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- PDB-4ixs: Native structure of xometc at ph 5.2 -

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Basic information

Entry
Database: PDB / ID: 4ixs
TitleNative structure of xometc at ph 5.2
ComponentsCystathionine gamma-lyase-like protein
KeywordsLYASE / PLP DEPENDENT ENZYME / XOMETC / Cys-Met metabolism PLP dependent enzyme / cystathionine gamma/beta 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
CARBONATE ION / Cystathionine gamma-lyase-like protein
Similarity search - Component
Biological speciesXanthomonas oryzae pv. oryzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 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: 3NNP
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 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,8794
Polymers85,7272
Non-polymers1522
Water4,918273
1
A: Cystathionine gamma-lyase-like protein
B: Cystathionine gamma-lyase-like protein
hetero molecules

A: Cystathionine gamma-lyase-like protein
B: Cystathionine gamma-lyase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,7598
Polymers171,4554
Non-polymers3044
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area18450 Å2
ΔGint-109 kcal/mol
Surface area42790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.722, 124.357, 146.164
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Cystathionine gamma-lyase-like protein


Mass: 42863.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas oryzae pv. oryzae (bacteria)
Strain: KACC 10331/KXO85 / Gene: metB, XOO0778 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5H4T8, cystathionine gamma-lyase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.27 Å3/Da / Density % sol: 45.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 23% PEG 3350, 0.2M LITHIUM SULFATE, 0.1M BIS-TRIS, 0.2M SODIUM THIOCYANATE, PH 5.2, 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
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 35240 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.29→2.35 Å / % possible all: 92

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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: 2.29→48.72 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.908 / SU B: 6.597 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.321 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1762 5 %RANDOM
Rwork0.18 ---
obs0.184 33405 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: 26.86 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.29→48.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5526 0 10 273 5809
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0225661
X-RAY DIFFRACTIONr_angle_refined_deg1.9921.9767679
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0745730
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.4422.946224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.49115906
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8791543
X-RAY DIFFRACTIONr_chiral_restr0.1540.2892
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214235
X-RAY DIFFRACTIONr_mcbond_it1.0091.53639
X-RAY DIFFRACTIONr_mcangle_it1.81725806
X-RAY DIFFRACTIONr_scbond_it3.1532022
X-RAY DIFFRACTIONr_scangle_it4.9264.51870
LS refinement shellResolution: 2.29→2.35 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 116 -
Rwork0.225 2354 -
obs--96 %

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