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- PDB-7c8m: Crystal structure of IscU wild-type -

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Basic information

Entry
Database: PDB / ID: 7c8m
TitleCrystal structure of IscU wild-type
ComponentsNitrogen-fixing NifU domain protein
KeywordsBIOSYNTHETIC PROTEIN / Iron-sulfur cluster biogenesis
Function / homologyNIF system FeS cluster assembly, NifU-like / NIF system FeS cluster assembly, NifU, N-terminal / NifU-like N terminal domain / iron-sulfur cluster assembly / 2 iron, 2 sulfur cluster binding / iron ion binding / FE2/S2 (INORGANIC) CLUSTER / Nitrogen-fixing NifU domain protein
Function and homology information
Biological speciesMethanothrix thermoacetophila (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsKunichika, K. / Takahashi, Y. / Fujishiro, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17K14510 Japan
CitationJournal: Biochemistry / Year: 2021
Title: The Structure of the Dimeric State of IscU Harboring Two Adjacent [2Fe-2S] Clusters Provides Mechanistic Insights into Cluster Conversion to [4Fe-4S].
Authors: Kunichika, K. / Nakamura, R. / Fujishiro, T. / Takahashi, Y.
History
DepositionJun 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Nitrogen-fixing NifU domain protein
C: Nitrogen-fixing NifU domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8814
Polymers30,5292
Non-polymers3522
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-32 kcal/mol
Surface area13020 Å2
Unit cell
Length a, b, c (Å)85.290, 67.140, 47.420
Angle α, β, γ (deg.)90.000, 123.610, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: _ / Auth seq-ID: 6 - 133 / Label seq-ID: 6 - 133

Dom-IDAuth asym-IDLabel asym-ID
1AA
2CB

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Components

#1: Protein Nitrogen-fixing NifU domain protein / IscU


Mass: 15264.462 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothrix thermoacetophila (archaea)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: A0B757
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
Has ligand of interestN

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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: 1.85 Å3/Da / Density % sol: 33.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 30 % (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 8, 2019
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, direct water cooling using micro-channel (1st crystal),indirect water cooling (2nd crystal)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→48.79 Å / Num. obs: 2867 / % possible obs: 98.1 % / Redundancy: 6.248 % / Biso Wilson estimate: 94.123 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.182 / Rrim(I) all: 0.199 / Χ2: 0.869 / Net I/σ(I): 6.35 / Num. measured all: 17912
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.5-3.65.1620.9831.3912082602340.6661.09590
3.6-3.76.0371.1241.5711411911890.7811.23199
3.7-3.86.6740.682.6912881911930.8950.737100
3.8-3.96.5460.6982.4512111911850.9440.75896.9
3.9-46.5230.5733.018351261280.950.622100
4-4.16.4710.6512.839061391400.7980.709100
4.1-4.56.1920.3624.7526814394330.9550.39698.6
4.5-4.66.7090.2896.1753084790.9740.31394
4.6-4.76.5440.2535.8251779790.9860.275100
4.7-4.86.2470.2256.7653185850.9750.246100
4.8-4.96.550.295.8739358600.9810.315100
4.9-56.3520.256.7234358540.9740.27393.1
5-66.2530.1927.8526704314270.9840.2199.1
6-106.3610.09712.8128374524460.9940.10698.7
10-48.796.0810.05918.428211401350.9990.06596.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z7E

2z7e


Resolution: 3.5→48.79 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.958 / SU B: 65.406 / SU ML: 0.922 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.886 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2917 144 5 %RANDOM
Rwork0.2211 ---
obs0.2251 2723 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 297.49 Å2 / Biso mean: 141.527 Å2 / Biso min: 77.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20.18 Å2
2---0.12 Å20 Å2
3----0.22 Å2
Refinement stepCycle: final / Resolution: 3.5→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1964 0 8 0 1972
Biso mean--100.98 --
Num. residues----256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122014
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.6352690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4195254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.81523.4100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.38515368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1581510
X-RAY DIFFRACTIONr_chiral_restr0.1250.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021508
Refine LS restraints NCS

Ens-ID: 1 / Number: 4126 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2C
LS refinement shellResolution: 3.502→3.592 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 11 -
Rwork0.333 206 -
all-217 -
obs--92.34 %

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