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- PDB-9j7r: Crystal structure of S. aureus MccB mutant K196A -

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Basic information

Entry
Database: PDB / ID: 9j7r
TitleCrystal structure of S. aureus MccB mutant K196A
ComponentsCystathionine gamma-synthase homolog
KeywordsLYASE / CGL / PLP / MccB
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 / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-PGU / Cystathionine gamma-synthase homolog
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHa, N.-C. / Lee, D. / Lee, H. / Byun, K.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)RS-2021-IP321036 Korea, Republic Of
National Research Foundation (NRF, Korea)2022R1A2C109178313 Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of S. aureus MccB mutant K196A
Authors: Ha, N.-C. / Lee, D. / Lee, H. / Byun, K.
History
DepositionAug 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cystathionine gamma-synthase homolog
B: Cystathionine gamma-synthase homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4064
Polymers82,6492
Non-polymers7572
Water1,67593
1
A: Cystathionine gamma-synthase homolog
B: Cystathionine gamma-synthase homolog
hetero molecules

A: Cystathionine gamma-synthase homolog
B: Cystathionine gamma-synthase homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,8128
Polymers165,2994
Non-polymers1,5134
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area19760 Å2
ΔGint-106 kcal/mol
Surface area42930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.998, 154.454, 150.038
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-536-

HOH

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Components

#1: Protein Cystathionine gamma-synthase homolog


Mass: 41324.660 Da / Num. of mol.: 2 / Mutation: K196A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Gene: yrhB, SAV0460 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3JQ19, cystathionine gamma-lyase
#2: Chemical ChemComp-PGU / N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-glutamic acid


Mass: 378.272 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H19N2O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.96 Å3/Da / Density % sol: 37.4 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M sodium citrate pH 5.5, 22% PEG1000

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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: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 6, 2023
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: 23029 / % possible obs: 92 % / Redundancy: 6.4 % / Biso Wilson estimate: 31.49 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rpim(I) all: 0.022 / Rrim(I) all: 0.068 / Net I/σ(I): 21.09
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 4.23 / Num. unique obs: 967 / CC1/2: 0.927 / CC star: 0.981 / Rpim(I) all: 0.086 / Rrim(I) all: 0.193 / % possible all: 84

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→36.26 Å / SU ML: 0.2831 / Cross valid method: FREE R-VALUE / σ(F): 1.6 / Phase error: 24.0096
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.266 1999 9.63 %
Rwork0.2163 18757 -
obs0.2211 20756 90.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.64 Å2
Refinement stepCycle: LAST / Resolution: 2.5→36.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5531 0 50 93 5674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00245705
X-RAY DIFFRACTIONf_angle_d0.50897765
X-RAY DIFFRACTIONf_chiral_restr0.0425936
X-RAY DIFFRACTIONf_plane_restr0.0043988
X-RAY DIFFRACTIONf_dihedral_angle_d7.0834807
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.34441070.26281004X-RAY DIFFRACTION68.16
2.56-2.630.29591200.25231125X-RAY DIFFRACTION77.72
2.63-2.710.28231300.24351220X-RAY DIFFRACTION83.38
2.71-2.790.28731380.24461288X-RAY DIFFRACTION87.59
2.79-2.890.3161390.23681310X-RAY DIFFRACTION89.67
2.89-3.010.29871400.23851317X-RAY DIFFRACTION89.22
3.01-3.150.30091430.24031336X-RAY DIFFRACTION90.68
3.15-3.310.29291470.22391371X-RAY DIFFRACTION92.73
3.31-3.520.28321480.2241396X-RAY DIFFRACTION94.49
3.52-3.790.2561520.22011426X-RAY DIFFRACTION96.1
3.79-4.170.24321530.19861446X-RAY DIFFRACTION96.79
4.17-4.780.23961570.18221470X-RAY DIFFRACTION97.48
4.78-6.010.24951580.20421473X-RAY DIFFRACTION97.14
6.02-36.260.22941670.20211575X-RAY DIFFRACTION98.64

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