[English] 日本語
- PDB-6rj4: Molybdenum storage protein - P6422, ADP -

Open data

ID or keywords:


Basic information

Database: PDB / ID: 6rj4
TitleMolybdenum storage protein - P6422, ADP
Components(Molybdenum storage protein subunit ...) x 2
KeywordsMETAL BINDING PROTEIN / Mo storage / ATP hydrolysis / polyoxomolybdate clusters / amino acid kinase
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
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / Molybdenum storage protein subunit beta / Molybdenum storage protein subunit alpha
Similarity search - Component
Biological speciesAzotobacter vinelandii (unknown)
AuthorsErmler, U. / Bruenle, S.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2019
Title: Molybdate pumping into the molybdenum storage protein via an ATP-powered piercing mechanism.
Authors: Steffen Brünle / Martin L Eisinger / Juliane Poppe / Deryck J Mills / Julian D Langer / Janet Vonck / Ulrich Ermler /
Abstract: The molybdenum storage protein (MoSto) deposits large amounts of molybdenum as polyoxomolybdate clusters in a heterohexameric (αβ) cage-like protein complex under ATP consumption. Here, we suggest ...The molybdenum storage protein (MoSto) deposits large amounts of molybdenum as polyoxomolybdate clusters in a heterohexameric (αβ) cage-like protein complex under ATP consumption. Here, we suggest a unique mechanism for the ATP-powered molybdate pumping process based on X-ray crystallography, cryoelectron microscopy, hydrogen-deuterium exchange mass spectrometry, and mutational studies of MoSto from First, we show that molybdate, ATP, and Mg consecutively bind into the open ATP-binding groove of the β-subunit, which thereafter becomes tightly locked by fixing the previously disordered N-terminal arm of the α-subunit over the β-ATP. Next, we propose a nucleophilic attack of molybdate onto the γ-phosphate of β-ATP, analogous to the similar reaction of the structurally related UMP kinase. The formed instable phosphoric-molybdic anhydride becomes immediately hydrolyzed and, according to the current data, the released and accelerated molybdate is pressed through the cage wall, presumably by turning aside the Metβ149 side chain. A structural comparison between MoSto and UMP kinase provides valuable insight into how an enzyme is converted into a molecular machine during evolution. The postulated direct conversion of chemical energy into kinetic energy via an activating molybdate kinase and an exothermic pyrophosphatase reaction to overcome a proteinous barrier represents a novelty in ATP-fueled biochemistry, because normally, ATP hydrolysis initiates large-scale conformational changes to drive a distant process.
DepositionApr 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release

Structure visualization

Structure viewerMolecule:

Downloads & links


Deposited unit
B: Molybdenum storage protein subunit beta
A: Molybdenum storage protein subunit alpha
D: Molybdenum storage protein subunit beta
C: Molybdenum storage protein subunit alpha
F: Molybdenum storage protein subunit beta
E: Molybdenum storage protein subunit alpha
hetero molecules

Theoretical massNumber of molelcules
Total (without water)175,97323
B: Molybdenum storage protein subunit beta
A: Molybdenum storage protein subunit alpha
D: Molybdenum storage protein subunit beta
C: Molybdenum storage protein subunit alpha
F: Molybdenum storage protein subunit beta
E: Molybdenum storage protein subunit alpha
hetero molecules

B: Molybdenum storage protein subunit beta
A: Molybdenum storage protein subunit alpha
D: Molybdenum storage protein subunit beta
C: Molybdenum storage protein subunit alpha
F: Molybdenum storage protein subunit beta
E: Molybdenum storage protein subunit alpha
hetero molecules

Theoretical massNumber of molelcules
Total (without water)351,94546
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area68160 Å2
ΔGint-620 kcal/mol
Surface area94830 Å2
Unit cell
Length a, b, c (Å)188.680, 188.680, 188.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions





Molybdenum storage protein subunit ... , 2 types, 6 molecules BDFACE

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

Mass: 28247.582 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (strain DJ / ATCC BAA-1303) (unknown)
Strain: DJ / ATCC BAA-1303 / Gene: mosB, Avin_43210 / Production host: Escherichia coli BL21(DE3) (unknown) / 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.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (strain DJ / ATCC BAA-1303) (unknown)
Strain: DJ / ATCC BAA-1303 / Gene: mosA, Avin_43200 / Production host: Escherichia coli BL21(DE3) (unknown) / References: UniProt: P84308

Non-polymers , 6 types, 815 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate

Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate

Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-NA / SODIUM ION

Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate

Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#7: Chemical

Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water / Water

Mass: 18.015 Da / Num. of mol.: 798 / Source method: isolated from a natural source / Formula: H2O

Experimental details


ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5 / Details: 1.2 M ammonium sulfate, 0.1 M Tris-HCl, pH 8.5

Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 154099 / % possible obs: 99.8 % / Redundancy: 6.6 % / Rsym value: 0.07 / Net I/σ(I): 16.4
Reflection shellResolution: 1.9→2 Å / Num. unique obs: 21666 / Rsym value: 1.032


PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ndo
Resolution: 1.9→47.167 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2003 7787 5.05 %
Rwork0.1716 --
obs0.1731 154075 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→47.167 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11507 0 209 798 12514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712112
X-RAY DIFFRACTIONf_angle_d0.94316566
X-RAY DIFFRACTIONf_dihedral_angle_d15.1557304
X-RAY DIFFRACTIONf_chiral_restr0.0541933
X-RAY DIFFRACTIONf_plane_restr0.0052154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.30912670.3024783X-RAY DIFFRACTION100
1.9216-1.94420.28852710.25564806X-RAY DIFFRACTION100
1.9442-1.9680.29132320.25484818X-RAY DIFFRACTION100
1.968-1.99290.29192370.24394824X-RAY DIFFRACTION100
1.9929-2.01910.252500.23324822X-RAY DIFFRACTION100
2.0191-2.04670.29292600.22164836X-RAY DIFFRACTION100
2.0467-2.0760.26762360.23164815X-RAY DIFFRACTION100
2.076-2.1070.24412650.2084839X-RAY DIFFRACTION100
2.107-2.13990.21812590.20374778X-RAY DIFFRACTION100
2.1399-2.1750.23882520.19774855X-RAY DIFFRACTION100
2.175-2.21250.22962500.18694800X-RAY DIFFRACTION99
2.2125-2.25270.2492550.19914824X-RAY DIFFRACTION100
2.2527-2.2960.23462760.19354825X-RAY DIFFRACTION100
2.296-2.34290.22852600.18214876X-RAY DIFFRACTION100
2.3429-2.39390.19962660.17344816X-RAY DIFFRACTION100
2.3939-2.44950.23062610.18044871X-RAY DIFFRACTION100
2.4495-2.51080.23942770.18014814X-RAY DIFFRACTION100
2.5108-2.57870.20982570.17354866X-RAY DIFFRACTION100
2.5787-2.65450.22932520.1754883X-RAY DIFFRACTION100
2.6545-2.74020.21472530.18684885X-RAY DIFFRACTION100
2.7402-2.83810.22722390.17754892X-RAY DIFFRACTION100
2.8381-2.95180.21772790.18294852X-RAY DIFFRACTION100
2.9518-3.08610.20962600.18144891X-RAY DIFFRACTION100
3.0861-3.24870.21942640.18544902X-RAY DIFFRACTION100
3.2487-3.45220.20062640.16844890X-RAY DIFFRACTION100
3.4522-3.71870.16762620.15344944X-RAY DIFFRACTION100
3.7187-4.09270.17772690.14864975X-RAY DIFFRACTION100
4.0927-4.68450.14932610.12534967X-RAY DIFFRACTION100
4.6845-5.90010.15462810.14455044X-RAY DIFFRACTION100
5.9001-47.18140.17192720.15965295X-RAY DIFFRACTION100
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)
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 2 through 37 )
2X-RAY DIFFRACTION2chain 'B' and (resid 38 through 68 )
3X-RAY DIFFRACTION3chain 'B' and (resid 69 through 168 )
4X-RAY DIFFRACTION4chain 'B' and (resid 169 through 270 )
5X-RAY DIFFRACTION5chain 'A' and (resid 33 through 47 )
6X-RAY DIFFRACTION6chain 'A' and (resid 48 through 68 )
7X-RAY DIFFRACTION7chain 'A' and (resid 69 through 123 )
8X-RAY DIFFRACTION8chain 'A' and (resid 124 through 143 )
9X-RAY DIFFRACTION9chain 'A' and (resid 144 through 169 )
10X-RAY DIFFRACTION10chain 'A' and (resid 170 through 204 )
11X-RAY DIFFRACTION11chain 'A' and (resid 205 through 221 )
12X-RAY DIFFRACTION12chain 'A' and (resid 222 through 261 )
13X-RAY DIFFRACTION13chain 'A' and (resid 262 through 276 )
14X-RAY DIFFRACTION14chain 'D' and (resid 4 through 28 )
15X-RAY DIFFRACTION15chain 'D' and (resid 29 through 68 )
16X-RAY DIFFRACTION16chain 'D' and (resid 69 through 121 )
17X-RAY DIFFRACTION17chain 'D' and (resid 122 through 141 )
18X-RAY DIFFRACTION18chain 'D' and (resid 142 through 199 )
19X-RAY DIFFRACTION19chain 'D' and (resid 200 through 270 )
20X-RAY DIFFRACTION20chain 'C' and (resid 33 through 68 )
21X-RAY DIFFRACTION21chain 'C' and (resid 69 through 123 )
22X-RAY DIFFRACTION22chain 'C' and (resid 124 through 143 )
23X-RAY DIFFRACTION23chain 'C' and (resid 144 through 169 )
24X-RAY DIFFRACTION24chain 'C' and (resid 170 through 190 )
25X-RAY DIFFRACTION25chain 'C' and (resid 191 through 204 )
26X-RAY DIFFRACTION26chain 'C' and (resid 205 through 221 )
27X-RAY DIFFRACTION27chain 'C' and (resid 222 through 261 )
28X-RAY DIFFRACTION28chain 'C' and (resid 262 through 276 )
29X-RAY DIFFRACTION29chain 'F' and (resid 4 through 28 )
30X-RAY DIFFRACTION30chain 'F' and (resid 29 through 95 )
31X-RAY DIFFRACTION31chain 'F' and (resid 96 through 133 )
32X-RAY DIFFRACTION32chain 'F' and (resid 134 through 168 )
33X-RAY DIFFRACTION33chain 'F' and (resid 169 through 270 )
34X-RAY DIFFRACTION34chain 'E' and (resid 18 through 33 )
35X-RAY DIFFRACTION35chain 'E' and (resid 34 through 97 )
36X-RAY DIFFRACTION36chain 'E' and (resid 98 through 169 )
37X-RAY DIFFRACTION37chain 'E' and (resid 170 through 204 )
38X-RAY DIFFRACTION38chain 'E' and (resid 205 through 221 )
39X-RAY DIFFRACTION39chain 'E' and (resid 222 through 260 )
40X-RAY DIFFRACTION40chain 'E' and (resid 261 through 276 )

About Yorodumi


Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive


Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more