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

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Basic information

Entry
Database: PDB / ID: 6khq
Titlebacterial cystathionine gamma-lyase MccB of Staphylococcus aureus with cofactor PLP
ComponentsCystathionine gamma lyase
KeywordsLYASE / Cystathionine gamma lyase / CGL / MccB / yhrB / PLP / Pyridoxal Phosphate / Cysteine synthesis
Function / homology
Function and homology information


cystathionine gamma-synthase activity / cystathionine gamma-lyase activity / cysteine biosynthetic process via cystathionine / transsulfuration / methionine biosynthetic process / 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
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 16, 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

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Assembly

Deposited unit
A: Cystathionine gamma lyase
B: Cystathionine gamma lyase


Theoretical massNumber of molelcules
Total (without water)87,1302
Polymers87,1302
Non-polymers00
Water2,504139
1
A: Cystathionine gamma lyase
B: Cystathionine gamma lyase

A: Cystathionine gamma lyase
B: Cystathionine gamma lyase


Theoretical massNumber of molelcules
Total (without water)174,2604
Polymers174,2604
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area20200 Å2
ΔGint-107 kcal/mol
Surface area43040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.281, 132.281, 97.954
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11A-449-

HOH

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Components

#1: Protein Cystathionine gamma lyase


Mass: 43565.016 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.65 Å3/Da / Density % sol: 53.55 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: PEG 400, Sodium Acetate

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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: Jun 19, 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: 39074 / % possible obs: 99.5 % / Redundancy: 14.1 % / Biso Wilson estimate: 26.43 Å2 / CC1/2: 1 / Rpim(I) all: 0.017 / Rrim(I) all: 0.072 / Net I/σ(I): 28.11
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 3.92 / Num. unique obs: 1914 / CC1/2: 0.701 / Rpim(I) all: 0.126 / Rrim(I) all: 0.373 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472model building
PHENIX1.15.2_3472refinement
MxDCdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KGZ

6kgz


Resolution: 2.3→42.2 Å / SU ML: 0.2616 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 21.8161
RfactorNum. reflection% reflection
Rfree0.2492 2000 5.19 %
Rwork0.2029 --
obs0.2052 38561 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 30.28 Å2
Refinement stepCycle: LAST / Resolution: 2.3→42.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5687 0 0 139 5826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00225782
X-RAY DIFFRACTIONf_angle_d0.49077855
X-RAY DIFFRACTIONf_chiral_restr0.0433942
X-RAY DIFFRACTIONf_plane_restr0.0033998
X-RAY DIFFRACTIONf_dihedral_angle_d4.77613464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.29351300.25582389X-RAY DIFFRACTION91.43
2.36-2.420.27491390.24352512X-RAY DIFFRACTION96.68
2.42-2.50.27761400.24172567X-RAY DIFFRACTION98.15
2.5-2.580.29131390.23272565X-RAY DIFFRACTION98.72
2.58-2.670.30641410.2252572X-RAY DIFFRACTION99.12
2.67-2.770.28961420.23462593X-RAY DIFFRACTION99.56
2.77-2.90.27981430.23312611X-RAY DIFFRACTION99.82
2.9-3.050.26651430.22552627X-RAY DIFFRACTION99.86
3.05-3.250.28331440.22532625X-RAY DIFFRACTION99.86
3.25-3.50.27581450.22022636X-RAY DIFFRACTION99.89
3.5-3.850.25371450.18932647X-RAY DIFFRACTION99.89
3.85-4.40.19981450.1652661X-RAY DIFFRACTION99.61
4.4-5.550.20091480.15592706X-RAY DIFFRACTION99.83
5.55-42.20.20391560.17832850X-RAY DIFFRACTION99.9

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