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- PDB-6ld9: Crystal structure of cystathionine gamma synthase from Xanthomona... -

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Basic information

Entry
Database: PDB / ID: 6ld9
TitleCrystal structure of cystathionine gamma synthase from Xanthomonas oryzae pv. oryzae in complex with cystathionine
ComponentsCystathionine gamma-synthase
KeywordsBIOSYNTHETIC PROTEIN / cysathionine gamma synthase / PLP dependent enzyme / methionine biosynthesis pathway
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
O-succinylhomoserine (thiol)-lyase / : / Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-E9U / Cystathionine gamma-synthase
Similarity search - Component
Biological speciesXanthomonas oryzae pv. oryzae KACC 10331 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNgo, H.P.T. / Nguyen, T.D.Q. / Kang, L.W.
CitationJournal: To Be Published
Title: Crystal structure of cystathionine gamma synthase from Xanthomonas oryzae pv. oryzae in complex with cystathionine
Authors: Ngo, H.P.T. / Nguyen, T.D.Q. / Kang, L.W.
History
DepositionNov 20, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cystathionine gamma-synthase
B: Cystathionine gamma-synthase
C: Cystathionine gamma-synthase
D: Cystathionine gamma-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,4818
Polymers172,6754
Non-polymers1,8064
Water8,053447
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20590 Å2
ΔGint-97 kcal/mol
Surface area45170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.146, 161.146, 245.259
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

#1: Protein
Cystathionine gamma-synthase


Mass: 43168.809 Da / Num. of mol.: 4 / Mutation: D5Y, H8D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas oryzae pv. oryzae KACC 10331 (bacteria)
Strain: KACC10331 / Gene: metB, XOO1818 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5H1U9
#2: Chemical
ChemComp-E9U / (2~{S})-4-[(2~{R})-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]sulfanyl-2-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]butanoic acid


Mass: 451.389 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H22N3O9PS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.87 Å3/Da / Density % sol: 74.74 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.12 M Ethylene Glycols Mix, 0.1 M Na HEPES/MOPS pH 7.5, 10%(w/v) PEG 4000, 20%(v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 106893 / % possible obs: 99.76 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 25.8
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.52 / Num. unique obs: 10462

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
HKL-2000data reduction
PDB_EXTRACT3.25data extraction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LD7

6ld7


Resolution: 2.5→47.06 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 11.36 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1861 5331 5 %RANDOM
Rwork0.1526 ---
obs0.1543 101562 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 112.7 Å2 / Biso mean: 30.917 Å2 / Biso min: 14.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å2-0 Å2-0 Å2
2--0.12 Å2-0 Å2
3----0.23 Å2
Refinement stepCycle: final / Resolution: 2.5→47.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11489 0 116 447 12052
Biso mean--32.59 33.1 -
Num. residues----1549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01311821
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711114
X-RAY DIFFRACTIONr_angle_refined_deg2.2041.64316091
X-RAY DIFFRACTIONr_angle_other_deg1.5421.57825597
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.34851545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.63721.489564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.968151800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8331584
X-RAY DIFFRACTIONr_chiral_restr0.1110.21569
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213507
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022485
LS refinement shellResolution: 2.503→2.568 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 401 -
Rwork0.204 7298 -
all-7699 -
obs--97.59 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1927-0.0551-0.11180.01760.03050.1815-0.00850.009-0.02620.00420.00370.00410.02320.01480.00480.04220.0040.03560.0139-0.01330.050952.3247-26.28119.9036
20.21230.0346-0.14450.0117-0.01330.1689-0.0091-0.0095-0.0231-0.00320.0038-0.00280.0275-0.00990.00530.0437-0.00530.03410.01430.01390.052528.2439-26.320234.6572
30.1206-0.0618-0.04120.0652-0.01220.12520.05260.01660.0278-0.013-0.0027-0.0062-0.05370.0081-0.04990.06250.00590.05680.0073-0.00020.058348.608910.66337.0491
40.11640.0562-0.07120.0535-0.00730.13970.0514-0.01360.02720.0167-0.01060.0105-0.054-0.0111-0.04080.0616-0.00450.05530.0058-0.00150.055931.960210.654937.4646
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 801
2X-RAY DIFFRACTION2B9 - 801
3X-RAY DIFFRACTION3C9 - 801
4X-RAY DIFFRACTION4D9 - 801

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