[English] 日本語
Yorodumi
- PDB-6gwv: Molybdenum storage protein without polymolybdate clusters and ATP -

+
Open data


ID or keywords:

Loading...

-
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 / Amino acid kinase family / Acetylglutamate kinase-like superfamily / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
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 / Sulfate


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


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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

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)
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)

+
About Yorodumi

-
News

-
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

-
Yorodumi

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