[English] 日本語
Yorodumi
- PDB-7aiz: Vanadium nitrogenase VFe protein, high CO state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7aiz
TitleVanadium nitrogenase VFe protein, high CO state
Components(Nitrogenase vanadium-iron protein ...) x 3
KeywordsOXIDOREDUCTASE / Nitrogenase / nitrogen fixation / CO reduction / atomic resolution
Function / homology
Function and homology information


vanadium-iron nitrogenase complex / vanadium ion binding / nitrogenase / nitrogenase activity / nitrogen fixation / iron-sulfur cluster binding / ATP binding / metal ion binding
Similarity search - Function
Nitrogenase vanadium-iron protein, alpha chain / Nitrogenase vanadium-iron, delta subunit / Nitrogenase vanadium-iron protein beta chain / Vanadium/alternative nitrogenase delta subunit / Vanadium/alternative nitrogenase delta subunit / Nitrogenase alpha chain / Nitrogenase component 1, alpha chain / Nitrogenase component 1, conserved site / Nitrogenases component 1 alpha and beta subunits signature 2. / Nitrogenases component 1 alpha and beta subunits signature 1. ...Nitrogenase vanadium-iron protein, alpha chain / Nitrogenase vanadium-iron, delta subunit / Nitrogenase vanadium-iron protein beta chain / Vanadium/alternative nitrogenase delta subunit / Vanadium/alternative nitrogenase delta subunit / Nitrogenase alpha chain / Nitrogenase component 1, alpha chain / Nitrogenase component 1, conserved site / Nitrogenases component 1 alpha and beta subunits signature 2. / Nitrogenases component 1 alpha and beta subunits signature 1. / Nitrogenase/oxidoreductase, component 1 / : / Nitrogenase component 1 type Oxidoreductase
Similarity search - Domain/homology
BICARBONATE ION / FE(8)-S(7) CLUSTER / CARBON MONOXIDE / FeV / 3-HYDROXY-3-CARBOXY-ADIPIC ACID / Nitrogenase vanadium-iron protein alpha chain / Nitrogenase vanadium-iron protein beta chain / Nitrogenase vanadium-iron protein delta chain
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsRohde, M. / Einsle, O.
Funding support Germany, 3items
OrganizationGrant numberCountry
European Research Council (ERC)310656 Germany
German Research Foundation (DFG)RTG 1976, project no. 235777276 Germany
German Research Foundation (DFG)PP 1927, project no. 311061829 Germany
CitationJournal: Sci Adv / Year: 2021
Title: Two ligand-binding sites in CO-reducing V nitrogenase reveal a general mechanistic principle.
Authors: Rohde, M. / Laun, K. / Zebger, I. / Stripp, S.T. / Einsle, O.
History
DepositionSep 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nitrogenase vanadium-iron protein alpha chain
B: Nitrogenase vanadium-iron protein beta chain
C: Nitrogenase vanadium-iron protein delta chain
D: Nitrogenase vanadium-iron protein alpha chain
E: Nitrogenase vanadium-iron protein beta chain
F: Nitrogenase vanadium-iron protein delta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,87836
Polymers240,3586
Non-polymers4,52030
Water45,0192499
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36780 Å2
ΔGint-139 kcal/mol
Surface area62350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.521, 80.041, 107.210
Angle α, β, γ (deg.)84.000, 72.480, 75.030
Int Tables number1
Space group name H-MP1

-
Components

-
Nitrogenase vanadium-iron protein ... , 3 types, 6 molecules ADBECF

#1: Protein Nitrogenase vanadium-iron protein alpha chain / Dinitrogenase 2 subunit alpha / Nitrogenase component I


Mass: 53951.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Gene: vnfD / Production host: Azotobacter vinelandii (bacteria) / References: UniProt: P16855, nitrogenase
#2: Protein Nitrogenase vanadium-iron protein beta chain / Dinitrogenase 2 subunit beta / Nitrogenase component I


Mass: 52839.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Gene: vnfK / Production host: Azotobacter vinelandii (bacteria) / References: UniProt: P16856, nitrogenase
#3: Protein Nitrogenase vanadium-iron protein delta chain / Dinitrogenase 2 subunit delta / Nitrogenase component I


Mass: 13387.959 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Gene: vnfG / Production host: Azotobacter vinelandii (bacteria) / References: UniProt: P16857, nitrogenase

-
Non-polymers , 9 types, 2529 molecules

#4: Chemical ChemComp-D6N / FeV


Mass: 692.329 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CFe7NS7V / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-HCA / 3-HYDROXY-3-CARBOXY-ADIPIC ACID


Mass: 206.150 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H10O7
#6: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#7: Chemical
ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#10: Chemical ChemComp-CLF / FE(8)-S(7) CLUSTER


Mass: 671.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe8S7
#11: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 2499 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Tris/HCl pH 7.5, magnesium chloride, ethylene glycol, PEG 8000, sodium dithionite

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.977944 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977944 Å / Relative weight: 1
ReflectionResolution: 1.05→48.39 Å / Num. obs: 1006898 / % possible obs: 93.3 % / Redundancy: 7 % / CC1/2: 0.999 / Net I/σ(I): 9.7
Reflection shellResolution: 1.05→1.07 Å / Num. unique obs: 47522 / CC1/2: 0.444

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ADR

7adr


Resolution: 1.05→48.39 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.982 / SU B: 0.92 / SU ML: 0.019 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.022 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1459 49972 5 %RANDOM
Rwork0.1244 ---
obs0.1255 956836 93.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.74 Å2 / Biso mean: 14.508 Å2 / Biso min: 4.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0.05 Å2-0.17 Å2
2---0.12 Å20.13 Å2
3----0.04 Å2
Refinement stepCycle: final / Resolution: 1.05→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16687 0 180 2602 19469
Biso mean--14.73 27.37 -
Num. residues----2098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.01317809
X-RAY DIFFRACTIONr_bond_other_d0.0010.01716665
X-RAY DIFFRACTIONr_angle_refined_deg3.081.67124192
X-RAY DIFFRACTIONr_angle_other_deg1.8571.58438455
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.50152201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.35622.42967
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.269153073
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.86915116
X-RAY DIFFRACTIONr_chiral_restr0.490.22283
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0221947
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024102
X-RAY DIFFRACTIONr_rigid_bond_restr5.984334472
LS refinement shellResolution: 1.05→1.077 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 3595 -
Rwork0.295 67492 -
all-71087 -
obs--88.88 %

+
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