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- PDB-7qqa: MgADP-bound Fe protein of the iron-only nitrogenase from Azotobac... -

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Basic information

Entry
Database: PDB / ID: 7qqa
TitleMgADP-bound Fe protein of the iron-only nitrogenase from Azotobacter vinelandii
ComponentsNitrogenase iron protein
KeywordsELECTRON TRANSPORT / Nitrogen fixation / Fe protein / iron-only nitrogenase / alternative nitrogenase
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 / Nitrogenase iron protein
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsTrncik, C. / Mueller, T. / Franke, P. / Einsle, O.
Funding supportEuropean Union, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)235777276European Union
German Research Foundation (DFG)273919336European Union
European Research Council (ERC)310656European Union
CitationJournal: Journal of Inorganic Biochemistry / Year: 2022
Title: MgADP-bound Fe protein of the iron-only nitrogenase from Azotobacter vinelandii
Authors: Trncik, C. / Mueller, T. / Franke, P. / Einsle, O.
History
DepositionJan 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitrogenase iron protein
B: Nitrogenase iron protein
C: Nitrogenase iron protein
D: Nitrogenase iron protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,34714
Polymers119,8374
Non-polymers2,50910
Water13,727762
1
A: Nitrogenase iron protein
B: Nitrogenase iron protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1737
Polymers59,9192
Non-polymers1,2555
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-75 kcal/mol
Surface area20860 Å2
2
C: Nitrogenase iron protein
D: Nitrogenase iron protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1737
Polymers59,9192
Non-polymers1,2555
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-75 kcal/mol
Surface area21260 Å2
Unit cell
Length a, b, c (Å)48.677, 80.366, 80.024
Angle α, β, γ (deg.)68.570, 75.850, 76.030
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRAA2 - 2711 - 270
21TYRTYRBB2 - 2711 - 270
12TYRTYRAA2 - 2711 - 270
22TYRTYRCC2 - 2711 - 270
13ALAALAAA2 - 2741 - 273
23ALAALADD2 - 2741 - 273
14GLYGLYBB2 - 2721 - 271
24GLYGLYCC2 - 2721 - 271
15TYRTYRBB2 - 2711 - 270
25TYRTYRDD2 - 2711 - 270
16TYRTYRCC2 - 2711 - 270
26TYRTYRDD2 - 2711 - 270

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 29959.307 Da / Num. of mol.: 4 / Mutation: 0 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / Strain: DJ / ATCC BAA-1303 / References: UniProt: C1DK95, nitrogenase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 762 / Source method: isolated from a natural source / Formula: H2O
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: 2.32 Å3/Da / Density % sol: 47.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.05 M magnesium chloride, 0.1 M HEPES/NaOH pH7.0, PEG 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→73.48 Å / Num. obs: 67524 / % possible obs: 90.5 % / Redundancy: 3.5 % / CC1/2: 0.997 / Net I/σ(I): 6.9
Reflection shellResolution: 1.8→1.99 Å / Num. unique obs: 3377 / CC1/2: 0.71

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Q93

6q93


Resolution: 1.79→73.48 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.91 / SU B: 4.687 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.238 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2486 3226 4.8 %RANDOM
Rwork0.197 ---
obs0.1995 64307 66.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 119.99 Å2 / Biso mean: 31.013 Å2 / Biso min: 10.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0.08 Å2-0.01 Å2
2--0.11 Å20.11 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 1.79→73.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8322 0 128 762 9212
Biso mean--24.31 36.76 -
Num. residues----1088
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0138590
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168240
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.65311592
X-RAY DIFFRACTIONr_angle_other_deg1.2851.5919048
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.00751084
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.21823.786412
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.196151544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4431540
X-RAY DIFFRACTIONr_chiral_restr0.0770.21146
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029680
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021820
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A82200.1
12B82200.1
21A80430.12
22C80430.12
31A84470.08
32D84470.08
41B81230.11
42C81230.11
51B82210.09
52D82210.09
61C80430.12
62D80430.12
LS refinement shellResolution: 1.79→1.836 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 14 -
Rwork0.242 157 -
all-171 -
obs--2.27 %

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