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- PDB-6o7m: Nitrogenase MoFeP mutant F99Y from Azotobacter vinelandii in the ... -

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Basic information

Entry
Database: PDB / ID: 6o7m
TitleNitrogenase MoFeP mutant F99Y from Azotobacter vinelandii in the indigo carmine oxidized state
Components(Nitrogenase molybdenum-iron protein ...) x 2
KeywordsOXIDOREDUCTASE / Nitrogenase / F99Y / 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: 1.4 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)233,27112
Polymers229,8304
Non-polymers3,4418
Water45,7762541
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, performed anaerobically
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31670 Å2
ΔGint-261 kcal/mol
Surface area57810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.457, 127.788, 107.539
Angle α, β, γ (deg.)90.00, 109.00, 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: 59551.879 Da / Num. of mol.: 2 / Mutation: F99Y / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P07329, nitrogenase

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Non-polymers , 5 types, 2549 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.: 2541 / 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: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 18% PEG 8000, 100 mM Tris pH 8.3, 500 mM NaCl, 5 mM indigo carmine (IDS)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9537 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: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.4→62.92 Å / Num. obs: 357803 / % possible obs: 93.7 % / Redundancy: 5.9 % / CC1/2: 0.958 / Rmerge(I) obs: 0.197 / Rpim(I) all: 0.13 / Rrim(I) all: 0.237 / Χ2: 0.89 / Net I/σ(I): 6.1
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 5.8 % / Rmerge(I) obs: 2.22 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 16856 / CC1/2: 0.187 / Rpim(I) all: 1.442 / Rrim(I) all: 2.661 / Χ2: 0.79 / % possible all: 89.1

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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: 1.4→40.109 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2083 35606 10.01 %Random selection
Rwork0.1826 ---
obs0.1851 355856 93.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→40.109 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15886 0 96 2541 18523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716553
X-RAY DIFFRACTIONf_angle_d0.88622873
X-RAY DIFFRACTIONf_dihedral_angle_d15.7726243
X-RAY DIFFRACTIONf_chiral_restr0.0722381
X-RAY DIFFRACTIONf_plane_restr0.0062872
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.41590.369110760.350710152X-RAY DIFFRACTION88
1.4159-1.43250.355210350.34049968X-RAY DIFFRACTION87
1.4325-1.450.3810740.361210046X-RAY DIFFRACTION88
1.45-1.46840.342711340.332710043X-RAY DIFFRACTION88
1.4684-1.48770.362910620.338510125X-RAY DIFFRACTION88
1.4877-1.50810.301710740.298310210X-RAY DIFFRACTION89
1.5081-1.52960.384210800.36379542X-RAY DIFFRACTION83
1.5296-1.55240.311230.279610064X-RAY DIFFRACTION88
1.5524-1.57670.282612310.246210632X-RAY DIFFRACTION93
1.5767-1.60250.273111950.236110831X-RAY DIFFRACTION94
1.6025-1.63020.258211750.2310852X-RAY DIFFRACTION95
1.6302-1.65980.24412790.221610860X-RAY DIFFRACTION95
1.6598-1.69170.244413290.210710855X-RAY DIFFRACTION96
1.6917-1.72630.251512470.212410931X-RAY DIFFRACTION96
1.7263-1.76380.226812600.189811074X-RAY DIFFRACTION97
1.7638-1.80480.213612480.180111024X-RAY DIFFRACTION97
1.8048-1.850.211412230.17410939X-RAY DIFFRACTION95
1.85-1.90.231411390.201710076X-RAY DIFFRACTION88
1.9-1.95590.263511250.225710269X-RAY DIFFRACTION89
1.9559-2.0190.193712150.160811234X-RAY DIFFRACTION98
2.019-2.09120.22412560.203611079X-RAY DIFFRACTION97
2.0912-2.17490.184212720.153311225X-RAY DIFFRACTION98
2.1749-2.27390.201913170.17211129X-RAY DIFFRACTION98
2.2739-2.39380.165311530.139411365X-RAY DIFFRACTION98
2.3938-2.54370.170912440.143711074X-RAY DIFFRACTION97
2.5437-2.74010.180211400.153610142X-RAY DIFFRACTION88
2.7401-3.01570.179811930.151411083X-RAY DIFFRACTION96
3.0157-3.45190.169812700.144311234X-RAY DIFFRACTION98
3.4519-4.34820.146212590.123111043X-RAY DIFFRACTION96
4.3482-40.12540.156211780.144711149X-RAY DIFFRACTION95

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