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- PDB-6o7q: Nitrogenase MoFeP mutant S188A from Azotobacter vinelandii in the... -

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Basic information

Entry
Database: PDB / ID: 6o7q
TitleNitrogenase MoFeP mutant S188A from Azotobacter vinelandii in the dithionite reduced state after redox cycling
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
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 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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)233,20712
Polymers229,7664
Non-polymers3,4418
Water24,3381351
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, performed anaerobically
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31490 Å2
ΔGint-268 kcal/mol
Surface area57330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.437, 130.413, 107.751
Angle α, β, γ (deg.)90.00, 109.09, 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 , 5 types, 1359 molecules

#3: Chemical ChemComp-CLF / FE(8)-S(7) CLUSTER


Mass: 671.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe8S7
#4: Chemical ChemComp-HCA / 3-HYDROXY-3-CARBOXY-ADIPIC ACID


Mass: 206.150 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H10O7
#5: Chemical ChemComp-ICS / iron-sulfur-molybdenum cluster with interstitial carbon


Mass: 787.451 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CFe7MoS9
#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.: 1351 / 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: 2.21 Å3/Da / Density % sol: 44.43 %
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. 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: ALS / Beamline: 5.0.2 / Wavelength: 1.7389 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2018
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7389 Å / Relative weight: 1
ReflectionResolution: 2→48.684 Å / Num. obs: 135987 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 20.243 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.213 / Rpim(I) all: 0.137 / Rrim(I) all: 0.54 / Χ2: 0.94 / Net I/σ(I): 5.9
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.099 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 6741 / CC1/2: 0.709 / Rpim(I) all: 0.713 / Rrim(I) all: 1.315 / Χ2: 0.56 / % possible all: 99.9

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Processing

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

2min


Resolution: 2→48.684 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.84
RfactorNum. reflection% reflection
Rfree0.2294 13206 9.72 %
Rwork0.1863 --
obs0.1904 135859 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→48.684 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15771 0 96 1351 17218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00316343
X-RAY DIFFRACTIONf_angle_d0.7522581
X-RAY DIFFRACTIONf_dihedral_angle_d13.6999747
X-RAY DIFFRACTIONf_chiral_restr0.062353
X-RAY DIFFRACTIONf_plane_restr0.0032837
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.30194530.26714017X-RAY DIFFRACTION100
2.0227-2.04650.30464370.26434134X-RAY DIFFRACTION100
2.0465-2.07150.32714450.28494000X-RAY DIFFRACTION99
2.0715-2.09770.32424490.27444057X-RAY DIFFRACTION99
2.0977-2.12530.26444080.24754097X-RAY DIFFRACTION100
2.1253-2.15440.28324620.23554100X-RAY DIFFRACTION100
2.1544-2.18520.27384790.2353950X-RAY DIFFRACTION100
2.1852-2.21780.2714770.21714076X-RAY DIFFRACTION100
2.2178-2.25250.32074860.27044032X-RAY DIFFRACTION100
2.2525-2.28940.32714330.26024097X-RAY DIFFRACTION100
2.2894-2.32890.26344070.2084082X-RAY DIFFRACTION100
2.3289-2.37120.24194400.20094097X-RAY DIFFRACTION100
2.3712-2.41680.23974580.19694093X-RAY DIFFRACTION100
2.4168-2.46620.244150.19534076X-RAY DIFFRACTION100
2.4662-2.51980.25474040.20294114X-RAY DIFFRACTION100
2.5198-2.57840.25064280.19894112X-RAY DIFFRACTION100
2.5784-2.64290.22944400.19094085X-RAY DIFFRACTION100
2.6429-2.71430.25544630.19744056X-RAY DIFFRACTION100
2.7143-2.79420.25654610.20284040X-RAY DIFFRACTION100
2.7942-2.88440.25344600.1894090X-RAY DIFFRACTION100
2.8844-2.98740.25494800.18814081X-RAY DIFFRACTION100
2.9874-3.1070.23354440.18324084X-RAY DIFFRACTION100
3.107-3.24840.19544350.17414098X-RAY DIFFRACTION100
3.2484-3.41960.20694020.1734131X-RAY DIFFRACTION100
3.4196-3.63380.21133930.1654146X-RAY DIFFRACTION100
3.6338-3.91430.1884410.14964105X-RAY DIFFRACTION100
3.9143-4.3080.17864130.14044135X-RAY DIFFRACTION100
4.308-4.93080.16544230.13344129X-RAY DIFFRACTION100
4.9308-6.21030.17884530.15344109X-RAY DIFFRACTION100
6.2103-48.69820.21074170.17924230X-RAY DIFFRACTION100

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