[English] 日本語
Yorodumi
- PDB-6q93: MgADP-bound Fe protein of Vanadium nitrogenase from Azotobacter v... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6q93
TitleMgADP-bound Fe protein of Vanadium nitrogenase from Azotobacter vinelandii
ComponentsNitrogenase iron protein
KeywordsELECTRON TRANSPORT / Biological nitrogen fixation / Dinitrogenase reductase / Vanadium nitrogenase / Fe protein / VnfH
Function / homology
Function and homology information


: / nitrogenase / nitrogenase activity / nitrogen fixation / 4 iron, 4 sulfur cluster binding / ATP binding / metal ion binding
Similarity search - Function
Nitrogenase iron protein NifH / NifH/frxC family / NifH/chlL conserved site / 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family / NifH/frxC family signature 2. / NifH/frxC family signature 1. / NIFH_FRXC family profile. / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase ...Nitrogenase iron protein NifH / NifH/frxC family / NifH/chlL conserved site / 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family / NifH/frxC family signature 2. / NifH/frxC family signature 1. / NIFH_FRXC family profile. / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / IRON/SULFUR CLUSTER / Nitrogenase iron protein
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRohde, M. / Gerhardt, S. / Einsle, O.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Research Council310656 Germany
CitationJournal: J. Biol. Inorg. Chem. / Year: 2018
Title: Crystal structure of VnfH, the iron protein component of vanadium nitrogenase.
Authors: Rohde, M. / Trncik, C. / Sippel, D. / Gerhardt, S. / Einsle, O.
History
DepositionDec 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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 iron protein
B: Nitrogenase iron protein
C: Nitrogenase iron protein
D: Nitrogenase iron protein
E: Nitrogenase iron protein
F: Nitrogenase iron protein
G: Nitrogenase iron protein
H: Nitrogenase iron protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,55330
Polymers248,4858
Non-polymers5,06722
Water7,008389
1
A: Nitrogenase iron protein
B: Nitrogenase iron protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3767
Polymers62,1212
Non-polymers1,2555
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-74 kcal/mol
Surface area20180 Å2
MethodPISA
2
C: Nitrogenase iron protein
D: Nitrogenase iron protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4008
Polymers62,1212
Non-polymers1,2796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-86 kcal/mol
Surface area20170 Å2
MethodPISA
3
E: Nitrogenase iron protein
F: Nitrogenase iron protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4008
Polymers62,1212
Non-polymers1,2796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-75 kcal/mol
Surface area19950 Å2
MethodPISA
4
G: Nitrogenase iron protein
H: Nitrogenase iron protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3767
Polymers62,1212
Non-polymers1,2555
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-78 kcal/mol
Surface area20210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.573, 176.857, 354.225
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein
Nitrogenase iron protein / Nitrogenase Fe protein / Nitrogenase component II / Nitrogenase reductase


Mass: 31060.686 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Source: (natural) Azotobacter vinelandii (strain DJ / ATCC BAA-1303) (bacteria)
Strain: DJ / ATCC BAA-1303 / References: UniProt: C1DI30, nitrogenase
#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 2.98 Å3/Da / Density % sol: 58.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: Tris/HCl buffer, magnesium chloride, ADP, PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→49.54 Å / Num. obs: 150174 / % possible obs: 99.9 % / Redundancy: 27.8 % / Biso Wilson estimate: 46.59 Å2 / Net I/σ(I): 13.2
Reflection shellResolution: 2.2→2.24 Å

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FP6

1fp6


Resolution: 2.2→49.1 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.942 / SU R Cruickshank DPI: 0.201 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.198 / SU Rfree Blow DPI: 0.157 / SU Rfree Cruickshank DPI: 0.159
RfactorNum. reflection% reflectionSelection details
Rfree0.215 7601 5.06 %RANDOM
Rwork0.2 ---
obs0.201 150093 99.9 %-
Displacement parametersBiso mean: 68.75 Å2
Baniso -1Baniso -2Baniso -3
1-8.734 Å20 Å20 Å2
2---14.1316 Å20 Å2
3---5.3976 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: 1 / Resolution: 2.2→49.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16541 0 258 389 17188
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00917027HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1223012HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6097SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3020HARMONIC5
X-RAY DIFFRACTIONt_it17027HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3
X-RAY DIFFRACTIONt_other_torsion18.34
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2249SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact19936SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.21 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2717 155 5.16 %
Rwork0.2324 2847 -
all0.2345 3002 -
obs--99.9 %
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)
10.49760.2927-0.06522.25170.40043.33750.08320.0489-0.06290.2412-0.0464-0.1122-0.1537-0.099-0.0368-0.02580.07960.0185-0.06910.0162-0.1083-12.605-32.5497-17.4172
22.5341-1.8287-0.1820-0.78851.6465-0.2455-0.14590.54180.3923-0.0504-0.5442-0.36370.38990.2959-0.11960.0442-0.1449-0.3040.04620.3046.1315-13.7204-27.9895
32.45090.3414-1.11830.612-0.75314.4432-0.10620.5442-0.03130.02290.07580.0134-0.1247-0.32030.0304-0.304-0.002-0.01460.2036-0.0302-0.2509-17.2673-44.9973-68.653
41.76910.7411-0.61052.5279-1.12452.3643-0.23090.1938-0.5442-0.07280.0826-0.41120.3584-0.06780.1483-0.23640.07550.0339-0.0711-0.07490.053-22.307-65.1861-49.9604
52.6191-0.2818-0.66461.3247-0.15661.48230.1552-0.12-0.01970.5442-0.13730.54420.3434-0.0265-0.01790.09850.01120.152-0.304-0.0880.11966.3954-80.9164-26.7316
60.92060.00840.44293.5646-0.18812.67150.01960.00990.00920.5008-0.21270.16270.0273-0.02440.193-0.02340.0640.0334-0.1079-0.0217-0.132525.9211-61.2672-18.5171
72.10010.59260.66022.31730.56262.40130.07290.36150.54420.18590.05620.2032-0.17230.0936-0.1291-0.24740.08680.0687-0.02740.13490.021934.4188-30.2986-52.0782
83.0780.46430.73010.79190.8113.4705-0.07730.5442-0.01230.10340.1781-0.03570.33630.5149-0.1008-0.3040.0729-0.00570.27470.0261-0.282930.3824-50.5172-70.6813
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }

+
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