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- PDB-7aiz: Vanadium nitrogenase VFe protein, high CO state -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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Components

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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

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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
#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

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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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

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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

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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 %

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