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- PDB-6o7o: Nitrogenase MoFeP mutant F99Y/S188A from Azotobacter vinelandii i... -

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Basic information

Entry
Database: PDB / ID: 6o7o
TitleNitrogenase MoFeP mutant F99Y/S188A from Azotobacter vinelandii in the dithionite reduced state after redox cycling
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: 1.89 Å
AuthorsRutledge, H.L. / 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
Water36,1562007
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, performed anaerobically
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31470 Å2
ΔGint-265 kcal/mol
Surface area57360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.746, 128.678, 107.536
Angle α, β, γ (deg.)90.00, 108.94, 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 / 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 / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P07329, nitrogenase

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Non-polymers , 5 types, 2015 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
#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.: 2007 / 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: 2.16 Å3/Da / Density % sol: 43.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 18% PEG 8000, 100 mM Tris pH 8.5, 500 mM NaCl, 10 mM dithionite. Protein was redox cycled with 5 mM indigo carmine and 10 mM dithionite prior to crystallization.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.5498 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2018 / Details: Flat Si Rh coated M0
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5498 Å / Relative weight: 1
ReflectionResolution: 1.89→79.8 Å / Num. obs: 147935 / % possible obs: 94 % / Redundancy: 6.3 % / Biso Wilson estimate: 15.88 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.092 / Rrim(I) all: 0.169 / Χ2: 0.95 / Net I/σ(I): 8
Reflection shellResolution: 1.89→1.92 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.867 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 7300 / CC1/2: 0.695 / Rpim(I) all: 0.582 / Rrim(I) all: 1.051 / Χ2: 0.68 / % possible all: 93.5

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2MIN

2min


Resolution: 1.89→39.462 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1859 14707 9.96 %
Rwork0.1486 --
obs0.1523 147608 93.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.89→39.462 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15853 0 96 2007 17956
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116436
X-RAY DIFFRACTIONf_angle_d1.17522709
X-RAY DIFFRACTIONf_dihedral_angle_d14.2629815
X-RAY DIFFRACTIONf_chiral_restr0.0672364
X-RAY DIFFRACTIONf_plane_restr0.0072856
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.91140.29394720.23924409X-RAY DIFFRACTION93
1.9114-1.93390.25735090.22144298X-RAY DIFFRACTION93
1.9339-1.95750.25715030.22124405X-RAY DIFFRACTION93
1.9575-1.98230.264830.2114351X-RAY DIFFRACTION93
1.9823-2.00840.24745020.19964353X-RAY DIFFRACTION93
2.0084-2.03590.25084320.19634355X-RAY DIFFRACTION91
2.0359-2.0650.25574580.20244137X-RAY DIFFRACTION87
2.065-2.09580.23214830.17994263X-RAY DIFFRACTION92
2.0958-2.12850.21445260.16464461X-RAY DIFFRACTION95
2.1285-2.16340.20434550.15654459X-RAY DIFFRACTION94
2.1634-2.20070.20524880.16034574X-RAY DIFFRACTION95
2.2007-2.24070.2174590.17694378X-RAY DIFFRACTION93
2.2407-2.28380.26744720.2074379X-RAY DIFFRACTION93
2.2838-2.33040.20244920.15384463X-RAY DIFFRACTION94
2.3304-2.38110.21634510.15544143X-RAY DIFFRACTION88
2.3811-2.43650.20084830.14614286X-RAY DIFFRACTION92
2.4365-2.49740.18645330.14574488X-RAY DIFFRACTION95
2.4974-2.56490.19595240.14594507X-RAY DIFFRACTION96
2.5649-2.64040.18864670.14724549X-RAY DIFFRACTION96
2.6404-2.72560.2015390.14974459X-RAY DIFFRACTION96
2.7256-2.8230.19665280.14754506X-RAY DIFFRACTION96
2.823-2.9360.18454610.14494345X-RAY DIFFRACTION92
2.936-3.06950.18014900.14524382X-RAY DIFFRACTION92
3.0695-3.23130.16675100.144609X-RAY DIFFRACTION98
3.2313-3.43360.16755000.13284641X-RAY DIFFRACTION98
3.4336-3.69860.15444910.12574645X-RAY DIFFRACTION98
3.6986-4.07040.1455010.11314524X-RAY DIFFRACTION95
4.0704-4.65860.13244440.1074327X-RAY DIFFRACTION90
4.6586-5.86630.14425700.12124627X-RAY DIFFRACTION98
5.8663-39.47110.16554810.15494578X-RAY DIFFRACTION94

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