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- PDB-9rj1: S-methylcysteine synthase (BSAS4) from common bean in complex wit... -

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Basic information

Entry
Database: PDB / ID: 9rj1
TitleS-methylcysteine synthase (BSAS4) from common bean in complex with PLP, BEZ, and GOL
ComponentsCysteine synthase
KeywordsTRANSFERASE / cysteine synthase / s-methylcysteine synthase / O-acetylserine sulfhydrylase / beta-substituted alanine synthase
Function / homology
Function and homology information


L-3-cyanoalanine synthase activity / cysteine synthase / cysteine synthase activity / L-cysteine biosynthetic process from L-serine / cytoplasm
Similarity search - Function
Cysteine synthase CysK / Cysteine synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / : / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme
Similarity search - Domain/homology
BENZOIC ACID / Cysteine synthase
Similarity search - Component
Biological speciesPhaseolus vulgaris (common bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWitek, W. / Jaskolski, M. / Ruszkowski, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Plant Physiol. / Year: 2025
Title: Benzoic and salicylic acids inhibit beta-substituted alanine synthase 4;1 in common bean.
Authors: Lu, Z. / Witek, W. / Ruszkowski, M. / Imiolczyk, B. / Paulish, N. / Joshi, J. / Jaskolski, M. / Marsolais, F.
History
DepositionJun 12, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 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: Cysteine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1436
Polymers34,7781
Non-polymers3655
Water4,882271
1
A: Cysteine synthase
hetero molecules

A: Cysteine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,28512
Polymers69,5562
Non-polymers73010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7850 Å2
ΔGint-79 kcal/mol
Surface area22790 Å2
Unit cell
Length a, b, c (Å)69.185, 69.185, 186.433
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cysteine synthase


Mass: 34777.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phaseolus vulgaris (common bean) / Gene: PHAVU_007G185200g / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: V7BIJ9, cysteine synthase

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Non-polymers , 5 types, 276 molecules

#2: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.61 Å3/Da / Density % sol: 23.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M MgCl2 x 6H2O, 0.1 M TRIS, 25% v/v PEG SMEAR HIGH, 20% Glycerol v/v

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.5→80 Å / Num. obs: 60777 / % possible obs: 99.9 % / Redundancy: 14.16 % / CC1/2: 1 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.07 / Net I/σ(I): 20.97
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 13.69 % / Rmerge(I) obs: 1.56 / Mean I/σ(I) obs: 1.65 / Num. unique obs: 9636 / CC1/2: 0.736 / % possible all: 99.5

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Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
PHASERphasing
PHENIX1.21.2_5419refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→47.32 Å / SU ML: 0.168 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.9585
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1683 1215 2 %
Rwork0.1413 59545 -
obs0.1418 60760 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.2 Å2
Refinement stepCycle: LAST / Resolution: 1.6→47.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2391 0 38 271 2700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092527
X-RAY DIFFRACTIONf_angle_d0.923423
X-RAY DIFFRACTIONf_chiral_restr0.0595391
X-RAY DIFFRACTIONf_plane_restr0.0064440
X-RAY DIFFRACTIONf_dihedral_angle_d13.2081966
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.660.27321320.22386457X-RAY DIFFRACTION99.17
1.66-1.740.21151330.17826510X-RAY DIFFRACTION99.98
1.74-1.830.19871330.14816517X-RAY DIFFRACTION99.91
1.83-1.950.18011330.13096512X-RAY DIFFRACTION99.98
1.95-2.10.15791340.11076585X-RAY DIFFRACTION99.99
2.1-2.310.15171350.11316594X-RAY DIFFRACTION99.97
2.31-2.640.16011350.12736621X-RAY DIFFRACTION100
2.64-3.330.18491370.14766709X-RAY DIFFRACTION99.99
3.33-47.320.1561430.14727040X-RAY DIFFRACTION99.92

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