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- PDB-4pui: BolA domain of SufE1 from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 4pui
TitleBolA domain of SufE1 from Arabidopsis thaliana
ComponentsSufE-like protein, chloroplastic
KeywordsPROTEIN BINDING / stress-responsive protein / METAL BINDING PROTEIN / PROTEIN BINDING PROTEIN
Function / homology
Function and homology information


embryo development ending in seed dormancy / chloroplast stroma / chloroplast / enzyme activator activity / mitochondrion / cytosol
Similarity search - Function
Fe-S metabolism associated domain, SufE-like / Fe-S metabolism associated domain / BolA-like / BolA protein / BolA-like superfamily / BolA-like protein / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
SufE-like protein 1, chloroplastic/mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.698 Å
AuthorsRoret, T. / Didierjean, C.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural and Spectroscopic Insights into BolA-Glutaredoxin Complexes.
Authors: Roret, T. / Tsan, P. / Couturier, J. / Zhang, B. / Johnson, M.K. / Rouhier, N. / Didierjean, C.
History
DepositionMar 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2Sep 20, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SufE-like protein, chloroplastic
B: SufE-like protein, chloroplastic


Theoretical massNumber of molelcules
Total (without water)21,2782
Polymers21,2782
Non-polymers00
Water2,972165
1
A: SufE-like protein, chloroplastic


Theoretical massNumber of molelcules
Total (without water)10,6391
Polymers10,6391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SufE-like protein, chloroplastic


Theoretical massNumber of molelcules
Total (without water)10,6391
Polymers10,6391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.833, 31.634, 68.631
Angle α, β, γ (deg.)90.00, 116.83, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein SufE-like protein, chloroplastic / Protein EMBRYO DEFECTIVE 1374 / Protein SULFUR E / AtSUFE / Protein SULFUR E 1 / AtSUFE1


Mass: 10639.063 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 277-371
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SUFE, EMB1374, SUFE1, At4g26500, M3E9.70 / Production host: Escherichia coli (E. coli) / References: UniProt: Q84W65
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43.61 %
Crystal growTemperature: 278 K / Method: oil microbatch method / pH: 6.5
Details: 12% PEG20000, 6% ethylene glycol, 0.02 M trimethylamine HCl and 0.1 M MES, pH 6.5, Oil microbatch method, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97911 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2012
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.698→46.182 Å / Num. all: 20575 / Num. obs: 20573 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 20.6
Reflection shellResolution: 1.698→1.79 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2902 / % possible all: 97.2

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Processing

Software
NameVersionClassification
Proxima1 SOLEILdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V60

1v60


Resolution: 1.698→46.182 Å / SU ML: 0.23 / σ(F): 0 / σ(I): 0 / Phase error: 22.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2132 1053 5.12 %RANDOM
Rwork0.1913 ---
all0.1924 20575 --
obs0.1924 20573 99.47 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.557 Å2 / ksol: 0.415 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.8388 Å2-0 Å21.078 Å2
2---0.1159 Å2-0 Å2
3---6.9547 Å2
Refinement stepCycle: LAST / Resolution: 1.698→46.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1360 0 0 165 1525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061386
X-RAY DIFFRACTIONf_angle_d1.0661860
X-RAY DIFFRACTIONf_dihedral_angle_d14.134532
X-RAY DIFFRACTIONf_chiral_restr0.067211
X-RAY DIFFRACTIONf_plane_restr0.005241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6981-1.77540.33191180.28822368X-RAY DIFFRACTION97
1.7754-1.8690.27221350.24552423X-RAY DIFFRACTION100
1.869-1.98610.30271320.22612431X-RAY DIFFRACTION100
1.9861-2.13950.1881100.192414X-RAY DIFFRACTION100
2.1395-2.35480.2251410.19142433X-RAY DIFFRACTION100
2.3548-2.69550.19741120.19122475X-RAY DIFFRACTION100
2.6955-3.39590.24011540.18612432X-RAY DIFFRACTION100
3.3959-46.19870.17341510.17352537X-RAY DIFFRACTION100

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