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- PDB-4iyo: Crystal structure of cystathionine gamma lyase from Xanthomonas o... -

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Basic information

Entry
Database: PDB / ID: 4iyo
TitleCrystal structure of cystathionine gamma lyase from Xanthomonas oryzae pv. oryzae (XometC) in complex with E-site serine, A-site serine, A-site external aldimine structure with aminoacrylate and A-site iminopropionate intermediates
Components(Cystathionine gamma-lyase-like ...) x 2
KeywordsLYASE / PLP DEPENDENT ENZYME / XOCGL / IMINOPROPIONATE / SERINE / 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 / cysteine biosynthetic process via 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
Chem-0JO / AMINO-ACRYLATE / PYRUVIC ACID / SERINE / Cystathionine gamma-lyase-like protein
Similarity search - Component
Biological speciesXanthomonas oryzae pv. oryzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 29, 2013Deposition site: RCSB / Processing site: RCSB
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_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model / Data collection
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact
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 / _pdbx_validate_close_contact.auth_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, LYS201A modified
C: Cystathionine gamma-lyase-like protein, LYS201A modified
D: Cystathionine gamma-lyase-like protein, LYS201A modified
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,70317
Polymers171,2274
Non-polymers1,47613
Water23,8521324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21500 Å2
ΔGint-128 kcal/mol
Surface area41940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.319, 86.344, 226.344
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: 21500 ANGSTROM**2 SURFACE AREA OF THE COMPLEX: 41940 ANGSTROM**2 CHANGE IN SOLVENT FREE ENERGY: -128.0 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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Cystathionine gamma-lyase-like ... , 2 types, 4 molecules ABCD

#1: Protein Cystathionine gamma-lyase-like protein


Mass: 42635.578 Da / Num. of mol.: 1
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: Protein Cystathionine gamma-lyase-like protein, LYS201A modified


Mass: 42863.695 Da / Num. of mol.: 3
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, 1337 molecules

#3: Chemical
ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H7NO3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: 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
#7: Chemical ChemComp-NAK / AMINO-ACRYLATE / 2-IMINIOPROPANOATE


Mass: 87.077 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5NO2
#8: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1324 / 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: 43.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 25.5% PEG4000, 0.17M LITHIUM SULFATE, 0.085M 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: 1.78→50 Å / Num. obs: 142510 / % possible obs: 95.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.78→1.81 Å / % possible all: 99.7

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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: 1.8→33.82 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.021 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18 6971 5 %RANDOM
Rwork0.136 ---
obs0.138 132060 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: 18.02 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→33.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11523 0 97 1324 12944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.02211917
X-RAY DIFFRACTIONr_angle_refined_deg2.1281.97516185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.69251553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49322.983476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.394151900
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8841589
X-RAY DIFFRACTIONr_chiral_restr0.2170.21858
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0219001
X-RAY DIFFRACTIONr_mcbond_it1.2551.57649
X-RAY DIFFRACTIONr_mcangle_it1.964212227
X-RAY DIFFRACTIONr_scbond_it3.57834268
X-RAY DIFFRACTIONr_scangle_it5.7534.53940
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 505 -
Rwork0.194 9605 -
obs--99.99 %

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