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- PDB-6ulb: Sex Hormone-binding globulin mutant E176K in complex with Danazol -

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Basic information

Entry
Database: PDB / ID: 6ulb
TitleSex Hormone-binding globulin mutant E176K in complex with Danazol
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 / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Danazol / Sex hormone-binding globulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsRound, P.W. / Das, S. / Van Petegem, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: To Be Published
Title: Structural and biochemical analyses of danazol interactions with sex hormone-binding globulin and effects on androgen action
Authors: Round, P.W. / Das, S. / Van Petegem, F. / Hammond, G.L.
History
DepositionOct 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)22,9883
Polymers22,6111
Non-polymers3782
Water2,468137
1
A: Sex hormone-binding globulin
hetero molecules

A: Sex hormone-binding globulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9766
Polymers45,2212
Non-polymers7554
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)52.007, 52.007, 149.238
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-453-

HOH

21A-461-

HOH

31A-527-

HOH

41A-534-

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 BL21(DE3) (bacteria) / 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-QA1 / Danazol / (1R,3aS,3bR,10aR,10bS,12aS)-1-ethynyl-10a,12a-dimethyl-2,3,3a,3b,4,5,10,10a,10b,11,12,12a-dodecahydro-1H-cyclopenta[7,8 ]phenanthro[3,2-d][1,2]oxazol-1-ol


Mass: 337.455 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H27NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% PEG 3350, 0.2M potassium thiocyanate / 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: Jul 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.75→29.572 Å / Num. obs: 21617 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.018 / Rrim(I) all: 0.065 / Net I/σ(I): 21.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.75-1.789.80.7261129411580.9460.2440.7673.1100
9.09-29.57100.03820392040.9980.0130.0452.197.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.92 Å29.57 Å
Translation4.92 Å29.57 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PYF

6pyf


Resolution: 1.75→29.572 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.39
RfactorNum. reflection% reflectionSelection details
Rfree0.2252 1999 9.28 %Random selection
Rwork0.1839 ---
obs0.1877 21537 99.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 104.59 Å2 / Biso mean: 35.6795 Å2 / Biso min: 16.45 Å2
Refinement stepCycle: final / Resolution: 1.75→29.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1333 0 53 137 1523
Biso mean--30.06 44.89 -
Num. residues----171
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.7501-1.79380.2721410.24481376
1.7938-1.84230.28561380.23111342
1.8423-1.89650.25191380.21541351
1.8965-1.95770.23561390.2011360
1.9577-2.02770.24571400.20141365
2.0277-2.10880.27141430.19851389
2.1088-2.20480.24721380.19641368
2.2048-2.3210.24561410.19111377
2.321-2.46630.24981430.19471405
2.4663-2.65660.22671410.19621376
2.6566-2.92380.24171460.20171412
2.9238-3.34630.19561440.1941413
3.3463-4.21410.19781480.15391447
4.2141-29.5720.21781590.16981557
Refinement TLS params.Method: refined / Origin x: 13.1098 Å / Origin y: 23.5528 Å / Origin z: -8.1732 Å
111213212223313233
T0.1641 Å2-0.0224 Å20.0039 Å2-0.1797 Å20.0028 Å2--0.1886 Å2
L2.2544 °20.0925 °2-1.1128 °2-1.0378 °2-0.0731 °2--3.4142 °2
S-0.046 Å °0.0052 Å °-0.1964 Å °0.0646 Å °-0.0206 Å °0.0669 Å °0.1646 Å °-0.2376 Å °0.0386 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA14 - 188
2X-RAY DIFFRACTION1allC1
3X-RAY DIFFRACTION1allS1 - 198
4X-RAY DIFFRACTION1allB1

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