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- PDB-8e3v: Cobalt-reconstituted nitrogenase MoFeP mutant S188A from Azotobac... -

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Basic information

Entry
Database: PDB / ID: 8e3v
TitleCobalt-reconstituted nitrogenase MoFeP mutant S188A from Azotobacter vinelandii after IDS oxidation
Components(Nitrogenase molybdenum-iron protein ...) x 2
KeywordsOXIDOREDUCTASE / MoFeP / MoFe-protein
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 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
Similarity search - Domain/homology
FE(8)-S(7) CLUSTER / : / 3-HYDROXY-3-CARBOXY-ADIPIC ACID / Chem-ICS / Nitrogenase molybdenum-iron protein beta chain / Nitrogenase molybdenum-iron protein alpha chain
Similarity search - Component
Biological speciesAzotobacter vinelandii DJ (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
National Aeronautic Space Administration (NASA, United States)80NSSC18M0093 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Role of Serine Coordination in the Structural and Functional Protection of the Nitrogenase P-Cluster.
Authors: Rutledge, H.L. / Field, M.J. / Rittle, J. / Green, M.T. / Tezcan, F.A.
History
DepositionAug 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
Water27,1131505
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31460 Å2
ΔGint-261 kcal/mol
Surface area56630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.127, 130.039, 107.760
Angle α, β, γ (deg.)90.00, 109.12, 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 genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii DJ (bacteria) / Strain: DJ / ATCC BAA-1303 / Production host: Azotobacter vinelandii DJ (bacteria) / Strain (production host): DJ / ATCC BAA-1303 / References: UniProt: P07328, nitrogenase
#2: Protein Nitrogenase molybdenum-iron protein beta chain / Dinitrogenase


Mass: 59519.879 Da / Num. of mol.: 2 / Mutation: S188A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii DJ (bacteria) / Strain: DJ / ATCC BAA-1303 / Production host: Azotobacter vinelandii DJ (bacteria) / Strain (production host): DJ / ATCC BAA-1303 / References: UniProt: C1DGZ8, nitrogenase

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Non-polymers , 5 types, 1513 molecules

#3: Chemical ChemComp-HCA / 3-HYDROXY-3-CARBOXY-ADIPIC ACID


Mass: 206.150 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C7H10O7
#4: Chemical ChemComp-ICS / iron-sulfur-molybdenum cluster with interstitial carbon


Mass: 787.451 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: CFe7MoS9
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Fe
#6: Chemical ChemComp-CLF / FE(8)-S(7) CLUSTER


Mass: 671.215 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Fe8S7 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1505 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.75
Details: 20% PEG 8000, 100 mM Tris pH 7.75, 500 mM NaCl, 10 mM dithionite

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.60388, 1.61223
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2019
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.603881
21.612231
ReflectionResolution: 2→80.17 Å / Num. obs: 127562 / % possible obs: 94.4 % / Redundancy: 6.3 % / CC1/2: 0.993 / Rmerge(I) obs: 0.134 / Net I/σ(I): 8.9
Reflection shellResolution: 2→2.03 Å / Redundancy: 6 % / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 6261 / CC1/2: 0.725 / % possible all: 93

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Processing

Software
NameVersionClassification
PHENIX1.19.1-4122refinement
iMOSFLMdata reduction
pointlessdata scaling
PHENIX1.19.1-4122phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2MIN

2min


Resolution: 2→80.17 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2084 25211 10.05 %
Rwork0.1817 --
obs0.1844 127562 93.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→80.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15710 0 96 1505 17311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716287
X-RAY DIFFRACTIONf_angle_d1.05122513
X-RAY DIFFRACTIONf_dihedral_angle_d15.776059
X-RAY DIFFRACTIONf_chiral_restr0.0682349
X-RAY DIFFRACTIONf_plane_restr0.0052830
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.32637560.30667350X-RAY DIFFRACTION91
2.02-2.050.31138660.28137488X-RAY DIFFRACTION93
2.05-2.070.31468350.27637437X-RAY DIFFRACTION93
2.07-2.10.28128430.26137472X-RAY DIFFRACTION94
2.1-2.130.28848350.24497561X-RAY DIFFRACTION94
2.13-2.150.27528060.23697532X-RAY DIFFRACTION93
2.15-2.190.27078190.24137476X-RAY DIFFRACTION93
2.19-2.220.26618650.22717515X-RAY DIFFRACTION93
2.22-2.250.27997250.2367351X-RAY DIFFRACTION92
2.25-2.290.25147740.22626928X-RAY DIFFRACTION86
2.29-2.330.25528620.2127270X-RAY DIFFRACTION91
2.33-2.370.22588370.20617585X-RAY DIFFRACTION95
2.37-2.420.25048110.20187532X-RAY DIFFRACTION94
2.42-2.470.25178630.19637594X-RAY DIFFRACTION95
2.47-2.520.23798960.20027548X-RAY DIFFRACTION95
2.52-2.580.24418410.20277740X-RAY DIFFRACTION96
2.58-2.640.22547910.1937632X-RAY DIFFRACTION95
2.64-2.710.23818960.19537513X-RAY DIFFRACTION95
2.71-2.790.25148320.20017149X-RAY DIFFRACTION89
2.79-2.880.217660.18277203X-RAY DIFFRACTION90
2.88-2.990.211910030.17777742X-RAY DIFFRACTION98
2.99-3.110.22378170.18867842X-RAY DIFFRACTION98
3.11-3.250.19838370.17037812X-RAY DIFFRACTION97
3.25-3.420.19028400.16257808X-RAY DIFFRACTION97
3.42-3.630.17789180.15057829X-RAY DIFFRACTION98
3.63-3.910.16338110.14187039X-RAY DIFFRACTION88
3.91-4.310.14287900.12927578X-RAY DIFFRACTION94
4.31-4.930.13429420.12867795X-RAY DIFFRACTION98
4.93-6.210.16638830.15017692X-RAY DIFFRACTION96
6.21-51.770.18148510.17227511X-RAY DIFFRACTION94

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