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- PDB-6op2: Selenium incorporated FeMo-cofactor of nitrogenase from azotobact... -

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Basic information

Entry
Database: PDB / ID: 6op2
TitleSelenium incorporated FeMo-cofactor of nitrogenase from azotobacter vinelandii at high concentration of selenium
Components(Nitrogenase molybdenum-iron protein ...) x 2
KeywordsOXIDOREDUCTASE / nitrogenase / selenium / femo-cofactor
Function / homology
Function and homology information


molybdenum-iron nitrogenase complex / carbonyl sulfide nitrogenase activity / 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, subunit B, domain 4 / Nitrogenase molybdenum-iron protein beta chain / Nitrogenase molybdenum-iron protein alpha chain / Nitrogenase component 1, alpha chain / Nitrogenases component 1 alpha and beta subunits signature 1. / Nitrogenases component 1 alpha and beta subunits signature 2. / Nitrogenase Molybdenum-iron Protein, subunit B; domain 4 / Nitrogenase component 1, conserved site ...Nitrogenase molybdenum-iron protein beta chain, N-terminal / Domain of unknown function (DUF3364) / Nitrogenase Molybdenum-iron Protein, subunit B, domain 4 / Nitrogenase molybdenum-iron protein beta chain / Nitrogenase molybdenum-iron protein alpha chain / Nitrogenase component 1, alpha chain / Nitrogenases component 1 alpha and beta subunits signature 1. / Nitrogenases component 1 alpha and beta subunits signature 2. / Nitrogenase Molybdenum-iron Protein, subunit B; domain 4 / Nitrogenase component 1, conserved site / 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
Nitrogenase molybdenum-iron protein alpha chain / FE(8)-S(7) CLUSTER / 3-HYDROXY-3-CARBOXY-ADIPIC ACID / SELENIUM ATOM / IMIDAZOLE / Chem-ICS / Nitrogenase molybdenum-iron protein beta chain
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsArias, R.J. / Rees, D.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM045162 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM007616 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Localized Electronic Structure of Nitrogenase FeMoco Revealed by Selenium K-Edge High Resolution X-ray Absorption Spectroscopy.
Authors: Henthorn, J.T. / Arias, R.J. / Koroidov, S. / Kroll, T. / Sokaras, D. / Bergmann, U. / Rees, D.C. / DeBeer, S.
History
DepositionApr 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 11, 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

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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)231,18727
Polymers226,8104
Non-polymers4,37623
Water20,6451146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34070 Å2
ΔGint-249 kcal/mol
Surface area57240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.761, 130.380, 106.896
Angle α, β, γ (deg.)90.000, 110.540, 90.000
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: 54000.559 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: 59404.684 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P07329, nitrogenase

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Non-polymers , 8 types, 1169 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 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical ChemComp-SE / SELENIUM ATOM / Hydrogen selenide


Mass: 78.960 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Se
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-CLF / FE(8)-S(7) CLUSTER


Mass: 671.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe8S7
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1146 / 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: 2.32 Å3/Da / Density % sol: 47.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 26% v/v PEG6000, 0.75 M sodium chloride, 12.5% v/v MPD, 0.1 M imidazole/malate buffer, pH 8.0, 5 mM Na2S2O4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2017
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.9→37.81 Å / Num. obs: 160550 / % possible obs: 98.7 % / Redundancy: 3.5 % / CC1/2: 0.941 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.072 / Rrim(I) all: 0.137 / Net I/σ(I): 6.5 / Num. measured all: 561170 / Scaling rejects: 1084
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.288 / Num. measured all: 28155 / Num. unique obs: 7979 / CC1/2: 0.485 / Rpim(I) all: 0.183 / Rrim(I) all: 0.343 / Net I/σ(I) obs: 3.1 / % possible all: 99.1

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Processing

Software
NameVersionClassification
Aimless0.6.2data scaling
REFMAC5.8.0230refinement
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3u7q
Resolution: 1.9→37.81 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.917 / SU B: 3.499 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.14
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2145 8048 5 %RANDOM
Rwork0.1766 ---
obs0.1785 152497 98.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 101.81 Å2 / Biso mean: 15.21 Å2 / Biso min: 1.57 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.9→37.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15847 0 153 1146 17146
Biso mean--20.01 19.54 -
Num. residues----1998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01416452
X-RAY DIFFRACTIONr_bond_other_d0.0010.01714563
X-RAY DIFFRACTIONr_angle_refined_deg1.6951.69822671
X-RAY DIFFRACTIONr_angle_other_deg0.9981.64434118
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.66451994
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55522.533841
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.031152814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.131591
X-RAY DIFFRACTIONr_chiral_restr1.0130.22080
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218312
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023169
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 596 -
Rwork0.198 11325 -
all-11921 -
obs--99.03 %

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