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- PDB-7z3h: Crystal structure of Iba57 from Chaetomium thermophilum -

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Basic information

Entry
Database: PDB / ID: 7z3h
TitleCrystal structure of Iba57 from Chaetomium thermophilum
ComponentsTransferase-like protein
KeywordsPROTEIN BINDING / 4Fe-4S / tetrahydrofolate
Function / homologyYgfZ/GcvT conserved site / YgfZ/GcvT / GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1 / transferase activity / mitochondrion / CITRIC ACID / Transferase-like protein
Function and homology information
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAltegoer, F. / Mrusek, D. / Bange, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Chem. / Year: 2022
Title: The iron-sulfur cluster assembly (ISC) protein Iba57 executes a tetrahydrofolate-independent function in mitochondrial [4Fe-4S] protein maturation.
Authors: Muhlenhoff, U. / Weiler, B.D. / Nadler, F. / Millar, R. / Kothe, I. / Freibert, S.A. / Altegoer, F. / Bange, G. / Lill, R.
History
DepositionMar 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 31, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Transferase-like protein
B: Transferase-like protein
C: Transferase-like protein
D: Transferase-like protein
E: Transferase-like protein
F: Transferase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)286,96312
Polymers285,8106
Non-polymers1,1536
Water4,125229
1
A: Transferase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8272
Polymers47,6351
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transferase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8272
Polymers47,6351
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transferase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8272
Polymers47,6351
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Transferase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8272
Polymers47,6351
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Transferase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8272
Polymers47,6351
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Transferase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8272
Polymers47,6351
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.530, 134.180, 107.010
Angle α, β, γ (deg.)90.000, 97.590, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Transferase-like protein


Mass: 47635.035 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0070650 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0SHN3
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.4 Å3/Da / Density % sol: 48.82 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Citric acid pH 4.0 5 % (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.4→47.34 Å / Num. obs: 104927 / % possible obs: 99.52 % / Redundancy: 3.7 % / Biso Wilson estimate: 57.2 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.09952 / Net I/σ(I): 9.19
Reflection shellResolution: 2.4→2.486 Å / Rmerge(I) obs: 1.474 / Mean I/σ(I) obs: 1.08 / Num. unique obs: 10450 / CC1/2: 0.357

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ESR

6esr
PDB Unreleased entry


Resolution: 2.4→47.34 Å / SU ML: 0.382 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.8257
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2735 5243 5 %
Rwork0.238 99684 -
obs0.2398 104927 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.15 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16835 0 78 229 17142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002917242
X-RAY DIFFRACTIONf_angle_d0.633423366
X-RAY DIFFRACTIONf_chiral_restr0.0482585
X-RAY DIFFRACTIONf_plane_restr0.00533048
X-RAY DIFFRACTIONf_dihedral_angle_d9.93212428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.430.36721710.33333297X-RAY DIFFRACTION99.8
2.43-2.460.36041730.3413298X-RAY DIFFRACTION99.83
2.46-2.490.36981750.33263330X-RAY DIFFRACTION99.69
2.49-2.520.33071730.32653280X-RAY DIFFRACTION99.62
2.52-2.550.36781760.33133340X-RAY DIFFRACTION99.35
2.55-2.590.39681750.33533311X-RAY DIFFRACTION99.57
2.59-2.620.40341730.37223314X-RAY DIFFRACTION99.8
2.62-2.660.41791740.39733303X-RAY DIFFRACTION99.66
2.66-2.70.39221740.35763306X-RAY DIFFRACTION99.57
2.7-2.750.41311780.33363368X-RAY DIFFRACTION99.86
2.75-2.790.36411740.30933313X-RAY DIFFRACTION99.77
2.79-2.850.33161740.28253302X-RAY DIFFRACTION99.83
2.85-2.90.32211760.27373338X-RAY DIFFRACTION99.72
2.9-2.960.32471740.2763312X-RAY DIFFRACTION99.8
2.96-3.020.29991750.27533312X-RAY DIFFRACTION99.6
3.02-3.090.32121750.27463327X-RAY DIFFRACTION99.63
3.09-3.170.31611730.28783308X-RAY DIFFRACTION99.29
3.17-3.260.33471750.28823320X-RAY DIFFRACTION99.71
3.26-3.350.28941760.25693356X-RAY DIFFRACTION99.83
3.35-3.460.27281760.23223334X-RAY DIFFRACTION99.83
3.46-3.580.29361740.22773317X-RAY DIFFRACTION99.57
3.58-3.730.25231760.22693326X-RAY DIFFRACTION99.49
3.73-3.90.26881740.22193309X-RAY DIFFRACTION99.6
3.9-4.10.21261730.20673291X-RAY DIFFRACTION98.69
4.1-4.360.23491750.1893332X-RAY DIFFRACTION99.1
4.36-4.70.20711750.18063322X-RAY DIFFRACTION99.54
4.7-5.170.19981780.18443374X-RAY DIFFRACTION99.66
5.17-5.920.23361750.2113318X-RAY DIFFRACTION98.87
5.92-7.440.25631760.21933352X-RAY DIFFRACTION99.16
7.45-47.340.25151770.20883374X-RAY DIFFRACTION98.67

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