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- PDB-4ixz: Native structure of cystathionine gamma lyase (XometC) from xanth... -

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Basic information

Entry
Database: PDB / ID: 4ixz
TitleNative structure of cystathionine gamma lyase (XometC) from xanthomonas oryzae pv. oryzae at pH 9.0
ComponentsCystathionine gamma-lyase-like protein
KeywordsLYASE / PLP DEPENDENT ENZYME / XOCGL / NATIVE / Cys-Met metabolism PLP dependent enzyme / cystathionine gamma lyase / PLP Binding
Function / homology
Function and homology information


cystathionine gamma-synthase activity / cystathionine gamma-lyase activity / L-cysteine biosynthetic process via L-cystathionine / 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 ...: / 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
BICARBONATE ION / BETA-MERCAPTOETHANOL / Cystathionine gamma-lyase-like protein
Similarity search - Component
Biological speciesXanthomonas oryzae pv. oryzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsNgo, H.P.T. / Kim, J.K. / Kang, L.W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: PLP undergoes conformational changes during the course of an enzymatic reaction.
Authors: Ngo, H.P. / Cerqueira, N.M. / Kim, J.K. / Hong, M.K. / Fernandes, P.A. / Ramos, M.J. / Kang, L.W.
History
DepositionJan 28, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionJan 29, 2014ID: 3NMY
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2May 3, 2017Group: Non-polymer description
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,8429
Polymers171,4554
Non-polymers3885
Water16,538918
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20610 Å2
ΔGint-122 kcal/mol
Surface area42760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.817, 86.308, 223.351
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. BIOMOLECULE: 1 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC SOFTWARE USED: PISA TOTAL BURIED SURFACE AREA: 20610 ANGSTROM**2 SURFACE AREA OF THE COMPLEX: 42760 ANGSTROM**2 CHANGE IN SOLVENT FREE ENERGY: -122.0 KCAL/MOL APPLY THE FOLLOWING TO CHAINS: A, B, C, D BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000

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Components

#1: Protein
Cystathionine gamma-lyase-like protein


Mass: 42863.695 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas oryzae pv. oryzae (bacteria)
Strain: KACC 10331/KXO85 / Gene: metB, XOCGL, XOO0778 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5H4T8, cystathionine gamma-lyase
#2: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 918 / 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: 2.22 Å3/Da / Density % sol: 44.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 25.5% PEG 4000, 15% GLYCEROL, 0.17MM LITHIUM SULFATE, 0.085MM TRIS, PH 9.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. obs: 93642 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.07→2.11 Å / % possible all: 99.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3E6G

3e6g


Resolution: 2.07→40.25 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.904 / SU B: 4.656 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.247 4688 5 %RANDOM
Rwork0.181 ---
obs0.184 88708 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.07→40.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11457 0 22 918 12397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.02211732
X-RAY DIFFRACTIONr_angle_refined_deg1.9721.97315911
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.95751516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75222.945472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.715151862
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6111589
X-RAY DIFFRACTIONr_chiral_restr0.1420.21828
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218823
X-RAY DIFFRACTIONr_mcbond_it1.081.57532
X-RAY DIFFRACTIONr_mcangle_it1.758212011
X-RAY DIFFRACTIONr_scbond_it3.10634200
X-RAY DIFFRACTIONr_scangle_it4.7564.53894
LS refinement shellResolution: 2.07→2.12 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 357 -
Rwork0.196 6365 -
obs--98.19 %

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