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- PDB-8zkc: iron-sulfur cluster transfer protein ApbC -

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Basic information

Entry
Database: PDB / ID: 8zkc
Titleiron-sulfur cluster transfer protein ApbC
ComponentsIron-sulfur cluster carrier protein
KeywordsCYTOSOLIC PROTEIN / Iron-sulfur clusters / dimerization / disulfide bonds
Function / homology
Function and homology information


ATP-dependent FeS chaperone activity / iron-sulfur cluster assembly / mitochondrial respiratory chain complex I assembly / 4 iron, 4 sulfur cluster binding / ATP hydrolysis activity / ATP binding / metal ion binding / cytosol
Similarity search - Function
Mrp, conserved site / Mrp family signature. / Iron-sulfur protein NUBPL-like / Mrp/NBP35 ATP-binding protein / Flagellum site-determining protein YlxH/ Fe-S cluster assembling factor NBP35 / NUBPL iron-transfer P-loop NTPase / Fe-S cluster assembly domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Iron-sulfur cluster carrier protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsYang, J. / Liu, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2024
Title: Crystal structure of the iron-sulfur cluster transfer protein ApbC from Escherichia coli.
Authors: Yang, J. / Duan, Y.F. / Liu, L.
History
DepositionMay 16, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Iron-sulfur cluster carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3233
Polymers44,2071
Non-polymers1162
Water181
1
A: Iron-sulfur cluster carrier protein
hetero molecules

A: Iron-sulfur cluster carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,6476
Polymers88,4142
Non-polymers2334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/41
Buried area2600 Å2
ΔGint-34 kcal/mol
Surface area28220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.270, 74.270, 167.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein Iron-sulfur cluster carrier protein


Mass: 44206.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mrp, b2113, JW2100 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AF08
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.61 Å3/Da / Density % sol: 52.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: tri-potassium citrate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.85→55.51 Å / Num. obs: 11707 / % possible obs: 99.9 % / Redundancy: 24.3 % / CC1/2: 1 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.026 / Rrim(I) all: 0.129 / Net I/σ(I): 21.1
Reflection shellResolution: 2.85→2.91 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 845 / CC1/2: 0.507 / Rpim(I) all: 0.706

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Processing

Software
NameVersionClassification
XDSdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing
PHENIX(1.20.1_4487: ???)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→55.51 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2791 508 5.09 %
Rwork0.2349 --
obs0.2371 9974 86.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→55.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2580 0 7 1 2588
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.478
X-RAY DIFFRACTIONf_dihedral_angle_d13.266945
X-RAY DIFFRACTIONf_chiral_restr0.04428
X-RAY DIFFRACTIONf_plane_restr0.003459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.140.3856480.35331207X-RAY DIFFRACTION45
3.14-3.590.35041420.28482679X-RAY DIFFRACTION100
3.6-4.530.28511620.22022693X-RAY DIFFRACTION100
4.53-55.510.23231560.20112887X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 8.1621 Å / Origin y: 40.5851 Å / Origin z: 18.7716 Å
111213212223313233
T0.3293 Å2-0.0865 Å2-0.1787 Å2-0.3717 Å2-0.1323 Å2--0.3152 Å2
L1.7334 °2-0.3107 °20.6723 °2-1.5614 °2-0.6384 °2--2.4688 °2
S-0.0682 Å °-0.0987 Å °0.1425 Å °-0.1071 Å °-0.0651 Å °0.2947 Å °0.2492 Å °-0.1916 Å °0.1005 Å °
Refinement TLS groupSelection details: all

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