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- PDB-1z7y: Crystal Structure of the Arabidopsis thaliana O-Acetylserine Sulf... -

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Basic information

Entry
Database: PDB / ID: 1z7y
TitleCrystal Structure of the Arabidopsis thaliana O-Acetylserine Sulfhydrylase K46A mutant
ComponentsCysteine synthase
KeywordsTRANSFERASE
Function / homology
Function and homology information


double fertilization forming a zygote and endosperm / pollen tube growth / cysteine synthase / cysteine synthase activity / cysteine biosynthetic process / apoplast / cysteine biosynthetic process from serine / plant-type vacuole / chloroplast stroma / response to cadmium ion ...double fertilization forming a zygote and endosperm / pollen tube growth / cysteine synthase / cysteine synthase activity / cysteine biosynthetic process / apoplast / cysteine biosynthetic process from serine / plant-type vacuole / chloroplast stroma / response to cadmium ion / chloroplast / peroxisome / mRNA binding / nucleus / plasma membrane / cytosol
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. / : / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold ...Cysteine synthase CysK / Cysteine synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / : / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-AA5 / Cysteine synthase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBonner, E.R. / Cahoon, R.E. / Knapke, S.M. / Jez, J.M.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Molecular Basis of Cysteine Biosynthesis in Plants: STRUCTURAL AND FUNCTIONAL ANALYSIS OF O-ACETYLSERINE SULFHYDRYLASE FROM ARABIDOPSIS THALIANA.
Authors: Bonner, E.R. / Cahoon, R.E. / Knapke, S.M. / Jez, J.M.
History
DepositionMar 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1602
Polymers33,7821
Non-polymers3781
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cysteine synthase
hetero molecules

A: Cysteine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3214
Polymers67,5642
Non-polymers7572
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_664-y+1,-x+1,-z-1/21
Buried area7200 Å2
ΔGint-58 kcal/mol
Surface area22730 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)105.856, 105.856, 100.159
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Cysteine synthase / O-acetylserine sulfhydrylase / O-acetylserine (Thiol)-lyase / CSase A / CS-A / OAS-TL A / Cys-3A / At.OAS.5-8


Mass: 33781.926 Da / Num. of mol.: 1 / Mutation: K46A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: OASA1, OAS1 / Plasmid: pET28a-AtOASSA-K46A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P47998, cysteine synthase
#2: Chemical ChemComp-AA5 / N-[(3-HYDROXY-2-METHYL-5-{[(TRIHYDROXYPHOSPHORANYL)OXY]METHYL}PYRIDIN-4-YL)METHYLENE]METHIONINE


Mass: 378.338 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19N2O7PS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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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: 2.03 Å3/Da / Density % sol: 39.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: sodium formate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Mar 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→60 Å / Num. all: 15955 / Num. obs: 15955 / % possible obs: 98.5 % / Observed criterion σ(I): 0
Reflection shellResolution: 2.7→2.8 Å / % possible all: 94.9

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Processing

Software
NameClassification
PROTEUM PLUSdata collection
PROTEUM PLUSdata reduction
CNSrefinement
PROTEUM PLUSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1OAS

1oas


Resolution: 2.7→15 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.277 795 random
Rwork0.251 --
all-16181 -
obs-15955 -
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2354 0 24 72 2450
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.4

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