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- PDB-6o7s: Nitrogenase MoFeP mutant S188A from Azotobacter vinelandii in the... -

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Basic information

Entry
Database: PDB / ID: 6o7s
TitleNitrogenase MoFeP mutant S188A from Azotobacter vinelandii in the indigo carmine oxidized state
Components(Nitrogenase molybdenum-iron protein ...) x 2
KeywordsOXIDOREDUCTASE / Nitrogenase / 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
: / 3-HYDROXY-3-CARBOXY-ADIPIC ACID / Chem-ICS / FE(6)-S(7) CLUSTER / 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. / 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)233,03014
Polymers229,7664
Non-polymers3,26410
Water23,6181311
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, performed anaerobically
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30810 Å2
ΔGint-221 kcal/mol
Surface area57280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.775, 128.050, 107.539
Angle α, β, γ (deg.)90.00, 108.97, 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: 59519.879 Da / Num. of mol.: 2 / Mutation: S188A / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P07329, nitrogenase

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Non-polymers , 6 types, 1321 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-LPJ / FE(6)-S(7) CLUSTER


Mass: 559.525 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe6S7
#7: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1311 / 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: 43.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% PEG 8000, 100 mM Tris pH 8.0, 500 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2017 / 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: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.27→79.64 Å / Num. obs: 83478 / % possible obs: 92.2 % / Redundancy: 6.5 % / Biso Wilson estimate: 18.218 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.071 / Rrim(I) all: 0.132 / Net I/σ(I): 11.9
Reflection shellResolution: 2.27→2.31 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 4629 / CC1/2: 0.927 / Rpim(I) all: 0.231 / Rrim(I) all: 0.437 / % possible all: 97.1

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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: 2.27→35.45 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2078 8445 10.19 %
Rwork0.17 --
obs0.1739 82909 91.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.27→35.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15742 0 94 1311 17147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716291
X-RAY DIFFRACTIONf_angle_d0.71422442
X-RAY DIFFRACTIONf_dihedral_angle_d15.2839689
X-RAY DIFFRACTIONf_chiral_restr0.0922345
X-RAY DIFFRACTIONf_plane_restr0.0042833
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2703-2.2960.2313060.19112615X-RAY DIFFRACTION97
2.296-2.32310.23753090.18912611X-RAY DIFFRACTION97
2.3231-2.35140.22852990.19122597X-RAY DIFFRACTION97
2.3514-2.38110.21612960.18252633X-RAY DIFFRACTION97
2.3811-2.41250.23122980.18212591X-RAY DIFFRACTION96
2.4125-2.44550.22572600.18782621X-RAY DIFFRACTION95
2.4455-2.48040.23312870.18342577X-RAY DIFFRACTION95
2.4804-2.51740.23793020.19262434X-RAY DIFFRACTION92
2.5174-2.55680.2332820.19312515X-RAY DIFFRACTION91
2.5568-2.59870.24652760.18682542X-RAY DIFFRACTION96
2.5987-2.64350.23893080.19082637X-RAY DIFFRACTION97
2.6435-2.69150.41871350.35481310X-RAY DIFFRACTION48
2.6915-2.74330.26742770.20422673X-RAY DIFFRACTION98
2.7433-2.79930.22962740.18222623X-RAY DIFFRACTION97
2.7993-2.86010.21062940.17852618X-RAY DIFFRACTION96
2.8601-2.92660.23063140.17742526X-RAY DIFFRACTION95
2.9266-2.99970.2252860.17632572X-RAY DIFFRACTION94
2.9997-3.08080.22152590.18612492X-RAY DIFFRACTION91
3.0808-3.17140.24252680.1822515X-RAY DIFFRACTION93
3.1714-3.27370.21763070.16542624X-RAY DIFFRACTION97
3.2737-3.39060.21833230.16562608X-RAY DIFFRACTION97
3.3906-3.52630.24042130.20431849X-RAY DIFFRACTION68
3.5263-3.68660.19962510.17472190X-RAY DIFFRACTION94
3.6866-3.88070.17772980.15652351X-RAY DIFFRACTION93
3.8807-4.12350.17062220.14941968X-RAY DIFFRACTION72
4.1235-4.44140.15032990.12052677X-RAY DIFFRACTION98
4.4414-4.88730.14453230.11842670X-RAY DIFFRACTION99
4.8873-5.59210.16842730.13342660X-RAY DIFFRACTION97
5.5921-7.03640.18913080.15792520X-RAY DIFFRACTION93
7.0364-35.45420.18452980.16612645X-RAY DIFFRACTION95

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