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- PDB-8af3: Sterol carrier protein Artifical metalloenzyme incorporating Q111... -

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Basic information

Entry
Database: PDB / ID: 8af3
TitleSterol carrier protein Artifical metalloenzyme incorporating Q111C mutation coupled to 2,2'-bipyridine
ComponentsEnoyl-CoA hydratase 2
KeywordsMETAL BINDING PROTEIN / de novo protein / artificial metalloenzyme / bipyridine adduct
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 / molecular replacement / Resolution: 1.52 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 1.1Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Feb 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 1.3Apr 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enoyl-CoA hydratase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0005
Polymers13,3921
Non-polymers6084
Water79344
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-32 kcal/mol
Surface area6870 Å2
Unit cell
Length a, b, c (Å)35.160, 51.050, 63.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 13391.677 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 2,2-Bipyridine was coupled to a cysteine at position 111
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.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.79 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: well solution 2.3M ammonium sulphate, 100 mM citric acid pH 5.6 and 200 mM NaCl

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Data collection

DiffractionMean temperature: 81 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.378 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.378 Å / Relative weight: 1
ReflectionResolution: 1.52→39.68 Å / Num. obs: 32696 / % possible obs: 97.14 % / Redundancy: 11.3 % / Biso Wilson estimate: 32.77 Å2 / CC1/2: 1 / Rrim(I) all: 0.044 / Net I/σ(I): 26.4
Reflection shellResolution: 1.52→1.574 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 1005 / CC1/2: 0.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
xia2data scaling
PHASERphasing
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IKT

1ikt


Resolution: 1.52→39.68 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 32.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2389 1559 4.77 %
Rwork0.2266 31137 -
obs0.2272 32696 96.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.73 Å2 / Biso mean: 56.8164 Å2 / Biso min: 25.13 Å2
Refinement stepCycle: final / Resolution: 1.52→39.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms910 0 72 44 1026
Biso mean--81.31 52.66 -
Num. residues----116
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.52-1.570.41851330.40182198233177
1.57-1.630.45071250.34272696282191
1.63-1.690.29521510.305629073058100
1.69-1.770.30931500.289329453095100
1.77-1.860.29991420.2928903032100
1.86-1.980.35111430.279229253068100
1.98-2.130.1871560.248529113067100
2.13-2.340.26761460.241929313077100
2.34-2.680.22491420.241329293071100
2.68-3.380.24821440.221629013045100
3.38-39.680.21161270.19782904303199
Refinement TLS params.Method: refined / Origin x: 28.1941 Å / Origin y: 31.4984 Å / Origin z: 10.9324 Å
111213212223313233
T0.3051 Å20.0014 Å20.0169 Å2-0.2048 Å20.0164 Å2--0.1935 Å2
L7.3092 °20.0013 °21.709 °2-4.6237 °2-1.5778 °2--3.6303 °2
S0.1599 Å °-0.3986 Å °-0.3993 Å °0.1594 Å °0.0601 Å °0.1563 Å °0.0388 Å °-0.1367 Å °-0.1643 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA5 - 120
2X-RAY DIFFRACTION1allA201
3X-RAY DIFFRACTION1allD1 - 52
4X-RAY DIFFRACTION1allE1 - 2
5X-RAY DIFFRACTION1allB1

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