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- PDB-3e6g: Crystal structure of XometC, a cystathionine c-lyase-like protein... -

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Basic information

Entry
Database: PDB / ID: 3e6g
TitleCrystal structure of XometC, a cystathionine c-lyase-like protein from Xanthomonas oryzae pv.oryzae
ComponentsCystathionine gamma-lyase-like protein
KeywordsLYASE / Bacterial blight / cystathionine lyase / reverse transsulfuration pathway / Xanthomonas oryzae pv.oryzae
Function / homology
Function and homology information


carbon-sulfur lyase activity / cystathionine gamma-synthase activity / transsulfuration / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase ...Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cystathionine gamma-lyase-like protein
Similarity search - Component
Biological speciesXanthomonas oryzae pv. oryzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsNgo, H.P.T. / Kim, J.K. / Kim, H.S. / Jung, J.H. / Ahn, Y.J. / Kim, J.G. / Lee, B.M. / Kang, H.W. / Kang, L.W.
CitationJournal: To be published
Title: Crystal structure of XometC, a cystathionine c-lyase-like protein from Xanthomonas oryzae pv.oryzae
Authors: Ngo, H.P.T. / Kim, J.K. / Kim, H.S. / Jung, J.H. / Ahn, Y.J. / Kim, J.G. / Lee, B.M. / Kang, H.W. / Kang, L.W.
History
DepositionAug 15, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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: Cystathionine gamma-lyase-like protein
B: Cystathionine gamma-lyase-like protein
C: Cystathionine gamma-lyase-like protein
D: Cystathionine gamma-lyase-like protein


Theoretical massNumber of molelcules
Total (without water)171,6714
Polymers171,6714
Non-polymers00
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13790 Å2
ΔGint-76.6 kcal/mol
Surface area45710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.351, 78.351, 300.989
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
Cystathionine gamma-lyase-like protein / XometC


Mass: 42917.852 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas oryzae pv. oryzae (bacteria)
Gene: metB, XOO0778 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q5H4T8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.69 Å3/Da / Density % sol: 54.29 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% PEG3350, 0.2M lithium sulfate monohydrate, 0.1M bis-Tris, pH5.5, sodium thiocyanate, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 11, 2008
RadiationMonochromator: flat Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 44441 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.8→2.9 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2I87

2i87


Resolution: 2.8→42.26 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.872 / SU B: 16.079 / SU ML: 0.321 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.423 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29549 2238 5 %RANDOM
Rwork0.21559 ---
all0.21957 42154 --
obs0.21957 42154 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.296 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.8→42.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10559 0 0 102 10661
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02210758
X-RAY DIFFRACTIONr_angle_refined_deg1.8061.96514582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.54251397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.49423430
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.215151756
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5661581
X-RAY DIFFRACTIONr_chiral_restr0.120.21704
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028051
X-RAY DIFFRACTIONr_nbd_refined0.260.25425
X-RAY DIFFRACTIONr_nbtor_refined0.3170.27209
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2405
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4280.22
X-RAY DIFFRACTIONr_mcbond_it0.771.57104
X-RAY DIFFRACTIONr_mcangle_it1.392211101
X-RAY DIFFRACTIONr_scbond_it1.8234005
X-RAY DIFFRACTIONr_scangle_it2.9554.53481
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 170 -
Rwork0.335 3104 -
obs--99.97 %

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