[English] 日本語
Yorodumi
- PDB-6h6w: Molybdenum storage protein- H156A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6h6w
TitleMolybdenum storage protein- H156A
Components(Molybdenum storage protein subunit ...) x 2
KeywordsMETAL BINDING PROTEIN / polyoxometalate cluster assembly / molybdenum storage protein / bionanolab
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
Chem-8M0 / ADENOSINE-5'-TRIPHOSPHATE / Mo5 Cluster / MOLYBDENUM ATOM / MOLYBDATE ION / PHOSPHATE ION / Molybdenum storage protein subunit beta / Molybdenum storage protein subunit alpha
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsErmler, U. / Bruenle, S.
CitationJournal: J. Inorg. Biochem. / Year: 2018
Title: The molybdenum storage protein - A bionanolab for creating experimentally alterable polyoxomolybdate clusters.
Authors: Brunle, S. / Poppe, J. / Hail, R. / Demmer, U. / Ermler, U.
History
DepositionJul 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,92712
Polymers57,4262
Non-polymers4,50110
Water6,341352
1
B: Molybdenum storage protein subunit beta
A: Molybdenum storage protein subunit alpha
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)185,78036
Polymers172,2786
Non-polymers13,50230
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 area33640 Å2
ΔGint-216 kcal/mol
Surface area44910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.270, 114.270, 234.140
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-304-

MOO

21A-426-

HOH

-
Components

-
Molybdenum storage protein subunit ... , 2 types, 2 molecules BA

#1: 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(DE3) (bacteria) / References: UniProt: P84253
#2: Protein Molybdenum storage protein subunit alpha / Mo storage protein subunit alpha / MoSto subunit alpha


Mass: 29178.512 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(DE3) (bacteria) / References: UniProt: P84308

-
Non-polymers , 8 types, 362 molecules

#3: 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
#4: Chemical ChemComp-FUQ / Mo5 Cluster


Mass: 899.844 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H20Mo5O25
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-8M0 / bis(mu4-oxo)-tetrakis(mu3-oxo)-hexakis(mu2-oxo)-hexadecaoxo-octamolybdenum (VI) / Octamolybdate [Mo(VI)8O28]8-


Mass: 1215.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mo8O28
#8: Chemical ChemComp-MOO / MOLYBDATE ION / MOLYBDATE / Molybdate


Mass: 159.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: MoO4
#9: Chemical ChemComp-MO / MOLYBDENUM ATOM


Mass: 95.940 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mo
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.84 Å3/Da / Density % sol: 67.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M sodium citrate, pH 5.6, 1 M ammonium phosphate, 10% glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.738 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.738 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 144386 / % possible obs: 98.6 % / Redundancy: 3.2 % / Rsym value: 0.062 / Net I/σ(I): 12.6
Reflection shellResolution: 1.9→2 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ndo

4ndo


Resolution: 1.9→49.48 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.31 / Phase error: 20.77
RfactorNum. reflection% reflection
Rfree0.2031 7170 4.97 %
Rwork0.1758 --
obs0.1772 144293 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→49.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3795 0 172 350 4317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124113
X-RAY DIFFRACTIONf_angle_d1.9795786
X-RAY DIFFRACTIONf_dihedral_angle_d8.323283
X-RAY DIFFRACTIONf_chiral_restr0.075643
X-RAY DIFFRACTIONf_plane_restr0.007709
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8710.76682220.67023972X-RAY DIFFRACTION86
1.871-1.8930.67052410.62014222X-RAY DIFFRACTION92
1.893-1.91610.46692260.49334464X-RAY DIFFRACTION96
1.9161-1.94040.36611950.39444539X-RAY DIFFRACTION97
1.9404-1.96590.35852230.31794514X-RAY DIFFRACTION98
1.9659-1.99290.28992350.25974535X-RAY DIFFRACTION98
1.9929-2.02130.26152290.21934588X-RAY DIFFRACTION99
2.0213-2.05150.21572230.19984624X-RAY DIFFRACTION99
2.0515-2.08360.24852490.19294610X-RAY DIFFRACTION100
2.0836-2.11770.20352460.18464603X-RAY DIFFRACTION100
2.1177-2.15420.2472190.17514660X-RAY DIFFRACTION100
2.1542-2.19340.20952460.17164601X-RAY DIFFRACTION100
2.1934-2.23560.19432040.16934661X-RAY DIFFRACTION100
2.2356-2.28120.22012770.17414579X-RAY DIFFRACTION100
2.2812-2.33080.2112500.16724630X-RAY DIFFRACTION100
2.3308-2.3850.21671790.16064681X-RAY DIFFRACTION100
2.385-2.44470.19232540.1594601X-RAY DIFFRACTION100
2.4447-2.51080.2042670.16174595X-RAY DIFFRACTION100
2.5108-2.58470.18432180.15294643X-RAY DIFFRACTION100
2.5847-2.66810.16872540.14914602X-RAY DIFFRACTION100
2.6681-2.76340.1872480.16274629X-RAY DIFFRACTION100
2.7634-2.87410.18762490.16724651X-RAY DIFFRACTION100
2.8741-3.00490.21472510.1634621X-RAY DIFFRACTION100
3.0049-3.16320.17382310.16064613X-RAY DIFFRACTION100
3.1632-3.36140.19152740.15534615X-RAY DIFFRACTION100
3.3614-3.62090.15962410.14774606X-RAY DIFFRACTION100
3.6209-3.98510.18082500.14394626X-RAY DIFFRACTION100
3.9851-4.56140.15252600.134617X-RAY DIFFRACTION100
4.5614-5.74550.15372580.15174601X-RAY DIFFRACTION100
5.7455-49.4980.23862510.21754620X-RAY DIFFRACTION100
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)
18.6357-0.64530.76967.8017-0.93538.5248-0.15750.5135-0.0728-0.63790.02761.0199-0.4058-0.84180.16040.30680.0885-0.07250.4866-0.03440.488619.678632.450822.5269
20.5853-0.09840.03820.46920.0290.6326-0.01660.1173-0.0363-0.1065-0.00120.01280.0842-0.04940.01860.2233-0.0233-0.01560.1846-0.03480.177451.466914.949917.9304
34.576-0.81173.12068.0982-3.75483.41690.0294-0.25680.51510.53360.1380.6639-0.8629-0.3614-0.13420.3540.0350.04210.2731-0.04670.312953.666425.399811.6404
41.6351-0.58140.80070.35880.37563.4378-0.05210.0101-0.06430.04570.01840.0560.0115-0.02770.03160.2258-0.0190.00370.1643-0.03650.228444.861513.730726.1901
52.4433-0.2528-0.95281.68070.95481.6132-0.128-0.1493-0.21790.0877-0.01940.17110.304-0.11080.13090.3366-0.0282-0.00290.245-0.03020.242943.73832.556811.5841
62.8288-2.13680.36962.6606-0.74511.77610.0019-0.0398-0.09680.08370.01170.1371-0.0012-0.11170.00210.1563-0.03120.01070.2029-0.0020.163337.080729.979447.551
70.2391-0.11650.21130.7748-0.12171.2130.01490.00210.0038-0.0453-0.00980.05480.0262-0.0644-0.00550.1462-0.00690.00870.187-0.00690.169437.676328.294636.8263
82.138-0.2865-0.38912.05490.65671.7588-0.0458-0.0005-0.23430.00760.03830.31390.2431-0.2934-0.01080.1688-0.0591-0.00130.23090.01940.20727.448717.777545.2552
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 3 through 14 )
2X-RAY DIFFRACTION2chain 'B' and (resid 15 through 121 )
3X-RAY DIFFRACTION3chain 'B' and (resid 122 through 147 )
4X-RAY DIFFRACTION4chain 'B' and (resid 148 through 180 )
5X-RAY DIFFRACTION5chain 'B' and (resid 181 through 270 )
6X-RAY DIFFRACTION6chain 'A' and (resid 33 through 68 )
7X-RAY DIFFRACTION7chain 'A' and (resid 69 through 204 )
8X-RAY DIFFRACTION8chain 'A' and (resid 205 through 276 )

+
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