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- PDB-6kgz: bacterial cystathionine gamma-lyase MccB of Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 6kgz
Titlebacterial cystathionine gamma-lyase MccB of Staphylococcus aureus
ComponentsCystathionine gamma-lyase
KeywordsLYASE / Cysteine biosynthesis pathway / MccB / PLP binding protein / Schiff-base / yhrB
Function / homology
Function and homology information


transsulfuration / catalytic activity / 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
Cystathionine gamma-synthase homolog
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHa, N.-C. / Lee, D.
CitationJournal: Crystals / Year: 2019
Title: Crystal Structure of Bacterial Cystathionine Gamma-Lyase in The Cysteine Biosynthesis Pathway of Staphylococcus aureus
Authors: Lee, D. / Jeong, S. / Ahn, J. / Ha, N.-C. / Kwon, A.-R.
History
DepositionJul 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 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-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4592
Polymers43,3371
Non-polymers1221
Water93752
1
A: Cystathionine gamma-lyase
hetero molecules

A: Cystathionine gamma-lyase
hetero molecules

A: Cystathionine gamma-lyase
hetero molecules

A: Cystathionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,8368
Polymers173,3484
Non-polymers4894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area18930 Å2
ΔGint-90 kcal/mol
Surface area47960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.567, 105.567, 287.986
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-522-

HOH

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Components

#1: Protein Cystathionine gamma-lyase


Mass: 43336.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Strain: Mu50 / Gene: yrhB, SAV0460 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3JQ19, cystathionine gamma-lyase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 5.02 Å3/Da / Density % sol: 75.49 %
Crystal growTemperature: 311 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Tacsimate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 36627 / % possible obs: 99.6 % / Redundancy: 14.7 % / Biso Wilson estimate: 26.52 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.125 / Net I/σ(I): 16.67
Reflection shellResolution: 2.3→2.34 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1774 / Rpim(I) all: 0.159 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4l0o

4l0o


Resolution: 2.3→46.59 Å / SU ML: 0.2897 / Cross valid method: FREE R-VALUE / σ(F): 1.54 / Phase error: 22.6016 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2364 1656 4.98 %
Rwork0.2102 31615 -
obs0.2116 33271 90.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.58 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2801 0 8 52 2861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00272854
X-RAY DIFFRACTIONf_angle_d0.55453877
X-RAY DIFFRACTIONf_chiral_restr0.0455472
X-RAY DIFFRACTIONf_plane_restr0.0042492
X-RAY DIFFRACTIONf_dihedral_angle_d2.82821716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.370.3378580.30081518X-RAY DIFFRACTION52.62
2.37-2.450.3512880.30511891X-RAY DIFFRACTION65.83
2.45-2.530.29851140.29712336X-RAY DIFFRACTION81.42
2.53-2.630.28441390.29362639X-RAY DIFFRACTION93.07
2.63-2.750.30321550.27352830X-RAY DIFFRACTION98.94
2.75-2.90.33111500.26122860X-RAY DIFFRACTION99.8
2.9-3.080.26411610.23652847X-RAY DIFFRACTION100
3.08-3.320.271530.2142903X-RAY DIFFRACTION99.93
3.32-3.650.21571410.18842912X-RAY DIFFRACTION100
3.65-4.180.20441680.16582895X-RAY DIFFRACTION99.97
4.18-5.270.16581670.14592950X-RAY DIFFRACTION99.97
5.27-46.590.1911620.17673034X-RAY DIFFRACTION97.68

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