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- PDB-6o0b: Structural and Mechanistic Insights into CO2 Activation by Nitrog... -

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Basic information

Entry
Database: PDB / ID: 6o0b
TitleStructural and Mechanistic Insights into CO2 Activation by Nitrogenase Iron Protein
ComponentsNitrogenase iron protein
KeywordsOXIDOREDUCTASE / Nitrogenase / Iron protein / Iron-sulfur cluster
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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold ...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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Nitrogenase iron protein
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsRettberg, L.A. / Stiebritz, M.T. / Kang, W. / Lee, C.C. / Ribbe, M.W. / Hu, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1651398 United States
CitationJournal: Chemistry / Year: 2019
Title: Structural and Mechanistic Insights into CO2Activation by Nitrogenase Iron Protein.
Authors: Rettberg, L.A. / Stiebritz, M.T. / Kang, W. / Lee, C.C. / Ribbe, M.W. / Hu, Y.
History
DepositionFeb 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 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 1.2Nov 27, 2019Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitrogenase iron protein
B: Nitrogenase iron protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1863
Polymers62,8342
Non-polymers3521
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-41 kcal/mol
Surface area21980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.071, 93.045, 60.796
Angle α, β, γ (deg.)90.000, 98.875, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

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


Mass: 31417.045 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (strain DJ / ATCC BAA-1303) (bacteria)
Strain: DJ / ATCC BAA-1303 / Gene: nifH, Avin_01380 / Production host: Azotobacter vinelandii DJ (bacteria) / References: UniProt: C1DGZ6, nitrogenase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
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: 2.58 Å3/Da / Density % sol: 52.39 %
Crystal growTemperature: 295 K / Method: liquid diffusion / pH: 8 / Details: PEG 4000, sodium chloride, Tris, Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97557 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97557 Å / Relative weight: 1
ReflectionResolution: 1.6→38.27 Å / Num. obs: 81373 / % possible obs: 98.14 % / Redundancy: 6 % / CC1/2: 0.995 / Rpim(I) all: 0.046 / Net I/σ(I): 8
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 6.1 % / Num. unique obs: 5737 / CC1/2: 0.452 / Rpim(I) all: 1.321 / % possible all: 98

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALA3.3.22data scaling
PHASER2.8.3phasing
PHENIX1.16-3549refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G1M

1g1m


Resolution: 1.6→38.27 Å / SU ML: 0.198 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.7931
RfactorNum. reflection% reflection
Rfree0.2185 1988 2.45 %
Rwork0.2062 --
obs0.2065 81050 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 33.48 Å2
Refinement stepCycle: LAST / Resolution: 1.6→38.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4128 0 8 252 4388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00724188
X-RAY DIFFRACTIONf_angle_d0.80395677
X-RAY DIFFRACTIONf_chiral_restr0.0631679
X-RAY DIFFRACTIONf_plane_restr0.0053736
X-RAY DIFFRACTIONf_dihedral_angle_d8.4542535
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.29211460.30545591X-RAY DIFFRACTION97.87
1.64-1.680.28051370.27265650X-RAY DIFFRACTION98.45
1.68-1.730.26741380.25965667X-RAY DIFFRACTION98.26
1.73-1.790.26751500.24495590X-RAY DIFFRACTION97.64
1.79-1.850.25131260.23945481X-RAY DIFFRACTION95.96
1.85-1.930.23491410.24665656X-RAY DIFFRACTION98.61
1.93-2.020.25081560.23445658X-RAY DIFFRACTION98.33
2.02-2.120.24671440.23425629X-RAY DIFFRACTION98.28
2.12-2.250.27181330.22545601X-RAY DIFFRACTION97.1
2.25-2.430.2261390.21865684X-RAY DIFFRACTION99.01
2.43-2.670.2341460.22215682X-RAY DIFFRACTION98.83
2.67-3.060.19921470.22635647X-RAY DIFFRACTION97.71
3.06-3.850.23931410.18945740X-RAY DIFFRACTION99.26
3.85-38.270.1631440.16225786X-RAY DIFFRACTION98.72

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