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

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Basic information

Entry
Database: PDB / ID: 7tpn
TitleSelenium-incorporated nitrogenase Fe protein (Av2-Se) from A. vinelandii (11 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: 1.38 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 25, 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
Water4,179232
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_555x,-y,-z1
Buried area5430 Å2
ΔGint-88 kcal/mol
Surface area19830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.996, 74.633, 75.137
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-532-

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, 236 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.: 232 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.04 Å3/Da / Density % sol: 39.82 %
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: Jun 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978691
20.980621
ReflectionResolution: 1.38→46.01 Å / Num. obs: 53696 / % possible obs: 99.6 % / Redundancy: 13 % / Biso Wilson estimate: 15.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.039 / Rrim(I) all: 0.101 / Net I/σ(I): 13.7
Reflection shellResolution: 1.38→1.4 Å / Redundancy: 12.4 % / Rmerge(I) obs: 1.669 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2653 / CC1/2: 0.775 / Rpim(I) all: 0.705 / Rrim(I) all: 1.816 / % possible all: 98.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.429
Highest resolutionLowest resolution
Rotation46 Å1.73 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: 1.38→46 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1973 4937 4.83 %
Rwork0.1763 97356 -
obs0.1773 53633 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.31 Å2 / Biso mean: 21.9527 Å2 / Biso min: 9.86 Å2
Refinement stepCycle: final / Resolution: 1.38→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2067 0 32 232 2331
Biso mean--16.64 31.29 -
Num. residues----274
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.38-1.40.33451710.31853234340599
1.4-1.410.28181570.29063182333999
1.41-1.430.28292060.28013226343299
1.43-1.450.25441570.26693216337399
1.45-1.470.27171720.25643238341099
1.47-1.490.25881420.249532773419100
1.49-1.510.31021550.23933204335999
1.51-1.530.26641590.23163241340099
1.53-1.550.22381700.21453241341199
1.55-1.580.26611240.2173295341999
1.58-1.610.22561550.21323231338699
1.61-1.640.22871520.201232683420100
1.64-1.670.24681370.232673404100
1.67-1.70.23281740.19532543428100
1.7-1.740.21031540.19133233338799
1.74-1.780.21422030.185431983401100
1.78-1.820.20191610.180732933454100
1.82-1.870.20112270.185632023429100
1.87-1.930.20281540.176832383392100
1.93-1.990.17031660.17383264343099
1.99-2.060.19671680.178932323400100
2.06-2.140.1791440.169933033447100
2.14-2.240.18891680.165832323400100
2.24-2.360.23781910.169932383429100
2.36-2.510.19371620.169732673429100
2.51-2.70.21891420.176332733415100
2.7-2.970.16241450.17433259340499
2.97-3.40.20011680.158632833451100
3.4-4.290.14081710.141832323403100
4.29-460.17891820.14763235341799

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