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- PDB-8e3u: Nickel-reconstituted nitrogenase MoFeP mutant S188A from Azotobac... -

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Basic information

Entry
Database: PDB / ID: 8e3u
TitleNickel-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
: / 3-HYDROXY-3-CARBOXY-ADIPIC ACID / Chem-ICS / FE(7)-S(7) CLUSTER / 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: 1.99 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)233,14114
Polymers229,7664
Non-polymers3,37610
Water18,1771009
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30540 Å2
ΔGint-222 kcal/mol
Surface area56340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.259, 129.009, 107.760
Angle α, β, γ (deg.)90.00, 109.22, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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 , 6 types, 1019 molecules

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


Mass: 615.370 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Fe7S7 / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: 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
#6: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Fe
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1009 / 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: 2.24 Å3/Da / Density % sol: 45.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.25
Details: 18% PEG 8000, 100 mM Tris pH 8.25, 500 mM NaCl, 10 mM dithionite

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.48484, 1.50832
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 2, 2018
RadiationMonochromator: Water-cooled flat double Si(111) Khozu monochromater
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.484841
21.508321
ReflectionResolution: 1.99→79.89 Å / Num. obs: 136546 / % possible obs: 99.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 30.36 Å2 / CC1/2: 0.939 / Net I/σ(I): 3.4
Reflection shellResolution: 1.99→2.02 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 6751 / CC1/2: 0.003 / % possible all: 99.9

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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: 1.99→79.89 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2529 6796 5.02 %
Rwork0.2023 --
obs0.2049 135397 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→79.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15657 0 96 1009 16762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01916207
X-RAY DIFFRACTIONf_angle_d1.79322352
X-RAY DIFFRACTIONf_dihedral_angle_d17.175992
X-RAY DIFFRACTIONf_chiral_restr0.1022343
X-RAY DIFFRACTIONf_plane_restr0.0142816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.010.42182320.3934199X-RAY DIFFRACTION97
2.01-2.030.37132080.37424230X-RAY DIFFRACTION97
2.03-2.060.38392350.36644123X-RAY DIFFRACTION97
2.06-2.090.38891990.34984242X-RAY DIFFRACTION97
2.09-2.110.40032050.34274214X-RAY DIFFRACTION97
2.11-2.140.35652490.334192X-RAY DIFFRACTION98
2.14-2.170.36872220.32254215X-RAY DIFFRACTION98
2.17-2.20.3632120.30854314X-RAY DIFFRACTION98
2.2-2.240.34912270.34226X-RAY DIFFRACTION99
2.24-2.280.34062280.29344292X-RAY DIFFRACTION99
2.28-2.310.31492150.27244268X-RAY DIFFRACTION99
2.31-2.360.32472470.27244264X-RAY DIFFRACTION99
2.36-2.40.30562070.25594313X-RAY DIFFRACTION99
2.4-2.450.31762030.25154352X-RAY DIFFRACTION99
2.45-2.50.31692500.24834255X-RAY DIFFRACTION99
2.5-2.560.31362210.2454307X-RAY DIFFRACTION99
2.56-2.630.32711910.25974322X-RAY DIFFRACTION99
2.63-2.70.31972190.24194332X-RAY DIFFRACTION100
2.7-2.780.33682050.22754311X-RAY DIFFRACTION100
2.78-2.870.25952290.20414331X-RAY DIFFRACTION100
2.87-2.970.28622150.20154332X-RAY DIFFRACTION100
2.97-3.090.28172050.19734336X-RAY DIFFRACTION100
3.09-3.230.27122370.18884330X-RAY DIFFRACTION100
3.23-3.40.23072540.17274291X-RAY DIFFRACTION100
3.4-3.610.20442310.14644321X-RAY DIFFRACTION100
3.61-3.890.17812510.13764310X-RAY DIFFRACTION100
3.89-4.280.18032420.12534322X-RAY DIFFRACTION100
4.28-4.90.18032610.12264323X-RAY DIFFRACTION100
4.9-6.180.19162290.14974332X-RAY DIFFRACTION100
6.18-79.890.18692670.1654402X-RAY DIFFRACTION100

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