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- PDB-6o7n: Nitrogenase MoFeP mutant F99Y/S188A from Azotobacter vinelandii i... -

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Basic information

Entry
Database: PDB / ID: 6o7n
TitleNitrogenase MoFeP mutant F99Y/S188A from Azotobacter vinelandii in the indigo carmine oxidized 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: 1.75 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)233,23912
Polymers229,7984
Non-polymers3,4418
Water38,3182127
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, performed anaerobically
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31740 Å2
ΔGint-265 kcal/mol
Surface area57550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.337, 127.960, 107.509
Angle α, β, γ (deg.)90.00, 109.01, 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) / Strain: DJ / 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) / Strain: DJ / References: UniProt: P07329, nitrogenase

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Non-polymers , 5 types, 2135 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.: 2127 / 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: 2.14 Å3/Da / Density % sol: 42.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 18% PEG 8000, 100 mM Tris pH 7.8, 500 mM NaCl, 5 mM indigo carmine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.54975 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: 1.54975 Å / Relative weight: 1
ReflectionResolution: 1.75→79.59 Å / Num. obs: 177299 / % possible obs: 90.5 % / Redundancy: 6 % / Biso Wilson estimate: 15.686 Å2 / CC1/2: 0.853 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.108 / Rrim(I) all: 0.194 / Χ2: 0.87 / Net I/σ(I): 6.5
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 4.6 % / Rmerge(I) obs: 1.476 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 5134 / CC1/2: 0.042 / Rpim(I) all: 1.172 / Rrim(I) all: 1.9 / Χ2: 0.64 / % possible all: 52.9

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Processing

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

2min


Resolution: 1.75→40.101 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.31
RfactorNum. reflection% reflection
Rfree0.2232 17637 10 %
Rwork0.1866 --
obs0.1902 176368 90 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→40.101 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15882 0 96 2127 18105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01716566
X-RAY DIFFRACTIONf_angle_d1.14122906
X-RAY DIFFRACTIONf_dihedral_angle_d14.4879948
X-RAY DIFFRACTIONf_chiral_restr0.1692388
X-RAY DIFFRACTIONf_plane_restr0.0062881
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.76990.38243360.33232983X-RAY DIFFRACTION51
1.7699-1.79070.32853920.31963318X-RAY DIFFRACTION57
1.7907-1.81250.32884010.30433760X-RAY DIFFRACTION64
1.8125-1.83550.32334680.284190X-RAY DIFFRACTION72
1.8355-1.85960.29724940.28034872X-RAY DIFFRACTION82
1.8596-1.88510.34395860.2995489X-RAY DIFFRACTION94
1.8851-1.9120.32266620.28865615X-RAY DIFFRACTION96
1.912-1.94060.33726420.30135502X-RAY DIFFRACTION94
1.9406-1.97090.29286720.23855536X-RAY DIFFRACTION96
1.9709-2.00320.26116190.22265626X-RAY DIFFRACTION96
2.0032-2.03780.27456070.23285432X-RAY DIFFRACTION93
2.0378-2.07480.29895180.25764859X-RAY DIFFRACTION82
2.0748-2.11470.27136600.20575675X-RAY DIFFRACTION97
2.1147-2.15790.23366580.1865714X-RAY DIFFRACTION98
2.1579-2.20480.22766320.19345724X-RAY DIFFRACTION97
2.2048-2.25610.31126460.25785509X-RAY DIFFRACTION94
2.2561-2.31250.24956510.19455463X-RAY DIFFRACTION94
2.3125-2.3750.23066070.17725248X-RAY DIFFRACTION90
2.375-2.44490.21285630.17315476X-RAY DIFFRACTION93
2.4449-2.52380.22566070.17645797X-RAY DIFFRACTION98
2.5238-2.6140.22056230.17725815X-RAY DIFFRACTION98
2.614-2.71860.23196410.1885717X-RAY DIFFRACTION97
2.7186-2.84230.2176260.17655692X-RAY DIFFRACTION97
2.8423-2.99210.20855820.17275257X-RAY DIFFRACTION90
2.9921-3.17950.2146600.16725773X-RAY DIFFRACTION98
3.1795-3.42490.19066050.15815818X-RAY DIFFRACTION99
3.4249-3.76930.17055890.15055833X-RAY DIFFRACTION98
3.7693-4.31420.15776390.13915346X-RAY DIFFRACTION91
4.3142-5.43330.16776180.13465887X-RAY DIFFRACTION99
5.4333-40.11150.19236330.17635805X-RAY DIFFRACTION97

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