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- PDB-6pyf: Sex Hormone-binding globulin mutant E176K in complex with Estradiol -

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Basic information

Entry
Database: PDB / ID: 6pyf
TitleSex Hormone-binding globulin mutant E176K in complex with Estradiol
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
ESTRADIOL / Sex hormone-binding globulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.73 Å
AuthorsRound, P.W. / Wu, T.S. / 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 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sex hormone-binding globulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9233
Polymers22,6111
Non-polymers3122
Water3,351186
1
A: Sex hormone-binding globulin
hetero molecules

A: Sex hormone-binding globulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8466
Polymers45,2212
Non-polymers6254
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/41
Unit cell
Length a, b, c (Å)51.876, 51.876, 149.613
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-417-

HOH

21A-577-

HOH

31A-578-

HOH

41A-584-

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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EST / ESTRADIOL


Mass: 272.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H24O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: hormone*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.59 Å3/Da / Density % sol: 52.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 3350, potassium thiocyanate / Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→42.63 Å / Num. obs: 22292 / % possible obs: 100 % / Redundancy: 1.8 % / CC1/2: 1 / Rmerge(I) obs: 0.019 / Net I/σ(I): 22.5 / Num. measured all: 41097
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.73-1.761.90.252222211740.8683.4100
8.99-42.631.40.007300211147.998.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.92 Å42.63 Å
Translation4.92 Å42.63 Å

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Processing

Software
NameVersionClassification
PHENIX1.15.23472refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LHU

1lhu


Resolution: 1.73→42.629 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2204 1995 9 %
Rwork0.1834 20164 -
obs0.1866 22159 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.84 Å2 / Biso mean: 31.4378 Å2 / Biso min: 15.46 Å2
Refinement stepCycle: final / Resolution: 1.73→42.629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1351 0 26 186 1563
Biso mean--19.82 34.8 -
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 (%)
1.7301-1.77330.26031380.22361390100
1.7733-1.82130.23371380.21521412100
1.8213-1.87490.25681410.2081416100
1.8749-1.93540.33651380.2709140999
1.9354-2.00450.24891400.19261405100
2.0045-2.08480.21731410.18671425100
2.0848-2.17970.20021400.17951416100
2.1797-2.29460.29781380.2143138497
2.2946-2.43830.23581410.18141435100
2.4383-2.62660.18131440.17471448100
2.6266-2.89090.22091450.17991459100
2.8909-3.3090.19671440.18061456100
3.309-4.16850.2081480.15641505100
4.1685-42.6290.20841590.1822160499

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