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- PDB-7c8n: Crystal structure of IscU H106A variant -

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Basic information

Entry
Database: PDB / ID: 7c8n
TitleCrystal structure of IscU H106A variant
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 / ferrous iron binding / 2 iron, 2 sulfur cluster binding / intracellular iron ion homeostasis / FE2/S2 (INORGANIC) CLUSTER / Nitrogen-fixing NifU domain protein
Function and homology information
Biological speciesMethanothrix thermoacetophila (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,3732
Polymers15,1971
Non-polymers1761
Water1,72996
1
A: Nitrogen-fixing NifU domain protein
hetero molecules

A: Nitrogen-fixing NifU domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7464
Polymers30,3952
Non-polymers3522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455-x+y-1,y,-z+1/21
Buried area1890 Å2
ΔGint-45 kcal/mol
Surface area12400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.021, 107.021, 65.753
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

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


Mass: 15197.394 Da / Num. of mol.: 1 / Mutation: H106A
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.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
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: 3.58 Å3/Da / Density % sol: 65.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 200 mM Ammonium sulfate, 100 mM CAPS, 30 % (v/v) PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 2, 2019
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→41.54 Å / Num. obs: 35180 / % possible obs: 98 % / Redundancy: 10.368 % / Biso Wilson estimate: 30.987 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.049 / Χ2: 0.924 / Net I/σ(I): 24.36 / Num. measured all: 364743
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
1.5-1.610.6080.9693.665291620061550.8111.01899.3
1.6-1.710.5270.5116.7250276482447760.9370.53899
1.7-1.810.0050.31910.1837740382237720.9710.33698.7
1.8-1.99.6970.17515.729449308730370.9880.18598.4
1.9-210.9780.13121.926864249224470.9960.13898.2
2-2.510.8560.0734.0579029738172800.9980.07398.6
2.5-310.1220.04147.5132806331632410.9990.04397.7
3-3.58.7660.03352.5514437170616470.9990.03596.5
3.5-410.0560.0360.792729679220.9990.03195.3
4-610.540.02863.0214061143313340.9990.02993.1
6-1010.0980.02762.37445349844110.02988.6
10-41.548.320.02855.8810651691280.9990.02975.7

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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: 1.5→41.54 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.569 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1966 1759 5 %RANDOM
Rwork0.1772 ---
obs0.1782 33421 98.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.22 Å2 / Biso mean: 33.747 Å2 / Biso min: 15.91 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.5→41.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms962 0 4 96 1062
Biso mean--17.86 42.63 -
Num. residues----127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0121007
X-RAY DIFFRACTIONr_angle_refined_deg2.8191.6361355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3675136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1323.95848
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4315187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.491155
X-RAY DIFFRACTIONr_chiral_restr0.1690.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.02754
LS refinement shellResolution: 1.501→1.54 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 128 -
Rwork0.267 2438 -
all-2566 -
obs--99.42 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9215-1.7372-1.13492.64470.61820.8261-0.23250.0678-0.25260.12210.13480.34710.1748-0.11140.09770.0458-0.0153-0.0040.0461-0.010.1083-64.707312.057412.3349
21.12670.05260.1130.8980.64490.46930.02990.1264-0.0343-0.05980.0491-0.1183-0.04070.0373-0.0790.0651-0.00630.01530.0395-0.03750.0503-44.05314.05534.9863
30.82770.5196-0.91950.354-0.92026.837-0.02860.1793-0.1227-0.04490.1156-0.07320.2132-0.0638-0.0870.0666-0.01350.01710.0636-0.04540.0383-44.57154.2235-9.3878
40.945-0.1898-0.45210.53930.2980.448-0.01550.108-0.1151-0.14570.04380.0351-0.0081-0.0777-0.02830.0759-0.0261-0.03920.05770.00640.0781-54.113.96511.1896
56.2468-3.0625-2.96971.50321.4531.41720.23110.23980.2951-0.1307-0.1139-0.1587-0.082-0.1192-0.11720.172-0.02250.14370.0498-0.01680.1224-37.090515.1417-11.8425
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 19
2X-RAY DIFFRACTION2A20 - 46
3X-RAY DIFFRACTION3A47 - 54
4X-RAY DIFFRACTION4A55 - 122
5X-RAY DIFFRACTION5A123 - 127

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