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- PDB-6pyb: Sex Hormone-binding globulin mutant E176K in complex with DVT -

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Basic information

Entry
Database: PDB / ID: 6pyb
TitleSex Hormone-binding globulin mutant E176K in complex with DVT
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
Chem-P5G / Sex hormone-binding globulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_entry_details.has_protein_modification / _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)22,9953
Polymers22,6111
Non-polymers3842
Water1,982110
1
A: Sex hormone-binding globulin
hetero molecules

A: Sex hormone-binding globulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9906
Polymers45,2212
Non-polymers7694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_664-y+1,-x+1,-z-1/41
Unit cell
Length a, b, c (Å)51.953, 51.953, 148.354
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-421-

HOH

21A-494-

HOH

31A-509-

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-P5G / 4,4'-[(3R,4R)-oxolane-3,4-diylbis(methylene)]bis(2-methoxyphenol)


Mass: 344.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24O5 / 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.: 110 / 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: 2.61 Å3/Da / Density % sol: 52.96 % / Description: Large diamond shaped crystals
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 3350, Potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid Nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.8→29.67 Å / Num. obs: 19752 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Net I/σ(I): 22.2 / Num. measured all: 254680
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.8-1.8413.31.0751506611330.8432.6100
9-29.679.60.03420062080.99959.897.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.01 Å29.49 Å

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Processing

Software
NameVersionClassificationNB
PHENIX(1.15.2_3472)refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.49 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.231 1969 10 %
Rwork0.2032 17719 -
obs0.206 19688 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 232.27 Å2 / Biso mean: 45.34 Å2 / Biso min: 18.78 Å2
Refinement stepCycle: final / Resolution: 1.8→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1327 0 50 110 1487
Biso mean--51.14 42.84 -
Num. residues----172
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.8-1.8450.29961370.28421226
1.845-1.89490.29511350.27571228
1.8949-1.95070.29651370.2651231
1.9507-2.01360.26841380.25221240
2.0136-2.08560.28461390.23811242
2.0856-2.1690.29321390.23521252
2.169-2.26770.24751370.22821238
2.2677-2.38720.31031390.2281248
2.3872-2.53670.26131400.22981258
2.5367-2.73240.24831410.21361266
2.7324-3.00720.24471400.21771265
3.0072-3.44180.21531440.21161299
3.4418-4.3340.17041470.16321319
4.334-29.490.22241560.17621407

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