[English] 日本語
Yorodumi
- PDB-3spx: Crystal structure of O-Acetyl Serine Sulfhydrylase from Leishmani... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3spx
TitleCrystal structure of O-Acetyl Serine Sulfhydrylase from Leishmania donovani
ComponentsO-acetyl serine sulfhydrylase
KeywordsTRANSFERASE / O-Acetyl Serine Sulfhydrylase / Cysteine Synthase / Type II PLP dependent enzyme / Cysteine biocynthesis / Serine Acetyl Transferase / cytosolic
Function / homology
Function and homology information


cysteine synthase activity / cysteine biosynthetic process from serine / cytoplasm
Similarity search - Function
Cysteine synthase CysK / Cysteine synthase / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / O-acetyl serine sulfhydrylase
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.79 Å
AuthorsRaj, I. / Gourinath, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: The narrow active-site cleft of O-acetylserine sulfhydrylase from Leishmania donovani allows complex formation with serine acetyltransferases with a range of C-terminal sequences
Authors: Raj, I. / Kumar, S. / Gourinath, S.
History
DepositionJul 4, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2012Group: Database references
Revision 1.2Mar 12, 2014Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: O-acetyl serine sulfhydrylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0724
Polymers35,9071
Non-polymers1653
Water3,531196
1
A: O-acetyl serine sulfhydrylase
hetero molecules

A: O-acetyl serine sulfhydrylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1448
Polymers71,8152
Non-polymers3296
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area6320 Å2
ΔGint-76 kcal/mol
Surface area23340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.266, 61.974, 43.427
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-389-

HOH

21A-502-

HOH

-
Components

#1: Protein O-acetyl serine sulfhydrylase


Mass: 35907.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Strain: MHOM/IM/1983/AG83 / Gene: OASS / Plasmid: pET21c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G1C2I2, cysteine synthase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.24 Å3/Da / Density % sol: 45.02 % / Mosaicity: 0.418 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: KSCN, PEG 3350, Bis-tris propane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. all: 29852 / Num. obs: 29629 / % possible obs: 99.3 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.064 / Χ2: 0.997 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.79-1.835.60.38613590.752192.1
1.83-1.866.50.41513990.741196.9
1.86-1.97.30.35414440.752196.8
1.9-1.947.70.30114290.747199.5
1.94-1.9880.25914860.7481100
1.98-2.038.10.21214390.7641100
2.03-2.088.10.18815010.7831100
2.08-2.138.20.15714450.81100
2.13-2.28.20.13214790.8131100
2.2-2.278.20.11514780.8161100
2.27-2.358.20.09314770.8211100
2.35-2.448.20.08514820.7971100
2.44-2.558.20.07414890.8091100
2.55-2.698.20.06515070.841100
2.69-2.868.10.05614790.9181100
2.86-3.088.10.05315131.1511100
3.08-3.3980.05514911.741100
3.39-3.887.90.05615312.4941100
3.88-4.887.90.03515541.4951100
4.88-507.40.02416470.918199.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.97 Å42.2 Å
Translation1.97 Å42.2 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→42.2 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.207 / WRfactor Rwork: 0.167 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8612 / SU B: 2.406 / SU ML: 0.076 / SU R Cruickshank DPI: 0.1238 / SU Rfree: 0.1207 / Cross valid method: THROUGHOUT / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2163 1437 4.9 %RANDOM
Rwork0.176 ---
obs0.178 29499 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 58.07 Å2 / Biso mean: 20.7145 Å2 / Biso min: 3.82 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å20 Å20 Å2
2--0.25 Å20 Å2
3---0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.79→42.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2396 0 9 196 2601
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0222441
X-RAY DIFFRACTIONr_angle_refined_deg2.1041.9923302
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3335319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.01624.48387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80215426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4191513
X-RAY DIFFRACTIONr_chiral_restr0.1590.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211782
X-RAY DIFFRACTIONr_mcbond_it1.3971.51584
X-RAY DIFFRACTIONr_mcangle_it2.28522547
X-RAY DIFFRACTIONr_scbond_it3.8773857
X-RAY DIFFRACTIONr_scangle_it6.1424.5755
LS refinement shellResolution: 1.794→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 84 -
Rwork0.298 1812 -
all-1896 -
obs--87.58 %

+
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