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- PDB-4pug: BolA1 from Arabidopsis thaliana -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4pug
TitleBolA1 from Arabidopsis thaliana
ComponentsBolA like protein
KeywordsDNA BINDING PROTEIN / stress-responsive protein / transcriptional regulator / morphogen / TRANSCRIPTION
Function / homology
Function and homology information


chloroplast / 2 iron, 2 sulfur cluster binding / metal ion binding
Similarity search - Function
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
Protein BOLA1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.998 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

Downloads & links

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Assembly

Deposited unit
A: BolA like protein
B: BolA like protein


Theoretical massNumber of molelcules
Total (without water)22,3762
Polymers22,3762
Non-polymers00
Water3,711206
1
A: BolA like protein


Theoretical massNumber of molelcules
Total (without water)11,1881
Polymers11,1881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BolA like protein


Theoretical massNumber of molelcules
Total (without water)11,1881
Polymers11,1881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.088, 179.875, 66.818
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-215-

HOH

21A-239-

HOH

31B-232-

HOH

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Components

#1: Protein BolA like protein / BolA-like protein


Mass: 11187.762 Da / Num. of mol.: 2 / Fragment: UNP residues 64-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AT1G55805, At1g55805 / Production host: Escherichia coli (E. coli) / References: UniProt: Q682I1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.02 Å3/Da / Density % sol: 39.11 %
Crystal growTemperature: 278 K / Method: oil microbatch method
Details: 18% PEG4000, 6% 2-propanol, 6% 2.5 hexanediol, 4% xylitol and 0.07 M sodium acetate, Oil microbatch method, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979733 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 18, 2013
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979733 Å / Relative weight: 1
ReflectionResolution: 1.998→44.969 Å / Num. all: 12798 / Num. obs: 12798 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 11.3
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1790 / % possible all: 98.9

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Processing

Software
NameVersionClassification
Xnemodata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4PUI

4pui


Resolution: 1.998→44.969 Å / SU ML: 0.25 / σ(F): 0 / σ(I): 0 / Phase error: 22.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2258 625 4.89 %RANDOM
Rwork0.1994 ---
all0.2007 12798 --
obs0.2007 12798 99.76 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.326 Å2 / ksol: 0.359 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.9811 Å2-0 Å20 Å2
2---11.6499 Å2-0 Å2
3---18.7329 Å2
Refinement stepCycle: LAST / Resolution: 1.998→44.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1435 0 0 206 1641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031477
X-RAY DIFFRACTIONf_angle_d0.8491986
X-RAY DIFFRACTIONf_dihedral_angle_d13.964576
X-RAY DIFFRACTIONf_chiral_restr0.059222
X-RAY DIFFRACTIONf_plane_restr0.004259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9982-2.19930.29891690.23812934X-RAY DIFFRACTION99
2.1993-2.51750.2381560.2113010X-RAY DIFFRACTION100
2.5175-3.17160.21791500.23025X-RAY DIFFRACTION100
3.1716-44.98010.20051500.18323195X-RAY DIFFRACTION100

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