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- PDB-8af2: Human Sterol Carrier Protein with unnatural amino acid 2,2'-bipyr... -

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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)-3-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)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / enoyl-CoA hydratase 2 / 3-hydroxyacyl-CoA dehydratase activity / alpha-linolenic acid (ALA) metabolism / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / Beta-oxidation of very long chain fatty acids / very long-chain fatty acid metabolic process / 3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / Sertoli cell development / enoyl-CoA hydratase activity / estradiol 17-beta-dehydrogenase [NAD(P)+] 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
: / MFE-2 hydratase 2 N-terminal domain / : / SCP2 sterol-binding domain / SCP-2 sterol transfer family / SCP2 sterol-binding domain superfamily / MaoC-like dehydratase domain / MaoC like domain / HotDog domain superfamily / short chain dehydrogenase ...: / MFE-2 hydratase 2 N-terminal domain / : / SCP2 sterol-binding domain / SCP-2 sterol transfer family / SCP2 sterol-binding domain superfamily / MaoC-like dehydratase domain / MaoC like domain / HotDog domain superfamily / short chain dehydrogenase / PKS_KR / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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: 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


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


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


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


Mass: 18.015 Da / Num. of mol.: 21 / 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 % 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

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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

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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

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