[English] 日本語
Yorodumi
- PDB-2ogx: The crystal structure of the molybdenum storage protein from Azot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ogx
TitleThe crystal structure of the molybdenum storage protein from Azotobacter vinelandii loaded with polyoxotungstates (WSto)
Components(Molybdenum storage protein subunit ...) x 2
KeywordsMETAL BINDING PROTEIN / open alpha/beta structure
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 / Amino acid kinase family / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Molybdenum storage protein subunit beta / ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / TRI-TUNGSTEN(VI) OXIDE COMPLEX / : / Molybdenum storage protein subunit alpha
Similarity search - Component
Biological speciesAzotobacter vinelandii (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsSchemberg, J. / Warkentin, E. / Ermler, U.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2007
Title: Towards Biological Supramolecular Chemistry: A Variety of Pocket-Templated, Individual Metal Oxide Cluster Nucleations in the Cavity of a Mo/W-Storage Protein.
Authors: Schemberg, J. / Schneider, K. / Demmer, U. / Warkentin, E. / Muller, A. / Ermler, U.
History
DepositionJan 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)63,98130
Polymers58,2712
Non-polymers5,70928
Water7,044391
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)191,94290
Polymers174,8146
Non-polymers17,12884
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 area39880 Å2
ΔGint-674 kcal/mol
Surface area45370 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)114.400, 114.400, 233.700
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-2008-

WO3

21B-2011-

W

DetailsThe biological assembly is a heterohexamer, (AB)3, generated from the heterodimer AB by the three fold axis: -y+1, x-y, z, and y-x+1, -x+1, z, respectively.

-
Components

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

#1: Protein Molybdenum storage protein subunit alpha / Mo storage protein alpha subunit / MoSto subunit alpha


Mass: 29564.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (unknown) / Strain: DSMZ 366 / References: UniProt: P84308
#2: Protein Molybdenum storage protein subunit beta / Mo storage protein subunit beta / MoSto subunit beta


Mass: 28707.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (unknown) / Strain: DSMZ 366 / References: UniProt: P84253

-
Non-polymers , 6 types, 419 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-WO3 / TRI-TUNGSTEN(VI) OXIDE COMPLEX


Mass: 759.512 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O13W3
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Chemical...
ChemComp-W / TUNGSTEN ION


Mass: 183.840 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: W
#7: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.78 Å3/Da / Density % sol: 67.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.05M MOPS, 0.05M sodium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X10SA10.9787
SYNCHROTRONSLS X10SA20.98
Detector
TypeIDDetectorDateDetails
MARMOSAIC 225 mm CCD1CCDApr 24, 2005mirrors
MARMOSAIC 225 mm CCD2CCDApr 24, 2005mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97871
20.981
ReflectionResolution: 1.6→10 Å / Num. all: 107052 / Num. obs: 107052 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rsym value: 6.5 / Net I/σ(I): 10.3
Reflection shellResolution: 0→0 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2 / Rsym value: 5.15 / % possible all: 82.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
XDSdata reduction
XDSdata scaling
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→10 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.905 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19645 5682 5 %RANDOM
Rwork0.17295 ---
all0.17414 107052 --
obs0.17414 107052 95.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20.39 Å20 Å2
2--0.78 Å20 Å2
3----1.17 Å2
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3812 0 70 391 4273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224010
X-RAY DIFFRACTIONr_angle_refined_deg1.911.9955466
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9865512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.74922.688160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52315650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7431538
X-RAY DIFFRACTIONr_chiral_restr0.1270.2642
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022997
X-RAY DIFFRACTIONr_nbd_refined0.2260.22107
X-RAY DIFFRACTIONr_nbtor_refined0.3230.22816
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2415
X-RAY DIFFRACTIONr_metal_ion_refined0.370.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.2138
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.229
X-RAY DIFFRACTIONr_mcbond_it1.2921.52606
X-RAY DIFFRACTIONr_mcangle_it2.02824122
X-RAY DIFFRACTIONr_scbond_it3.06331518
X-RAY DIFFRACTIONr_scangle_it4.6994.51343
LS refinement shellResolution: 1.603→1.644 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 334 -
Rwork0.259 6058 -
obs--76.21 %
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)
10.3605-0.2012-0.06030.83440.02240.8431-0.0127-0.0063-0.0567-0.0010.0050.12480.0803-0.15110.0077-0.0395-0.01710.00280.00350.001-0.016433.9923.16343.207
20.4214-0.1259-0.1740.48070.39870.8343-0.02620.0519-0.0794-0.0408-0.02270.05880.0731-0.04030.04890.0302-0.0097-0.0049-0.0415-0.0434-0.026747.6479.29113.31
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA31 - 8031 - 80
2X-RAY DIFFRACTION1AA131 - 276131 - 276
3X-RAY DIFFRACTION2BB32 - 8032 - 80
4X-RAY DIFFRACTION2BB131 - 270131 - 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