559-2.01910.19745510.19081089111442100
2.0191-2.09120.22585900.18681088111471100
2.0912-2.1750.17396050.17461086611471100
2.175-2.27390.17975380.16671090011438100
2.2739-2.39380.1975570.17541090111458100
2.3938-2.54380.19635250.18111092611451100
2.5438-2.74020.1995760.17821089711473100
2.7402-3.01590.20745380.18651094111479100
3.0159-3.45220.18765450.18741087811423100
3.4522-4.34880.16626080.15681088111489100
4.3488-45.98560.2055480.2006108611140999
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)
14.7814-0.54430.78950.0558-0.22714.9528-0.1315-0.1937-0.65380.21250.15550.22370.5360.10170.01750.2341-0.04160.01860.19470.01440.235444.405517.528547.3229
20.63520.05130.40680.5239-0.05261.6610.0099-0.0171-0.0134-0.00180.01720.0378-0.028-0.0659-0.02270.19270.00290.0080.2031-0.0030.200139.382933.924839.3423
30.3008-0.18790.28831.06650.04361.82750.00370.0274-0.0314-0.14170.0190.16130.0873-0.1862-0.02820.1792-0.0235-0.00260.2131-0.00110.199534.346923.881737.1356
49.3134-5.5192-1.70497.66162.73172.3924-0.03020.3577-0.5153-0.1413-0.11880.85270.2791-0.6741-0.00550.2398-0.12620.00260.46260.00910.423518.709917.372843.3047
51.676-1.5846-0.14353.80740.90422.3648-0.00630.0236-0.134-0.01550.05530.20360.2151-0.2745-0.06060.1646-0.07050.02880.24030.0280.222330.771319.433444.3884
67.0944-0.7637-3.34993.44874.00995.5472-0.3377-0.2599-0.81510.81310.167-0.02080.897-0.04450.13370.3546-0.04150.02860.28760.06320.32330.132414.129250.7874
76.58470.3964-5.16320.5693-0.43437.63430.09220.39860.2902-0.07930.07650.2725-0.0443-0.942-0.1740.2183-0.0104-0.07190.3356-0.00780.301125.440627.470719.8186
87.5046-2.14151.61911.1496-0.30034.135-0.00910.14040.0569-0.17530.0181-0.02550.10190.2253-0.01070.2784-0.03830.00150.1436-0.07930.176959.885410.6459.1788
90.350.2728-0.70871.0165-1.42315.1881-0.00860.0283-0.0379-0.0376-0.0249-0.01210.0411-0.04220.0080.2378-0.0026-0.00350.1998-0.03680.204357.960413.478922.9249
104.8336-5.27935.16485.9713-5.18526.4684-0.0616-0.06370.2965-0.03850.02410.0483-0.6718-0.37110.18290.33550.0033-0.00620.2817-0.04050.330455.260727.30169.1719
117.85460.647-6.16060.6672-0.73954.8511-0.03310.1281-0.1653-0.13690.0304-0.08180.0966-0.07880.02550.2212-0.0068-0.00910.1116-0.03550.165450.936419.834321.8225
123.2933-1.76462.52511.0967-2.0126.8558-0.04660.0411-0.12840.0149-0.07730.09330.0425-0.08740.11970.2357-0.0344-0.00660.1448-0.06470.208744.222513.045524.2089
134.6517-2.8743-0.92396.98153.35851.8039-0.1826-0.2204-0.2477-0.02550.21090.11740.3443-0.07570.00860.2989-0.0512-0.00960.2799-0.02990.167147.83233.59811.2285
148.0324-0.3423-2.57548.70633.26857.9608-0.2852-0.3772-0.78870.6781-0.09610.31760.87210.2010.33330.4674-0.08730.05120.25670.02540.33742.2394-5.830413.2328
158.08630.0629-1.52528.64255.64383.993-0.2773-0.615-1.00040.90780.26740.08041.160.24220.11860.53810.00230.03070.34580.01310.305540.56622.970820.2215
161.2073-1.288-1.6061.87791.08823.4176-0.02890.1518-0.1501-0.2158-0.10170.23320.103-0.31660.130.3173-0.0194-0.03440.2367-0.06950.268545.3366.87746.2945
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 143 )A48 - 143
3X-RAY DIFFRACTION3chain 'A' and (resid 144 through 204 )A144 - 204
4X-RAY DIFFRACTION4chain 'A' and (resid 205 through 220 )A205 - 220
5X-RAY DIFFRACTION5chain 'A' and (resid 221 through 261 )A221 - 261
6X-RAY DIFFRACTION6chain 'A' and (resid 262 through 276 )A262 - 276
7X-RAY DIFFRACTION7chain 'B' and (resid 3 through 37 )B3 - 37
8X-RAY DIFFRACTION8chain 'B' and (resid 38 through 68 )B38 - 68
9X-RAY DIFFRACTION9chain 'B' and (resid 69 through 121 )B69 - 121
10X-RAY DIFFRACTION10chain 'B' and (resid 122 through 140 )B122 - 140
11X-RAY DIFFRACTION11chain 'B' and (resid 141 through 155 )B141 - 155
12X-RAY DIFFRACTION12chain 'B' and (resid 156 through 180 )B156 - 180
13X-RAY DIFFRACTION13chain 'B' and (resid 181 through 198 )B181 - 198
14X-RAY DIFFRACTION14chain 'B' and (resid 199 through 218 )B199 - 218
15X-RAY DIFFRACTION15chain 'B' and (resid 219 through 235 )B219 - 235
16X-RAY DIFFRACTION16chain 'B' and (resid 236 through 270 )B236 - 270

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