[English] 日本語
Yorodumi
- PDB-8af2: Human Sterol Carrier Protein with unnatural amino acid 2,2'-bipyr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8af2
TitleHuman Sterol Carrier Protein with unnatural amino acid 2,2'-bipyridine alanine incorporated at position 111
ComponentsEnoyl-CoA hydratase 2
KeywordsMETAL BINDING PROTEIN / de novo protein / artificial metalloenzyme incorporating unnatural amino acid 2 / 2-bipyridine / copper ion bound
Function / homology
Function and homology information


3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase / 3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity / very long-chain fatty-acyl-CoA metabolic process / Beta-oxidation of pristanoyl-CoA / TYSND1 cleaves peroxisomal proteins / medium-chain fatty-acyl-CoA metabolic process / (3R)-hydroxyacyl-CoA dehydrogenase (NAD+) activity / : / enoyl-CoA hydratase 2 / 3-hydroxyacyl-CoA dehydratase activity ...3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase / 3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity / very long-chain fatty-acyl-CoA metabolic process / Beta-oxidation of pristanoyl-CoA / TYSND1 cleaves peroxisomal proteins / medium-chain fatty-acyl-CoA metabolic process / (3R)-hydroxyacyl-CoA dehydrogenase (NAD+) activity / : / enoyl-CoA hydratase 2 / 3-hydroxyacyl-CoA dehydratase activity / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / alpha-linolenic acid (ALA) metabolism / Beta-oxidation of very long chain fatty acids / very long-chain fatty acid metabolic process / 3-hydroxyacyl-CoA dehydrogenase activity / Sertoli cell development / estradiol 17-beta-dehydrogenase [NAD(P)] activity / enoyl-CoA hydratase activity / peroxisomal membrane / estrogen metabolic process / fatty acid beta-oxidation / peroxisomal matrix / androgen metabolic process / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / isomerase activity / Peroxisomal protein import / osteoblast differentiation / peroxisome / protein homodimerization activity / membrane / cytosol
Similarity search - Function
SCP2 sterol-binding domain / SCP-2 sterol transfer family / SCP2 sterol-binding domain superfamily / MaoC-like dehydratase domain / MaoC like domain / short chain dehydrogenase / PKS_KR / HotDog domain superfamily / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. ...SCP2 sterol-binding domain / SCP-2 sterol transfer family / SCP2 sterol-binding domain superfamily / MaoC-like dehydratase domain / MaoC like domain / short chain dehydrogenase / PKS_KR / HotDog domain superfamily / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
COPPER (II) ION / Peroxisomal multifunctional enzyme type 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsRichardson, J.M. / Klemencic, E. / Jarvis, A.G.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)MR/S017402/1 United Kingdom
Wellcome Trust204804/Z/16/Z United Kingdom
CitationJournal: Catalysis Science And Technology / Year: 2024
Title: Using BpyAla to generate copper artificial metalloenzymes: a catalytic and structural study.
Authors: Klemencic, E. / Brewster, R.C. / Ali, H.S. / Richardson, J.M. / Jarvis, A.G.
History
DepositionJul 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id
Revision 2.1Feb 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.2Apr 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Enoyl-CoA hydratase 2
B: Enoyl-CoA hydratase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9789
Polymers28,6012
Non-polymers1,3777
Water37821
1
A: Enoyl-CoA hydratase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1655
Polymers14,3011
Non-polymers8654
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Enoyl-CoA hydratase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8134
Polymers14,3011
Non-polymers5123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.512, 50.523, 62.211
Angle α, β, γ (deg.)90.000, 90.732, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Enoyl-CoA hydratase 2 / / 3-alpha / 7-alpha / 12-alpha-trihydroxy-5-beta-cholest-24-enoyl-CoA hydratase


Mass: 14300.565 Da / Num. of mol.: 2
Mutation: 2,2'-bipyridine alanine incorporated at position 111
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSD17B4, EDH17B4, SDR8C1 / Production host: Escherichia coli (E. coli)
References: UniProt: P51659, 3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase, enoyl-CoA hydratase 2
#2: Chemical ChemComp-TRT / FRAGMENT OF TRITON X-100 / 1-{2-[2-(2-METHOXYETHOXY)ETHOXY]ETHOXY}-4-(1,1,3,3-TETRAMETHYLBUTYL)BENZENE / Triton X-100


Mass: 352.508 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H36O4 / Comment: detergent*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity % sol: 35.13 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop
Details: well solution 2.3M ammonium sulphate, 100 mM citric acid pH 5.6 and 200 mM NaCl

-
Data collection

DiffractionMean temperature: 81 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.51→62.21 Å / Num. obs: 7377 / % possible obs: 99.4 % / Redundancy: 5.2 % / Biso Wilson estimate: 47.02 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.182 / Net I/σ(I): 6.6
Reflection shellResolution: 2.514→2.558 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 370 / CC1/2: 0.352 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.19.1_4122refinement
autoPROCdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IKT

1ikt


Resolution: 2.51→62.21 Å / SU ML: 0.3523 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.4113
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2997 333 4.52 %
Rwork0.2338 7032 -
obs0.2366 7365 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.14 Å2
Refinement stepCycle: LAST / Resolution: 2.51→62.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1944 0 87 21 2052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00342064
X-RAY DIFFRACTIONf_angle_d0.72712766
X-RAY DIFFRACTIONf_chiral_restr0.0409288
X-RAY DIFFRACTIONf_plane_restr0.0023338
X-RAY DIFFRACTIONf_dihedral_angle_d11.1941294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-3.170.32811570.26193495X-RAY DIFFRACTION99.13
3.17-62.210.2911760.2243537X-RAY DIFFRACTION99.36

+
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