[English] 日本語
Yorodumi
- PDB-3p47: Crystal structure of Entamoeba histolytica Serine acetyltransfera... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3p47
TitleCrystal structure of Entamoeba histolytica Serine acetyltransferase 1 in complex with L-cysteine
ComponentsSerine acetyltransferase
KeywordsTRANSFERASE / Serine acetyltransferase / cysteine synthase / Acetyltransferase
Function / homology
Function and homology information


serine O-acetyltransferase / serine O-acetyltransferase activity
Similarity search - Function
serine acetyltransferase, domain 1 / serine acetyltransferase, domain 1 / Serine acetyltransferase, LbH domain / Serine acetyltransferase, N-terminal domain superfamily / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid ...serine acetyltransferase, domain 1 / serine acetyltransferase, domain 1 / Serine acetyltransferase, LbH domain / Serine acetyltransferase, N-terminal domain superfamily / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
CYSTEINE / serine O-acetyltransferase
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 Å
AuthorsKumar, S. / Gourinath, S.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural and biochemical studies of serine acetyltransferase reveal why the parasite Entamoeba histolytica cannot form a cysteine synthase complex
Authors: Kumar, S. / Raj, I. / Nagpal, I. / Subbarao, N. / Gourinath, S.
History
DepositionOct 6, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8993
Polymers35,6821
Non-polymers2172
Water2,900161
1
A: Serine acetyltransferase
hetero molecules

A: Serine acetyltransferase
hetero molecules

A: Serine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,6979
Polymers107,0463
Non-polymers6526
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area10600 Å2
ΔGint-28 kcal/mol
Surface area27550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.047, 110.047, 64.002
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-315-

SO4

21A-315-

SO4

31A-398-

HOH

41A-401-

HOH

-
Components

#1: Protein Serine acetyltransferase


Mass: 35681.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM1:IMSS / Gene: CysE / Plasmid: pET21c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9U8X2, serine O-acetyltransferase
#2: Chemical ChemComp-CYS / CYSTEINE / Cysteine


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.09 Å3/Da / Density % sol: 41.15 % / Mosaicity: 0.949 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Peg 2000, NaCl, Glycerol, Tris, L-cysteine, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.0337 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0337 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 26982 / % possible obs: 97.1 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.073 / Χ2: 1.042 / Net I/σ(I): 12.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.78-1.844.50.29622350.962180.8
1.84-1.924.90.25325631.048192.1
1.92-25.30.21727411.09198.6
2-2.115.60.17727691.0571100
2.11-2.245.70.1427901.0451100
2.24-2.425.70.11727621.0691100
2.42-2.665.70.09828041.051100
2.66-3.045.60.07927791.0441100
3.04-3.835.60.06527691.031199.9
3.83-505.80.04427701.001199.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.98 Å38.22 Å
Translation1.98 Å38.22 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.906 / WRfactor Rfree: 0.2581 / WRfactor Rwork: 0.2006 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8447 / SU B: 2.723 / SU ML: 0.088 / SU R Cruickshank DPI: 0.1314 / SU Rfree: 0.135 / Cross valid method: THROUGHOUT / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2454 1361 5 %RANDOM
Rwork0.1908 ---
obs0.1935 26973 97.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 59.24 Å2 / Biso mean: 26.3688 Å2 / Biso min: 14.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å2-0.78 Å20 Å2
2---1.57 Å20 Å2
3---2.35 Å2
Refinement stepCycle: LAST / Resolution: 1.78→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2148 0 12 161 2321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222211
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.9412993
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6255269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.21523.2100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33115372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6471512
X-RAY DIFFRACTIONr_chiral_restr0.1010.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211665
X-RAY DIFFRACTIONr_mcbond_it0.9131.51342
X-RAY DIFFRACTIONr_mcangle_it1.51922169
X-RAY DIFFRACTIONr_scbond_it2.4393869
X-RAY DIFFRACTIONr_scangle_it3.4574.5824
LS refinement shellResolution: 1.778→1.824 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 62 -
Rwork0.244 1545 -
all-1607 -
obs--78.58 %

+
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