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- PDB-6z1x: Crystal structure of human steroid carrier protein SL (SCP-2L) mu... -

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Basic information

Entry
Database: PDB / ID: 6z1x
TitleCrystal structure of human steroid carrier protein SL (SCP-2L) mutant V83C
ComponentsPeroxisomal multifunctional enzyme type 2
KeywordsOXIDOREDUCTASE / ALFA-BETA FOLD / PROTEIN-TRITON X-100 COMPLEX / HYDROPHOBIC TUNNEL
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
Peroxisomal multifunctional enzyme type 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.09 Å
AuthorsRozeboom, H.J. / Janssen, D.B.
CitationJournal: Acs Catalysis / Year: 2021
Title: Engineering Thermostability in Artificial Metalloenzymes to Increase Catalytic Activity
Authors: Doble, M.V. / Obrecht, L. / Joosten, H.J. / Lee, M. / Rozeboom, H.J. / Branigan, E. / Naismith, J.H. / Janssen, D.B. / Jarvis, A.G. / Kamer, P.C.J.
History
DepositionMay 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxisomal multifunctional enzyme type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6584
Polymers13,2681
Non-polymers1,3903
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-3 kcal/mol
Surface area6460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.690, 48.850, 63.740
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 Peroxisomal multifunctional enzyme type 2 / MFE-2 / 17-beta-hydroxysteroid dehydrogenase 4 / 17-beta-HSD 4 / D-bifunctional protein / DBP / ...MFE-2 / 17-beta-hydroxysteroid dehydrogenase 4 / 17-beta-HSD 4 / D-bifunctional protein / DBP / Multifunctional protein 2 / MPF-2 / Short chain dehydrogenase/reductase family 8C member 1


Mass: 13268.479 Da / Num. of mol.: 1 / Mutation: V83C
Source method: isolated from a genetically manipulated source
Details: DHB4_HUMAN 618 736 / Source: (gene. exp.) Homo sapiens (human) / Gene: HSD17B4, EDH17B4, SDR8C1 / Production host: Escherichia coli (E. coli)
References: UniProt: P51659, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor, 3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase, enoyl-CoA hydratase 2
#2: Chemical ChemComp-OXN / OXTOXYNOL-10 / ALPHA-[4-(1,1,3,3-TETRAMETHYLBUTYL)PHENYL]-OMEGA-HYDROXYPOLY(OXY-1,2-ETHANEDIYL) / TRITON X-100 / Triton X-100


Mass: 646.849 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H62O11 / Comment: detergent*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.1 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 2.2 M ammonium sulfate, 0.2 M NaCl and 0.1 M citric acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.09→28.82 Å / Num. obs: 6538 / % possible obs: 99.1 % / Redundancy: 6.8 % / Rsym value: 0.059 / Net I/σ(I): 23.4
Reflection shellResolution: 2.09→2.13 Å / Num. unique obs: 319 / Rsym value: 0.181

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IKT

1ikt


Resolution: 2.09→28.82 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.904 / SU B: 4.458 / SU ML: 0.122 / SU R Cruickshank DPI: 0.2477 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.248 / ESU R Free: 0.2
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.237 326 4.7 %RANDOM
Rwork0.1806 ---
obs0.1833 6538 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 56.51 Å2 / Biso mean: 20.315 Å2 / Biso min: 10.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--0.32 Å2-0 Å2
3----0.51 Å2
Refinement stepCycle: final / Resolution: 2.09→28.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms897 0 58 62 1017
Biso mean--29.84 26.8 -
Num. residues----115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.013969
X-RAY DIFFRACTIONr_bond_other_d0.0020.017976
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.651297
X-RAY DIFFRACTIONr_angle_other_deg1.31.5852260
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7755114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.76223.2540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.07715179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.328154
X-RAY DIFFRACTIONr_chiral_restr0.0720.2117
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021017
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02191
LS refinement shellResolution: 2.095→2.149 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 26 -
Rwork0.184 443 -
all-469 -
obs--95.52 %

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