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- PDB-2isq: Crystal Structure of O-Acetylserine Sulfhydrylase from Arabidopsi... -

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Basic information

Entry
Database: PDB / ID: 2isq
TitleCrystal Structure of O-Acetylserine Sulfhydrylase from Arabidopsis Thaliana in Complex with C-Terminal Peptide from Arabidopsis Serine Acetyltransferase
Components
  • Cysteine synthase
  • Serine acetyltransferase 1
KeywordsTRANSFERASE / alpha beta structrual domain
Function / homology
Function and homology information


double fertilization forming a zygote and endosperm / pollen tube growth / cellular response to sulfate starvation / serine O-acetyltransferase / serine O-acetyltransferase activity / cysteine synthase / cysteine biosynthetic process / cysteine synthase activity / cysteine biosynthetic process from serine / plant-type vacuole ...double fertilization forming a zygote and endosperm / pollen tube growth / cellular response to sulfate starvation / serine O-acetyltransferase / serine O-acetyltransferase activity / cysteine synthase / cysteine biosynthetic process / cysteine synthase activity / cysteine biosynthetic process from serine / plant-type vacuole / apoplast / chloroplast stroma / response to cadmium ion / response to cold / chloroplast / peroxisome / mRNA binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Serine O-acetyltransferase / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal domain superfamily / Cysteine synthase CysK / Cysteine synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / Hexapeptide transferase, conserved site ...Serine O-acetyltransferase / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal domain superfamily / Cysteine synthase CysK / Cysteine synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Rossmann fold - #1100 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Trimeric LpxA-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Cysteine synthase 1 / Serine acetyltransferase 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsFrancois, J.A. / Kumaran, S. / Jez, J.M.
CitationJournal: Plant Cell / Year: 2006
Title: Structural basis for interaction of o-acetylserine sulfhydrylase and serine acetyltransferase in the Arabidopsis cysteine synthase complex.
Authors: Francois, J.A. / Kumaran, S. / Jez, J.M.
History
DepositionOct 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine synthase
B: Serine acetyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9934
Polymers34,6502
Non-polymers3432
Water2,018112
1
A: Cysteine synthase
B: Serine acetyltransferase 1
hetero molecules

A: Cysteine synthase
B: Serine acetyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9868
Polymers69,3004
Non-polymers6864
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_664-y+1,-x+1,-z-1/21
Buried area9590 Å2
ΔGint-77 kcal/mol
Surface area22730 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)104.860, 104.860, 99.315
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsPhysiologic dimer is generated by crystallographic 2-fold symmetry.

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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: 33637.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: OASA1 / Plasmid: pET28a-AtOASS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P47998, cysteine synthase
#2: Protein/peptide Serine acetyltransferase 1 / AtSAT-1 / SAT-p / AtSERAT2 / 1


Mass: 1012.071 Da / Num. of mol.: 1 / Fragment: SAT peptide
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SAT1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q42588, serine O-acetyltransferase
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 3.94 Å3/Da / Density % sol: 68.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.5 M ammonium sulfate; 0.1 M PIPES, pH 6.5, 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: 1.54 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Jun 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 19828 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Rsym value: 0.145 / Net I/σ(I): 7.36
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 10 % / Mean I/σ(I) obs: 2.01 / Num. unique all: 1381 / Rsym value: 0.526 / % possible all: 100

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
CNSrefinement
SAINTdata reduction
PROTEUM PLUSPLUSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1Z7W

1z7w


Resolution: 2.8→100 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 991 -random
Rwork0.188 ---
all-19828 --
obs-19828 100 %-
Refinement stepCycle: LAST / Resolution: 2.8→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2431 0 20 112 2563
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.28

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