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

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Basic information

Entry
Database: PDB / ID: 7tqf
TitleSelenium-incorporated nitrogenase Fe protein (Av2-Se) from A. vinelandii (22 mM KSeCN)
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: 1.45 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
Water3,981221
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 area5380 Å2
ΔGint-88 kcal/mol
Surface area19850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.595, 74.173, 74.688
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-499-

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, 225 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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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 Å3/Da / Density % sol: 38.55 %
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: 0.97869, 0.98062
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978691
20.980621
ReflectionResolution: 1.45→45.58 Å / Num. obs: 45611 / % possible obs: 99.9 % / Redundancy: 12.9 % / Biso Wilson estimate: 17.55 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.026 / Rrim(I) all: 0.069 / Net I/σ(I): 19
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 12.4 % / Rmerge(I) obs: 1.057 / Num. unique obs: 2363 / CC1/2: 0.917 / Rpim(I) all: 0.445 / Rrim(I) all: 1.149 / % possible all: 98.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.449
Highest resolutionLowest resolution
Rotation38.85 Å1.85 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: 1.45→38.84 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2034 4128 4.77 %
Rwork0.1836 82352 -
obs0.1845 45514 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.71 Å2 / Biso mean: 25.3337 Å2 / Biso min: 13.19 Å2
Refinement stepCycle: final / Resolution: 1.45→38.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2061 0 36 221 2318
Biso mean--19.68 29.46 -
Num. residues----273
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.470.34021310.31892737286896
1.47-1.490.27481350.300528723007100
1.49-1.50.31341360.273128272963100
1.5-1.520.28341260.270728692995100
1.52-1.540.27831510.259728152966100
1.54-1.570.22771110.23328903001100
1.57-1.590.26611110.222928672978100
1.59-1.610.30561450.219628492994100
1.61-1.640.25591260.217228562982100
1.64-1.670.23551330.201728172950100
1.67-1.70.24451700.209128262996100
1.7-1.730.27111340.203928412975100
1.73-1.770.21721740.198128252999100
1.77-1.810.26541370.199828562993100
1.81-1.850.22951830.195227932976100
1.85-1.890.20921680.196428353003100
1.89-1.950.1931280.184728452973100
1.95-20.2331720.188727932965100
2-2.070.24611200.188228803000100
2.07-2.140.20071460.187628312977100
2.14-2.230.18761360.178728482984100
2.23-2.330.22691740.189928142988100
2.33-2.450.19121320.187428472979100
2.45-2.610.20441300.189328703000100
2.61-2.810.2121140.188228802994100
2.81-3.090.19861480.184528613009100
3.09-3.530.16231520.163328432995100
3.54-4.450.15771390.143128332972100
4.45-38.840.1861660.161728322998100

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