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- PDB-4gqy: Crystal structure of CBSX2 in complex with AMP -

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Basic information

Entry
Database: PDB / ID: 4gqy
TitleCrystal structure of CBSX2 in complex with AMP
ComponentsCBS domain-containing protein CBSX2, chloroplastic
KeywordsPROTEIN BINDING / CBS domain / Thioredoxin / Chloroplast in plant
Function / homology
Function and homology information


chloroplast stroma / cell redox homeostasis / chloroplast / plasma membrane
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
ADENOSINE MONOPHOSPHATE / CBS domain-containing protein CBSX2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.193 Å
AuthorsJeong, B.C. / Song, H.K.
CitationJournal: J.Struct.Biol. / Year: 2013
Title: Change in single cystathionine beta-synthase domain-containing protein from a bent to flat conformation upon adenosine monophosphate binding
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 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CBS domain-containing protein CBSX2, chloroplastic
B: CBS domain-containing protein CBSX2, chloroplastic
C: CBS domain-containing protein CBSX2, chloroplastic
D: CBS domain-containing protein CBSX2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1038
Polymers72,7144
Non-polymers1,3894
Water6,017334
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11220 Å2
ΔGint-75 kcal/mol
Surface area26390 Å2
MethodPISA
2
A: CBS domain-containing protein CBSX2, chloroplastic
B: CBS domain-containing protein CBSX2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0524
Polymers36,3572
Non-polymers6942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-28 kcal/mol
Surface area14790 Å2
MethodPISA
3
C: CBS domain-containing protein CBSX2, chloroplastic
D: CBS domain-containing protein CBSX2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0524
Polymers36,3572
Non-polymers6942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-26 kcal/mol
Surface area14640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.974, 103.634, 69.983
Angle α, β, γ (deg.)90.00, 112.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
CBS domain-containing protein CBSX2, chloroplastic / CBS domain-containing protein 1 / AtCDCP1 / Protein LOSS OF THE TIMING OF ET AND JA BIOSYNTHESIS 1 / AtLEJ1


Mass: 18178.619 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 76-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At4g34120, CBSX2, CDCP1, F28A23.120 / Plasmid: pET-GST / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9C5D0
#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.45 Å3/Da / Density % sol: 49.71 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 17, 2011
RadiationMonochromator: Double-crystal Si(111) liquid-nitrogen-cooled
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.193→50 Å / Num. obs: 35664 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.1 % / Rsym value: 0.117 / Net I/σ(I): 17.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.193→31.859 Å / SU ML: 0.26 / σ(F): 0 / Phase error: 24.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2411 1861 5.68 %
Rwork0.2009 --
obs0.2032 32757 91.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.193→31.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4349 0 92 334 4775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084504
X-RAY DIFFRACTIONf_angle_d1.2416133
X-RAY DIFFRACTIONf_dihedral_angle_d14.8811682
X-RAY DIFFRACTIONf_chiral_restr0.07764
X-RAY DIFFRACTIONf_plane_restr0.005754
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1931-2.25240.26671360.23152251X-RAY DIFFRACTION87
2.2524-2.31860.30741320.22862307X-RAY DIFFRACTION88
2.3186-2.39340.25661330.23772268X-RAY DIFFRACTION88
2.3934-2.4790.35241370.25442182X-RAY DIFFRACTION86
2.479-2.57820.2571360.23292168X-RAY DIFFRACTION83
2.5782-2.69550.30781420.2252363X-RAY DIFFRACTION90
2.6955-2.83750.29871310.24532317X-RAY DIFFRACTION90
2.8375-3.01510.31461380.24412208X-RAY DIFFRACTION85
3.0151-3.24770.281460.2212420X-RAY DIFFRACTION94
3.2477-3.57420.22361580.18732617X-RAY DIFFRACTION100
3.5742-4.09040.21271590.17212593X-RAY DIFFRACTION99
4.0904-5.150.1861530.15872582X-RAY DIFFRACTION99
5.15-31.86230.20291600.19382620X-RAY DIFFRACTION99

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