[English] 日本語
Yorodumi
- PDB-1pz4: The structural determination of an insect (mosquito) Sterol Carri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pz4
TitleThe structural determination of an insect (mosquito) Sterol Carrier Protein-2 with a ligand bound C16 Fatty Acid at 1.35 A resolution
Componentssterol carrier protein 2
KeywordsLIPID BINDING PROTEIN / alpha and beta
Function / homology
Function and homology information


SCP2 sterol-binding domain / SCP-2 sterol transfer family / SCP2 sterol-binding domain / Nonspecific Lipid-transfer Protein; Chain A / SCP2 sterol-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PALMITIC ACID / Sterol carrier protein 2
Similarity search - Component
Biological speciesAedes aegypti (yellow fever mosquito)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsDyer, D.H. / Lovell, S. / Thoden, J.B. / Holden, H.M. / Rayment, I. / Lan, Q.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: The Structural Determination of an Insect Sterol Carrier Protein-2 with a Ligand-bound C16 Fatty Acid at 1.35A Resolution
Authors: Dyer, D.H. / Lovell, S. / Thoden, J.B. / Holden, H.M. / Rayment, I. / Lan, Q.
History
DepositionJul 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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: sterol carrier protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1122
Polymers12,8561
Non-polymers2561
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.300, 46.100, 70.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein sterol carrier protein 2


Mass: 12855.876 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q86PR3
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 1.85 Å3/Da / Density % sol: 33.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2M sodium malonate, 100 mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Crystal-IDSol-IDDetails
110 mg/ml1drop
22 M1reservoir
3100 mM1reservoirpH7.5

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 / Wavelength: 1.54178 Å
DetectorType: Bruker X1000 / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.35→100 Å / Num. all: 21157 / Num. obs: 21157 / % possible obs: 97 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.038
Reflection shellResolution: 1.35→1.41 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2383 / % possible all: 92
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 97 % / Num. measured all: 78412
Reflection shell
*PLUS
% possible obs: 91.5 % / Num. unique obs: 2383 / Num. measured obs: 5542

-
Processing

Software
NameClassification
smartdata collection
SAINTdata reduction
EPMRphasing
TNTrefinement
SMARTdata reduction
SAINTdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→100 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2107 -random
Rwork0.187 ---
obs0.187 21157 97 %-
all-21157 --
Refinement stepCycle: LAST / Resolution: 1.35→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms890 0 18 88 996
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg2.23
X-RAY DIFFRACTIONt_dihedral_angle_d16.6
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rwork: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.234
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg16.6
X-RAY DIFFRACTIONt_planar_d0.007
X-RAY DIFFRACTIONt_plane_restr0.012
LS refinement shell
*PLUS
Highest resolution: 1.35 Å / Lowest resolution: 1.41 Å / Num. reflection Rfree: 2107 / Num. reflection Rwork: 19050 / Num. reflection obs: 21157

+
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