[English] 日本語
Yorodumi
- PDB-6o7l: Nitrogenase MoFeP mutant S188A from Azotobacter vinelandii in the... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6o7l
TitleNitrogenase MoFeP mutant S188A from Azotobacter vinelandii in the dithionite reduced state after redox cycling
Components(Nitrogenase molybdenum-iron protein ...) x 2
KeywordsOXIDOREDUCTASE / Nitrogenase / S188A / MoFeP
Function / homology
Function and homology information


molybdenum-iron nitrogenase complex / nitrogenase / nitrogenase activity / nitrogen fixation / iron-sulfur cluster binding / ATP binding / metal ion binding
Similarity search - Function
Nitrogenase Molybdenum-iron Protein, subunit B, domain 4 / Nitrogenase Molybdenum-iron Protein, subunit B; domain 4 / Nitrogenase molybdenum-iron protein beta chain, N-terminal / Domain of unknown function (DUF3364) / Nitrogenase molybdenum-iron protein alpha chain / Nitrogenase molybdenum-iron protein beta 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 Molybdenum-iron Protein, subunit B, domain 4 / Nitrogenase Molybdenum-iron Protein, subunit B; domain 4 / Nitrogenase molybdenum-iron protein beta chain, N-terminal / Domain of unknown function (DUF3364) / Nitrogenase molybdenum-iron protein alpha chain / Nitrogenase molybdenum-iron protein beta 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 / Nitrogenase molybdenum iron protein domain / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE(8)-S(7) CLUSTER / : / 3-HYDROXY-3-CARBOXY-ADIPIC ACID / Chem-ICS / Nitrogenase molybdenum-iron protein alpha chain / Nitrogenase molybdenum-iron protein beta chain
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsRutledge, H.L. / Tezcan, F.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM099813 United States
Other privateHerman Frasch Foundation 735-HF12 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Redox-Dependent Metastability of the Nitrogenase P-Cluster.
Authors: Rutledge, H.L. / Rittle, J. / Williamson, L.M. / Xu, W.A. / Gagnon, D.M. / Tezcan, F.A.
History
DepositionMar 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nitrogenase molybdenum-iron protein alpha chain
B: Nitrogenase molybdenum-iron protein beta chain
C: Nitrogenase molybdenum-iron protein alpha chain
D: Nitrogenase molybdenum-iron protein beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,20712
Polymers229,7664
Non-polymers3,4418
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, performed anaerobically
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31270 Å2
ΔGint-258 kcal/mol
Surface area56020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.562, 131.029, 107.616
Angle α, β, γ (deg.)90.00, 110.85, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Nitrogenase molybdenum-iron protein ... , 2 types, 4 molecules ACBD

#1: Protein Nitrogenase molybdenum-iron protein alpha chain / Dinitrogenase / Nitrogenase component I


Mass: 55363.043 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / Variant: DJ / References: UniProt: P07328, nitrogenase
#2: Protein Nitrogenase molybdenum-iron protein beta chain / Dinitrogenase / Nitrogenase component I


Mass: 59519.879 Da / Num. of mol.: 2 / Mutation: S188A / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / Variant: DJ / References: UniProt: P07329, nitrogenase

-
Non-polymers , 5 types, 272 molecules

#3: Chemical ChemComp-HCA / 3-HYDROXY-3-CARBOXY-ADIPIC ACID


Mass: 206.150 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H10O7
#4: Chemical ChemComp-ICS / iron-sulfur-molybdenum cluster with interstitial carbon


Mass: 787.451 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CFe7MoS9
#5: Chemical ChemComp-CLF / FE(8)-S(7) CLUSTER


Mass: 671.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe8S7
#6: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.28 Å3/Da / Density % sol: 46.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 18% PEG 8000, 100 mM Tris pH 7.5, 500 mM NaCl, 10 mM dithionite

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.7389 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2018
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7389 Å / Relative weight: 1
ReflectionResolution: 2.26→49.422 Å / Num. obs: 97426 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 32.234 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.178 / Rpim(I) all: 0.114 / Rrim(I) all: 0.212 / Χ2: 0.9 / Net I/σ(I): 5.9
Reflection shellResolution: 2.26→2.3 Å / Redundancy: 2.2 % / Rmerge(I) obs: 1.164 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4788 / CC1/2: 0.845 / Rpim(I) all: 0.754 / Rrim(I) all: 1.392 / Χ2: 0.67 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2MIN

2min


Resolution: 2.26→49.422 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.61
RfactorNum. reflection% reflection
Rfree0.2537 9577 9.85 %
Rwork0.2082 --
obs0.2128 97426 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.26→49.422 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15676 0 96 264 16036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816240
X-RAY DIFFRACTIONf_angle_d1.03822460
X-RAY DIFFRACTIONf_dihedral_angle_d15.649656
X-RAY DIFFRACTIONf_chiral_restr0.0822349
X-RAY DIFFRACTIONf_plane_restr0.0042825
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.28570.43283290.38682847X-RAY DIFFRACTION100
2.2857-2.31260.41223210.3542915X-RAY DIFFRACTION100
2.3126-2.34080.42662890.352939X-RAY DIFFRACTION100
2.3408-2.37040.35662860.34832960X-RAY DIFFRACTION100
2.3704-2.40160.3762810.31972924X-RAY DIFFRACTION100
2.4016-2.43450.35522880.30842931X-RAY DIFFRACTION100
2.4345-2.46930.3173190.30522919X-RAY DIFFRACTION100
2.4693-2.50610.32953110.28312921X-RAY DIFFRACTION100
2.5061-2.54530.34012970.28882925X-RAY DIFFRACTION100
2.5453-2.5870.34423410.26762904X-RAY DIFFRACTION100
2.587-2.63160.31913400.26572861X-RAY DIFFRACTION100
2.6316-2.67950.32433120.26442981X-RAY DIFFRACTION100
2.6795-2.7310.33053360.2522892X-RAY DIFFRACTION100
2.731-2.78670.29883500.26932891X-RAY DIFFRACTION100
2.7867-2.84730.33563200.26012891X-RAY DIFFRACTION100
2.8473-2.91360.31813270.24192908X-RAY DIFFRACTION100
2.9136-2.98640.31183270.23912942X-RAY DIFFRACTION100
2.9864-3.06720.29892910.23042918X-RAY DIFFRACTION100
3.0672-3.15740.28143320.23222914X-RAY DIFFRACTION100
3.1574-3.25930.28693220.21922911X-RAY DIFFRACTION100
3.2593-3.37570.27683510.21572898X-RAY DIFFRACTION100
3.3757-3.51090.25882960.21442947X-RAY DIFFRACTION100
3.5109-3.67060.27143120.19362930X-RAY DIFFRACTION100
3.6706-3.86410.21072820.16882977X-RAY DIFFRACTION100
3.8641-4.1060.19263470.16072882X-RAY DIFFRACTION100
4.106-4.42290.18313440.15162895X-RAY DIFFRACTION100
4.4229-4.86760.18243000.14262954X-RAY DIFFRACTION100
4.8676-5.57120.19473090.15162958X-RAY DIFFRACTION100
5.5712-7.01590.2053590.16832927X-RAY DIFFRACTION100
7.0159-49.43350.18843580.15972976X-RAY DIFFRACTION100

+
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