[English] 日本語
Yorodumi
- PDB-1iuq: The 1.55 A Crystal Structure of Glycerol-3-Phosphate Acyltransferase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1iuq
TitleThe 1.55 A Crystal Structure of Glycerol-3-Phosphate Acyltransferase
ComponentsGlycerol-3-Phosphate Acyltransferase
KeywordsTRANSFERASE / OPEN TWISTED ALPHA/BETA / FOUR HELIX BUNDLE
Function / homology
Function and homology information


: / glycerol-3-phosphate 1-O-acyltransferase / glycerol-3-phosphate O-acyltransferase activity / sn-1-glycerol-3-phosphate C16:0-DCA-CoA acyl transferase activity / CDP-diacylglycerol biosynthetic process / chloroplast stroma
Similarity search - Function
Glycerol-3-phosphate acyltransferase, alpha helical bundle, N-terminal / Glycerol-3-phosphate (1)-acyltransferase / Glycerol-3-phosphate (1)-acyltransferase / Glycerol-3-phosphate O-acyltransferase, chloroplast / Glycerol-3-phosphate O-acyltransferase, alpha helical bundle, N-terminal / GPAT, N-terminal domain superfamily / Glycerol-3-phosphate acyltransferase N-terminal / Phospholipid/glycerol acyltransferase / Acyltransferase / Phosphate acyltransferases ...Glycerol-3-phosphate acyltransferase, alpha helical bundle, N-terminal / Glycerol-3-phosphate (1)-acyltransferase / Glycerol-3-phosphate (1)-acyltransferase / Glycerol-3-phosphate O-acyltransferase, chloroplast / Glycerol-3-phosphate O-acyltransferase, alpha helical bundle, N-terminal / GPAT, N-terminal domain superfamily / Glycerol-3-phosphate acyltransferase N-terminal / Phospholipid/glycerol acyltransferase / Acyltransferase / Phosphate acyltransferases / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glycerol-3-phosphate acyltransferase ATS12, chloroplastic
Similarity search - Component
Biological speciesCucurbita moschata (crookneck pumpkin)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsTamada, T. / Feese, M.D. / Kato, Y. / Kuroki, R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Substrate recognition and selectivity of plant glycerol-3-phosphate acyltransferases (GPATs) from Cucurbita moscata and Spinacea oleracea.
Authors: Tamada, T. / Feese, M.D. / Ferri, S.R. / Kato, Y. / Yajima, R. / Toguri, T. / Kuroki, R.
History
DepositionMar 6, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: Glycerol-3-Phosphate Acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,19912
Polymers41,1661
Non-polymers1,03311
Water7,026390
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.138, 63.604, 115.862
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Glycerol-3-Phosphate Acyltransferase


Mass: 41165.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cucurbita moschata (crookneck pumpkin) / Plasmid: pET-17B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P10349, glycerol-3-phosphate 1-O-acyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2.36 Å3/Da / Density % sol: 47.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.6-1.8M AMMONIUM SULFATE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 277 K / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMsodium phosphate1droppH8.0
20.5 M1dropNaCl
314 mg/mlprotein1drop
420 mMsodium phosphate1droppH8.0
54-25 %PEG40001reservoir
6100 mMammonium acetate1reservoir
710 %(v/v)2-propanol1reservoir
8100 mMcitrate1reservoirpH5.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 14, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.548→27.125 Å / Num. all: 61882 / Num. obs: 60415 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 20.27 Å2 / Rsym value: 0.035 / Net I/σ(I): 9.2
Reflection shellResolution: 1.548→1.61 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 5411 / Rsym value: 0.292 / % possible all: 86.6
Reflection
*PLUS
Highest resolution: 1.55 Å / Num. obs: 61882 / Rmerge(I) obs: 0.035
Reflection shell
*PLUS
Highest resolution: 1.55 Å / % possible obs: 86.6 % / Rmerge(I) obs: 0.292

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
REFMAC5refinement
RefinementMethod to determine structure: MAD / Resolution: 1.55→15 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.996 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21906 3127 5.1 %RANDOM
Rwork0.20124 ---
obs0.20216 58534 97.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.957 Å2
Baniso -1Baniso -2Baniso -3
1-2 Å20 Å20 Å2
2---1.39 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.55→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2796 0 61 390 3247
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0212910
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8621.9793940
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2933355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.65815529
X-RAY DIFFRACTIONr_chiral_restr0.1190.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022183
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2480.31532
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.5360
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.354
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.516
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.1221.51788
X-RAY DIFFRACTIONr_mcangle_it2.0522891
X-RAY DIFFRACTIONr_scbond_it3.76631122
X-RAY DIFFRACTIONr_scangle_it5.7834.51049
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.296 196
Rwork0.296 3676
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.55 Å / Lowest resolution: 15 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.217 / Rfactor Rwork: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.022
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.862
LS refinement shell
*PLUS
Highest resolution: 1.55 Å / Lowest resolution: 1.61 Å

+
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