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- PDB-4gqv: Crystal structure of CBS-pair protein, CBSX1 from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 4gqv
TitleCrystal structure of CBS-pair protein, CBSX1 from Arabidopsis thaliana
ComponentsCBS domain-containing protein CBSX1, chloroplastic
KeywordsPROTEIN BINDING / CBS domain / Thioredoxin / Chloroplast / plant
Function / homology
Function and homology information


cell redox homeostasis / chloroplast
Similarity search - Function
: / CBS-domain / CBS-domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
CBS domain-containing protein CBSX1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.392 Å
AuthorsJeong, B.-C. / Park, S.H. / Yoo, K.S. / Shin, J.S. / Song, H.K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2013
Title: Crystal structure of the single cystathionine beta-synthase domain-containing protein CBSX1 from Arabidopsis thaliana
Authors: Jeong, B.C. / Park, S.H. / Yoo, K.S. / Shin, J.S. / Song, H.K.
History
DepositionAug 24, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: CBS domain-containing protein CBSX1, chloroplastic


Theoretical massNumber of molelcules
Total (without water)18,2271
Polymers18,2271
Non-polymers00
Water61334
1
A: CBS domain-containing protein CBSX1, chloroplastic

A: CBS domain-containing protein CBSX1, chloroplastic


Theoretical massNumber of molelcules
Total (without water)36,4542
Polymers36,4542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area1720 Å2
ΔGint-9 kcal/mol
Surface area13210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.361, 56.361, 82.595
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein CBS domain-containing protein CBSX1, chloroplastic / CBS domain-containing protein 2 / AtCDCP2 / Protein LOSS OF THE TIMING OF ET AND JA BIOSYNTHESIS 2 / AtLEJ2


Mass: 18226.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AP22.61, At4g36910, C7A10.450, CBSX1, CDCP2 / Plasmid: pET-GST / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O23193
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.08 Å3/Da / Density % sol: 40.8 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 100mM phophate-acetate pH 4.2, 200mM NaCl, 20%(w/w) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 23, 2007
RadiationMonochromator: Double-crystal Si(111) liquid-nitrogen-cooled
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.392→50 Å / Num. obs: 11556 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10.1 % / Biso Wilson estimate: 60.27 Å2 / Rsym value: 0.069 / Net I/σ(I): 60.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.392→31.527 Å / SU ML: 0.4 / σ(F): 1.36 / Phase error: 32.78 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.3095 1158 10.02 %
Rwork0.2484 --
obs0.2547 11556 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.392→31.527 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms946 0 0 34 980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009957
X-RAY DIFFRACTIONf_angle_d1.191299
X-RAY DIFFRACTIONf_dihedral_angle_d18.18359
X-RAY DIFFRACTIONf_chiral_restr0.07165
X-RAY DIFFRACTIONf_plane_restr0.004161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3922-2.5010.39561570.28111293X-RAY DIFFRACTION98
2.501-2.63280.33271440.27671282X-RAY DIFFRACTION100
2.6328-2.79770.38311320.27771326X-RAY DIFFRACTION100
2.7977-3.01360.37961380.26561289X-RAY DIFFRACTION100
3.0136-3.31650.33161640.25491321X-RAY DIFFRACTION100
3.3165-3.79570.2671350.22361298X-RAY DIFFRACTION100
3.7957-4.77960.26321460.22441303X-RAY DIFFRACTION100
4.7796-31.52970.32541420.26371286X-RAY DIFFRACTION98

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