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- PDB-1d2s: CRYSTAL STRUCTURE OF THE N-TERMINAL LAMININ G-LIKE DOMAIN OF SHBG... -

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Basic information

Entry
Database: PDB / ID: 1d2s
TitleCRYSTAL STRUCTURE OF THE N-TERMINAL LAMININ G-LIKE DOMAIN OF SHBG IN COMPLEX WITH DIHYDROTESTOSTERONE
ComponentsSEX HORMONE-BINDING GLOBULIN
KeywordsTRANSPORT PROTEIN / STEROID TRANSPORT / LAMININ G-LIKE DOMAIN / JELLYROLL / ANDROGEN BINDING PROTEIN (ABP) / SEX STEROID BINDING PROTEIN (SBP)
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
5-ALPHA-DIHYDROTESTOSTERONE / Sex hormone-binding globulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.55 Å
AuthorsGrishkovskaya, I. / Avvakumov, G.V. / Sklenar, G. / Dales, D. / Hammond, G.L. / Muller, Y.A.
CitationJournal: EMBO J. / Year: 2000
Title: Crystal structure of human sex hormone-binding globulin: steroid transport by a laminin G-like domain.
Authors: Grishkovskaya, I. / Avvakumov, G.V. / Sklenar, G. / Dales, D. / Hammond, G.L. / Muller, Y.A.
History
DepositionSep 28, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp

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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)19,2264
Polymers18,8551
Non-polymers3713
Water2,216123
1
A: SEX HORMONE-BINDING GLOBULIN
hetero molecules

A: SEX HORMONE-BINDING GLOBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4528
Polymers37,7112
Non-polymers7416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+11
Unit cell
Length a, b, c (Å)104.040, 104.040, 84.430
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Cell settinghexagonal
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-601-

HOH

21A-691-

HOH

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Components

#1: Protein SEX HORMONE-BINDING GLOBULIN / SHBG


Mass: 18855.418 Da / Num. of mol.: 1 / Fragment: RESIDUES 1 TO 205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: P04278
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-DHT / 5-ALPHA-DIHYDROTESTOSTERONE


Mass: 290.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H30O2 / Comment: hormone*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

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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: 2.33 Å3/Da / Density % sol: 47.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG400, HEPES, CALCIUM CHLORIDE, DIHYDROTESTOSTERONE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Crystal grow
*PLUS
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
113 mg/mlprotein1drop
250 mMHEPES1drop
32.5 mM1dropCaCl2
40.003 mM5alpha-DHT1drop
520 %isopropanol1reservoir
610 %PEG4001reservoir
7100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X11 / Wavelength: 0.9116
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Apr 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9116 Å / Relative weight: 1
ReflectionResolution: 1.55→40 Å / Num. all: 24678 / Num. obs: 24678 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 29.3 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 16.5
Reflection shellResolution: 1.55→1.75 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.234 / % possible all: 95
Reflection shell
*PLUS
% possible obs: 95 % / Mean I/σ(I) obs: 3.35

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Processing

Software
NameClassification
MAR345data collection
XDSdata reduction
MLPHAREphasing
REFMACrefinement
XDSdata scaling
RefinementResolution: 1.55→40 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.251 2461 RANDOM
Rwork0.205 --
all0.21 22208 -
obs0.21 22208 -
Displacement parametersBiso mean: 29.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.004 Å2-0.074 Å20 Å2
2---0.038 Å20 Å2
3---0.092 Å2
Refinement stepCycle: LAST / Resolution: 1.55→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1375 0 23 123 1521
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.030.03
X-RAY DIFFRACTIONp_planar_d0.0340.05
X-RAY DIFFRACTIONp_mcbond_it2.7864
X-RAY DIFFRACTIONp_mcangle_it3.7816
X-RAY DIFFRACTIONp_scbond_it3.5854
X-RAY DIFFRACTIONp_scangle_it5.0516

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