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- PDB-4iy7: crystal structure of cystathionine gamma lyase (XometC) from Xant... -

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Basic information

Entry
Database: PDB / ID: 4iy7
Titlecrystal structure of cystathionine gamma lyase (XometC) from Xanthomonas oryzae pv. oryzae in complex with E-site serine, A-site external aldimine structure with serine and A-site external aldimine structure with aminoacrylate intermediates
ComponentsCystathionine gamma-lyase-like protein
KeywordsLYASE / XOCGL / SERINE EXTERNAL SCHIFF BASE / AMINOACRYLATE EXTERNAL SCHIFF BASE / PLP DEPENDENT ENZYME / Cys-Met metabolism PLP dependent enzyme / cystathionine gamma lyase / PLP binding
Function / homology
Function and homology information


transsulfuration / pyridoxal phosphate binding
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
Chem-0JO / Chem-KOU / PYRUVIC ACID / SERINE / Cystathionine gamma-lyase-like protein
Similarity search - Component
Biological speciesXanthomonas oryzae pv. oryzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2Sep 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)172,73817
Polymers170,5424
Non-polymers2,19613
Water25,7251428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20870 Å2
ΔGint-120 kcal/mol
Surface area41620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.219, 86.069, 225.997
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: 20870 ANGSTROM**2 SURFACE AREA OF THE COMPLEX: 41620 ANGSTROM**2 CHANGE IN SOLVENT FREE ENERGY: -120.0 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

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Cystathionine gamma-lyase-like protein


Mass: 42635.578 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

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Non-polymers , 7 types, 1441 molecules

#2: Chemical
ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7NO3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-0JO / 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid


Mass: 316.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13N2O7P
#6: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#7: Chemical ChemComp-KOU / (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine


Mass: 334.219 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H15N2O8P
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1428 / 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: 2.17 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 25.5% PEG 4000, 0.17M LITHIUM SULFATE, 0.085 TRIS, 15% GLYCEROL, 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: Nov 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.67→50 Å / Num. obs: 171413 / % possible obs: 85.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.67→1.7 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4IXZ

4ixz


Resolution: 1.7→30.23 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.554 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.169 8207 5 %RANDOM
Rwork0.134 ---
obs0.136 155517 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.26 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11469 0 144 1428 13041
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.02211977
X-RAY DIFFRACTIONr_angle_refined_deg2.2621.97516281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59751574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.21522.887478
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.617151938
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2231592
X-RAY DIFFRACTIONr_chiral_restr0.280.21867
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0219060
X-RAY DIFFRACTIONr_mcbond_it1.3031.57684
X-RAY DIFFRACTIONr_mcangle_it2.05212299
X-RAY DIFFRACTIONr_scbond_it3.58734293
X-RAY DIFFRACTIONr_scangle_it5.6934.53956
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 609 -
Rwork0.197 11352 -
obs--99.93 %

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