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- PDB-6o7r: Nitrogenase MoFeP mutant F99Y, S188A from Azotobacter vinelandii ... -

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Basic information

Entry
Database: PDB / ID: 6o7r
TitleNitrogenase MoFeP mutant F99Y, S188A from Azotobacter vinelandii in the dithionite reduced state
Components(Nitrogenase molybdenum-iron protein ...) x 2
KeywordsOXIDOREDUCTASE / Nitrogenase / F99Y/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: 2.27 Å
AuthorsRutledge, H.L. / Williamson, L.M. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)233,23912
Polymers229,7984
Non-polymers3,4418
Water23,9061327
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, performed anaerobically
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31540 Å2
ΔGint-259 kcal/mol
Surface area57260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.610, 128.810, 107.640
Angle α, β, γ (deg.)90.00, 109.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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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 / Details: nifD / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P07328, nitrogenase
#2: Protein Nitrogenase molybdenum-iron protein beta chain / Dinitrogenase / Nitrogenase component I


Mass: 59535.879 Da / Num. of mol.: 2 / Mutation: F99Y, S188A / Source method: isolated from a natural source / Details: nifD / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P07329, nitrogenase

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Non-polymers , 5 types, 1335 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 / Feature type: SUBJECT OF INVESTIGATION
#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.: 1327 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG 8000, 100 mM Tris pH 8.0, 500 mM NaCl, 10 mM dithionite

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.7388 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2018 / Details: Rh coated flat bent M0
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7388 Å / Relative weight: 1
ReflectionResolution: 2.27→79.84 Å / Num. obs: 82483 / % possible obs: 90.7 % / Redundancy: 5.8 % / CC1/2: 0.984 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.079 / Rrim(I) all: 0.14 / Χ2: 0.99 / Net I/σ(I): 9.7
Reflection shellResolution: 2.27→2.31 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 4590 / CC1/2: 0.901 / Rpim(I) all: 0.269 / Rrim(I) all: 0.471 / Χ2: 0.96 / % possible all: 95.3

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Processing

Software
NameClassification
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2MIN

2min


Resolution: 2.27→47.311 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.51
RfactorNum. reflection% reflection
Rfree0.2077 8174 9.92 %
Rwork0.1637 --
obs0.1681 82389 90.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.27→47.311 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15805 0 96 1329 17230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716411
X-RAY DIFFRACTIONf_angle_d0.79122696
X-RAY DIFFRACTIONf_dihedral_angle_d15.4599800
X-RAY DIFFRACTIONf_chiral_restr0.0592371
X-RAY DIFFRACTIONf_plane_restr0.0052856
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2704-2.29620.25932860.19772613X-RAY DIFFRACTION95
2.2962-2.32320.24272750.1852603X-RAY DIFFRACTION95
2.3232-2.35150.27683000.19292532X-RAY DIFFRACTION94
2.3515-2.38130.23492660.19142555X-RAY DIFFRACTION93
2.3813-2.41260.22822790.17812458X-RAY DIFFRACTION91
2.4126-2.44570.24232420.18492308X-RAY DIFFRACTION84
2.4457-2.48060.26762500.18342452X-RAY DIFFRACTION89
2.4806-2.51760.22662850.18072640X-RAY DIFFRACTION97
2.5176-2.5570.23012840.1772696X-RAY DIFFRACTION97
2.557-2.59890.21723080.17712586X-RAY DIFFRACTION97
2.5989-2.64370.2393010.18822647X-RAY DIFFRACTION97
2.6437-2.69170.28391620.20471417X-RAY DIFFRACTION53
2.6917-2.74350.24572940.1952636X-RAY DIFFRACTION96
2.7435-2.79950.25153000.1912533X-RAY DIFFRACTION95
2.7995-2.86040.24732610.18362614X-RAY DIFFRACTION95
2.8604-2.92690.24242550.1872554X-RAY DIFFRACTION92
2.9269-3.00010.22852610.18172247X-RAY DIFFRACTION83
3.0001-3.08120.22252680.17952495X-RAY DIFFRACTION91
3.0812-3.17180.21743190.17762640X-RAY DIFFRACTION98
3.1718-3.27420.22992950.16912657X-RAY DIFFRACTION98
3.2742-3.39120.20642680.16832708X-RAY DIFFRACTION97
3.3912-3.52690.22192310.15981906X-RAY DIFFRACTION71
3.5269-3.68740.18632600.14682209X-RAY DIFFRACTION96
3.6874-3.88170.17442740.13842433X-RAY DIFFRACTION94
3.8817-4.12480.16482130.12631906X-RAY DIFFRACTION70
4.1248-4.4430.1552730.12482507X-RAY DIFFRACTION91
4.443-4.88970.15663240.11992681X-RAY DIFFRACTION99
4.8897-5.59630.17912870.13642706X-RAY DIFFRACTION98
5.5963-7.0470.1762920.16272637X-RAY DIFFRACTION95
7.047-47.32130.18492610.17152639X-RAY DIFFRACTION93

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