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- PDB-6pya: Sex Hormone-binding globulin mutant E176K in complex with IPI -

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Basic information

Entry
Database: PDB / ID: 6pya
TitleSex Hormone-binding globulin mutant E176K in complex with IPI
ComponentsSex hormone-binding globulin
KeywordsHORMONE / Sex Steroid Transport Binding Globulin
Function / homology
Function and homology information


androgen binding / steroid binding / extracellular exosome / extracellular region
Similarity search - Function
: / Laminin G domain / Laminin G domain profile. / Laminin G domain / Laminin G domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
3-[(1H-imidazol-1-yl)methyl]-2-phenyl-1H-indole / Sex hormone-binding globulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsRound, P.W. / Das, S. / Van Petegem, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Molecular interactions between sex hormone-binding globulin and nonsteroidal ligands that enhance androgen activity.
Authors: Round, P. / Das, S. / Wu, T.S. / Wahala, K. / Van Petegem, F. / Hammond, G.L.
History
DepositionJul 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 12, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sex hormone-binding globulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9243
Polymers22,6111
Non-polymers3132
Water2,180121
1
A: Sex hormone-binding globulin
hetero molecules

A: Sex hormone-binding globulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8486
Polymers45,2212
Non-polymers6274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_444-y-1,-x-1,-z-1/41
Unit cell
Length a, b, c (Å)52.241, 52.241, 147.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+1/4
#8: -y,-x,-z+3/4
Components on special symmetry positions
IDModelComponents
11A-416-

HOH

21A-435-

HOH

31A-439-

HOH

41A-520-

HOH

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Components

#1: Protein Sex hormone-binding globulin / SHBG / Sex steroid-binding protein / SBP / Testis-specific androgen-binding protein / ABP / ...SHBG / Sex steroid-binding protein / SBP / Testis-specific androgen-binding protein / ABP / Testosterone-estradiol-binding globulin / TeBG / Testosterone-estrogen-binding globulin


Mass: 22610.689 Da / Num. of mol.: 1 / Mutation: E176K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHBG / Production host: Escherichia coli (E. coli) / References: UniProt: P04278
#2: Chemical ChemComp-P57 / 3-[(1H-imidazol-1-yl)methyl]-2-phenyl-1H-indole


Mass: 273.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H15N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.58 Å3/Da / Density % sol: 52.35 % / Description: Crystals were diamond shaped
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% Peg 3350, 0.2 M potassium thiocyanate, HEPES pH 7.5, 2.5 mM Calcium Chloride
Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 17, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.71→26.12 Å / Num. obs: 23105 / % possible obs: 100 % / Redundancy: 12 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.2 / Num. measured all: 277976 / Scaling rejects: 173
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.71-1.7412.90.5921578212240.9243.8100
9.05-26.129.90.03820172030.99946.596.2

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472)refinement
Aimless0.5.23data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→26.12 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.04
RfactorNum. reflection% reflectionSelection details
Rfree0.2158 1998 8.68 %Random selection
Rwork0.1852 ---
obs0.1879 23009 99.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.5 Å2 / Biso mean: 32.5125 Å2 / Biso min: 14.79 Å2
Refinement stepCycle: final / Resolution: 1.71→26.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1357 0 22 121 1500
Biso mean--27.4 37.38 -
Num. residues----175
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.71-1.75280.2661400.23961476100
1.7528-1.80020.27661400.21851469100
1.8002-1.85310.25841390.21181465100
1.8531-1.91290.24531370.2426144099
1.9129-1.98130.31231400.27031462100
1.9813-2.06060.23831410.20141480100
2.0606-2.15430.22341410.20711485100
2.1543-2.26780.26911400.21051482100
2.2678-2.40980.24091410.20081484100
2.4098-2.59570.27281430.19821504100
2.5957-2.85660.23041450.19251514100
2.8566-3.26930.20861450.19011529100
3.2693-4.11640.18041480.16241557100
4.1164-26.120.1781580.15251664100

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