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- PDB-7tq9: Selenium-incorporated nitrogenase Fe protein (Av2-Se) from A. vin... -

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Basic information

Entry
Database: PDB / ID: 7tq9
TitleSelenium-incorporated nitrogenase Fe protein (Av2-Se) from A. vinelandii (22 mM KSeCN, with Av1)
ComponentsNitrogenase iron protein 1
KeywordsOXIDOREDUCTASE / nitrogenase / metalloprotein / iron sulfur cluster
Function / homology
Function and homology information


nitrogenase / : / nitrogenase activity / nitrogen fixation / 4 iron, 4 sulfur cluster binding / ATP binding / metal ion binding
Similarity search - Function
Nitrogenase iron protein NifH / NifH/frxC family / NifH/chlL conserved site / 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family / NifH/frxC family signature 2. / NifH/frxC family signature 1. / NIFH_FRXC family profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / IRON/SULFUR CLUSTER / Fe4-Se4 cluster / Nitrogenase iron protein 1
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsBuscagan, T.M. / Kaiser, J.T. / Rees, D.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Elife / Year: 2022
Title: Selenocyanate derived Se-incorporation into the Nitrogenase Fe protein cluster.
Authors: Buscagan, T.M. / Kaiser, J.T. / Rees, D.C.
History
DepositionJan 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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Assembly

Deposited unit
A: Nitrogenase iron protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8915
Polymers31,5481
Non-polymers1,3424
Water2,918162
1
A: Nitrogenase iron protein 1
hetero molecules

A: Nitrogenase iron protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,78110
Polymers63,0962
Non-polymers2,6858
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545x,-y-1,-z1
Buried area5270 Å2
ΔGint-88 kcal/mol
Surface area19880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.835, 74.406, 74.689
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-493-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Nitrogenase iron protein 1 / Nitrogenase Fe protein 1 / Nitrogenase component II / Nitrogenase reductase


Mass: 31548.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P00459, nitrogenase

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Non-polymers , 5 types, 166 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-SFS / Fe4-Se4 cluster


Mass: 539.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4Se4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Nonpolymer detailsIndividual instances of the Fe-S/Se cluster represented by residues 301 SF4 and 302 SFS may contain ...Individual instances of the Fe-S/Se cluster represented by residues 301 SF4 and 302 SFS may contain both sulfur and selenium. The primary citation should be consulted for a detailed description of the cluster refinement.

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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: 2.02 Å3/Da / Density % sol: 39.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 36-41% PEG400, 0.1-0.3 M sodium chloride, 0.1 M HEPES, pH 7.5, 2.5 mM dithionite, 0.17 mM Cymal-7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97239, 0.98062
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.972391
20.980621
ReflectionResolution: 1.6→45.85 Å / Num. obs: 34297 / % possible obs: 99.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 20.18 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.034 / Rrim(I) all: 0.064 / Net I/σ(I): 14.1
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.902 / Num. unique obs: 1623 / CC1/2: 0.851 / Rpim(I) all: 0.568 / Rrim(I) all: 1.07 / % possible all: 97.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.458
Highest resolutionLowest resolution
Rotation39.03 Å1.87 Å

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
MOLREPphasing
PHENIX1.19.2-4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6N4L

6n4l


Resolution: 1.6→39.02 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1942 3147 4.88 %
Rwork0.1712 61350 -
obs0.1723 34134 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.3 Å2 / Biso mean: 27.6176 Å2 / Biso min: 14.78 Å2
Refinement stepCycle: final / Resolution: 1.6→39.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2057 0 36 162 2255
Biso mean--21.91 35.7 -
Num. residues----272
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.630.30831240.30222797292198
1.63-1.650.24671190.27452805292499
1.65-1.680.3131430.266427792922100
1.68-1.710.27731650.24792792295799
1.71-1.740.27621330.2412829296299
1.74-1.780.25041570.22012752290999
1.78-1.820.23571410.21822819296099
1.82-1.860.22391930.20212682287598
1.86-1.910.20111500.1932818296899
1.91-1.960.16641250.17527712896100
1.96-2.020.22041770.167627702947100
2.02-2.080.23031180.167528682986100
2.08-2.160.16661280.16272769289799
2.16-2.240.17411400.16082801294199
2.24-2.340.2461700.15822736290698
2.34-2.470.17781320.16752790292299
2.47-2.620.21641240.170728382962100
2.62-2.820.21461190.168528562975100
2.82-3.110.18341470.16512813296099
3.11-3.560.1651410.15062728286998
3.56-4.480.14861370.14272791292899
4.48-39.020.1851640.16472746291098

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