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- PDB-9j7q: Crystal structure of S. aureus MccB with PLP -

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Basic information

Entry
Database: PDB / ID: 9j7q
TitleCrystal structure of S. aureus MccB with PLP
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
DI(HYDROXYETHYL)ETHER / Cystathionine gamma-synthase homolog
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 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 with PLP
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9485
Polymers41,5241
Non-polymers4244
Water3,711206
1
A: Cystathionine gamma-synthase homolog
hetero molecules

A: Cystathionine gamma-synthase homolog
hetero molecules

A: Cystathionine gamma-synthase homolog
hetero molecules

A: Cystathionine gamma-synthase homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,79320
Polymers166,0954
Non-polymers1,69816
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area22340 Å2
ΔGint-85 kcal/mol
Surface area47640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.747, 80.261, 161.387
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#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-503-

HOH

21A-619-

HOH

31A-698-

HOH

41A-701-

HOH

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Components

#1: Protein Cystathionine gamma-synthase homolog


Mass: 41523.805 Da / Num. of mol.: 1
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
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.45 Å3/Da / Density % sol: 49.73 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.1M Sodium Acetate trihydrate pH4.5, 30% PEG 300

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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: Nov 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 50071 / % possible obs: 97.2 % / Redundancy: 13.3 % / Biso Wilson estimate: 12.8 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rpim(I) all: 0.016 / Rrim(I) all: 0.059 / Net I/σ(I): 41.59
Reflection shellResolution: 1.64→1.67 Å / Redundancy: 13.3 % / Mean I/σ(I) obs: 8.64 / Num. unique obs: 2393 / CC1/2: 0.987 / CC star: 0.997 / Rpim(I) all: 0.086 / Rrim(I) all: 0.312 / % possible all: 96.4

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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: 1.64→31.26 Å / SU ML: 0.1683 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.7379
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2006 1997 4.11 %
Rwork0.1735 46594 -
obs0.1746 48591 97.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.71 Å2
Refinement stepCycle: LAST / Resolution: 1.64→31.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2918 0 28 206 3152
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01033008
X-RAY DIFFRACTIONf_angle_d1.17084082
X-RAY DIFFRACTIONf_chiral_restr0.0761489
X-RAY DIFFRACTIONf_plane_restr0.0104517
X-RAY DIFFRACTIONf_dihedral_angle_d8.9484433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.680.26871380.22363200X-RAY DIFFRACTION94.99
1.68-1.730.24491400.19173261X-RAY DIFFRACTION95.99
1.73-1.780.25281400.18713257X-RAY DIFFRACTION96.01
1.78-1.840.19541410.17753277X-RAY DIFFRACTION96.15
1.84-1.90.18631390.16953272X-RAY DIFFRACTION96.36
1.9-1.980.2441400.17613274X-RAY DIFFRACTION96.77
1.98-2.070.21471410.18163318X-RAY DIFFRACTION97.08
2.07-2.180.20141420.17353327X-RAY DIFFRACTION97.39
2.18-2.310.21131440.16543327X-RAY DIFFRACTION97.47
2.31-2.490.2031420.17133343X-RAY DIFFRACTION98
2.49-2.740.19431460.17573389X-RAY DIFFRACTION98.19
2.74-3.140.21831460.18033396X-RAY DIFFRACTION98.53
3.14-3.960.18061450.16963410X-RAY DIFFRACTION97.58
3.96-31.260.16391530.1583543X-RAY DIFFRACTION97.6

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