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- PDB-7ady: CO-removed state of the active site of vanadium nitrogenase VFe p... -

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Basic information

Entry
Database: PDB / ID: 7ady
TitleCO-removed state of the active site of vanadium nitrogenase VFe protein
Components(Nitrogenase vanadium-iron protein ...) x 3
KeywordsOXIDOREDUCTASE / Nitrogenase / CO-turnover / CO-removal
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 / FeV / HYDROSULFURIC ACID / 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. / Grunau, K. / Einsle, O.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Research Council (ERC)310656 Germany
Citation
Journal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: CO Binding to the FeV Cofactor of CO-Reducing Vanadium Nitrogenase at Atomic Resolution.
Authors: Rohde, M. / Grunau, K. / Einsle, O.
#1: Journal: Angewandte Chemie / Year: 2020
Title: CO binding to the FeV Cofactor of CO-reducing Vanadium Nitrogenase at Atomic Resolution
Authors: Rohde, M. / Grunau, K. / Einsle, O.
History
DepositionSep 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: 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 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)244,71032
Polymers240,3586
Non-polymers4,35226
Water46,0642557
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36220 Å2
ΔGint-151 kcal/mol
Surface area62710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.576, 80.027, 107.200
Angle α, β, γ (deg.)83.990, 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, 2583 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-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2S / Feature type: SUBJECT OF INVESTIGATION
#8: 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
#9: Chemical ChemComp-CLF / FE(8)-S(7) CLUSTER


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


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#11: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2557 / 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: 50.48 %
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: 0.9116 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9116 Å / Relative weight: 1
ReflectionResolution: 1.05→46.66 Å / Num. obs: 1016322 / % possible obs: 94.1 % / Redundancy: 7 % / CC1/2: 0.999 / Net I/σ(I): 10.2
Reflection shellResolution: 1.05→1.07 Å / Num. unique obs: 40988 / CC1/2: 0.449

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FEA

6fea


Resolution: 1.05→46.66 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.963 / SU ML: 0.019 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.02 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.141 5039 0.5 %RANDOM
Rwork0.1208 ---
obs0.1208 1011232 94.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.62 Å2 / Biso mean: 13.231 Å2 / Biso min: 4.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.18 Å20.39 Å2
2--0.55 Å2-0.15 Å2
3----0.4 Å2
Refinement stepCycle: final / Resolution: 1.05→46.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16711 0 178 2678 19567
Biso mean--13.48 26.01 -
Num. residues----2101
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.01317903
X-RAY DIFFRACTIONr_bond_other_d0.0010.01716495
X-RAY DIFFRACTIONr_angle_refined_deg3.1161.67124330
X-RAY DIFFRACTIONr_angle_other_deg1.8641.58138312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg19.9865.3452287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92922.413945
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.448153056
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.65915116
X-RAY DIFFRACTIONr_chiral_restr0.4950.22293
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0221938
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023815
X-RAY DIFFRACTIONr_rigid_bond_restr4.388334396
LS refinement shellResolution: 1.05→1.077 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 363 -
Rwork0.296 71965 -
all-72328 -
obs--90.42 %

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