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- PDB-6ld7: Native Structure of cystathionine gamma synthase (XometB) from Xa... -

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Basic information

Entry
Database: PDB / ID: 6ld7
TitleNative Structure of cystathionine gamma synthase (XometB) from Xanthomonas oryzae pv. oryzae
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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Cystathionine gamma-synthase
Similarity search - Component
Biological speciesXanthomonas oryzae pv. oryzae KACC 10331 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsNgo, H.P.T. / Nguyen, T.D.Q. / Kang, L.W.
CitationJournal: To Be Published
Title: Native Structure of cystathionine gamma synthase (XometB) from Xanthomonas oryzae pv. oryzae
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)174,49312
Polymers173,4244
Non-polymers1,0698
Water12,106672
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23130 Å2
ΔGint-73 kcal/mol
Surface area46590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.424, 165.424, 241.735
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: 43355.945 Da / Num. of mol.: 4 / Mutation: D134V
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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 672 / 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: 5.03 Å3/Da / Density % sol: 75.55 %
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: Jun 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 187462 / % possible obs: 99.89 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.012 / Net I/σ(I): 36.5
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.046 / Mean I/σ(I) obs: 5.9 / Num. unique obs: 18556

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CS1

1cs1


Resolution: 2.1→48.8 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.97 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1903 9421 5 %RANDOM
Rwork0.1615 ---
obs0.1629 178046 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 134.33 Å2 / Biso mean: 34.466 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å2-0 Å2
2--0.02 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: final / Resolution: 2.1→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11527 0 71 672 12270
Biso mean--71.72 40.75 -
Num. residues----1547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01311834
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711182
X-RAY DIFFRACTIONr_angle_refined_deg2.3531.62916092
X-RAY DIFFRACTIONr_angle_other_deg1.6381.56725760
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.20751555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.78121.413559
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.508151786
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.5451584
X-RAY DIFFRACTIONr_chiral_restr0.150.21562
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213477
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022488
LS refinement shellResolution: 2.102→2.157 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 707 -
Rwork0.258 13014 -
all-13721 -
obs--99.31 %
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)
10.0449-0.04420.0160.2503-0.16210.14890.01710.02560.00140.0125-0.0539-0.0269-0.00040.04660.03680.0182-0.0021-0.010.05280.040.040425.935-54.0956-12.7659
20.0399-0.0372-0.02780.1334-0.08760.1509-0.01260.00090.00590.01820.03050.01110.0064-0.0312-0.01790.0101-0.0009-0.00250.04450.03840.0348-10.8611-50.1981-9.6332
30.04660.05320.02660.136-0.06880.1488-0.01180.0018-0.0045-0.01670.03050.0137-0.0089-0.0272-0.01870.01020.00070.00150.04350.0380.0345-10.8687-32.5103-40.2451
40.03680.0407-0.00250.2293-0.15020.16290.014-0.0238-0.0002-0.0099-0.0537-0.02580.00090.04610.03970.01730.00020.01010.05380.03980.042125.9401-28.5747-36.9916
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 395
2X-RAY DIFFRACTION2B10 - 395
3X-RAY DIFFRACTION3C9 - 396
4X-RAY DIFFRACTION4D10 - 395

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