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- PDB-1kdk: THE STRUCTURE OF THE N-TERMINAL LG DOMAIN OF SHBG IN CRYSTALS SOA... -

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Basic information

Entry
Database: PDB / ID: 1kdk
TitleTHE STRUCTURE OF THE N-TERMINAL LG DOMAIN OF SHBG IN CRYSTALS SOAKED WITH EDTA
ComponentsSex Hormone-Binding Globulin
KeywordsTRANSPORT PROTEIN / SHBG / DHT
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 / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsGrishkovskaya, I. / Avvakumov, G.V. / Hammond, G.L. / Muller, Y.A.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Resolution of a disordered region at the entrance of the human sex hormone-binding globulin steroid-binding site.
Authors: Grishkovskaya, I. / Avvakumov, G.V. / Hammond, G.L. / Muller, Y.A.
History
DepositionNov 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / software / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)19,9462
Polymers19,6551
Non-polymers2901
Water1,60389
1
A: Sex Hormone-Binding Globulin
hetero molecules

A: Sex Hormone-Binding Globulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8924
Polymers39,3112
Non-polymers5812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+11
Unit cell
Length a, b, c (Å)103.720, 103.720, 85.760
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Sex Hormone-Binding Globulin


Mass: 19655.336 Da / Num. of mol.: 1 / Fragment: N-terminal LG-domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P04278
#2: Chemical ChemComp-DHT / 5-ALPHA-DIHYDROTESTOSTERONE


Mass: 290.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H30O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
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: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG400, Isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Details: Grishkovskaya, I., (1999) Acta Crystallog. D55, 2053.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
113 mg/mlprotein1drop
250 mMsodium HEPES1droppH7.5
32.5 mM1dropCaCl2
40.003 mMDHT1drop
520 %2-propanol1reservoir
610 %PEG4001reservoir
7100 mMsodium HEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.93 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: diamond(111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. all: 19262 / Num. obs: 19262 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 33.1 Å2 / Rmerge(I) obs: 0.064
Reflection shellResolution: 1.7→1.8 Å / Rmerge(I) obs: 0.37 / % possible all: 99.2
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 40 Å / Num. measured all: 90466 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 1.8 Å / % possible obs: 99.2 %

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Processing

Software
NameClassification
MAR345data collection
XDSdata reduction
REFMACrefinement
XDSdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1D2S

1d2s


Resolution: 1.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.245 1924 RANDOM
Rwork0.194 --
all-17326 -
obs-17326 -
Displacement parametersBiso mean: 36.2 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1389 0 21 89 1499
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_d0.037
LS refinement shellHighest resolution: 1.7 Å
RfactorNum. reflection
Rfree0.245 1924
Rwork0.194 -
obs-17326
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 20 Å / Rfactor obs: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS

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