[English] 日本語
Yorodumi
- PDB-2isq: Crystal Structure of O-Acetylserine Sulfhydrylase from Arabidopsi... -

+
Open data


ID or keywords:

Loading...

-
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 synthase activity / cysteine biosynthetic process / apoplast / cysteine biosynthetic process from serine ...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 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
Serine O-acetyltransferase / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / : / Serine acetyltransferase, N-terminal domain superfamily / Serine acetyltransferase, LbH domain / Cysteine synthase CysK / Cysteine synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site ...Serine O-acetyltransferase / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / : / Serine acetyltransferase, N-terminal domain superfamily / Serine acetyltransferase, LbH domain / 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 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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.

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more