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- PDB-1lho: CRYSTAL STRUCTURE OF THE N-TERMINAL LG-DOMAIN OF SHBG IN COMPLEX ... -

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Basic information

Entry
Database: PDB / ID: 1lho
TitleCRYSTAL STRUCTURE OF THE N-TERMINAL LG-DOMAIN OF SHBG IN COMPLEX WITH 5ALPHA-ANDROSTANE-3BETA,17BETA-DIOL
ComponentsSEX HORMONE-BINDING GLOBULIN
KeywordsTRANSPORT PROTEIN / SHBG / 17b-DHA
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-ANDROSTANE-3-BETA,17BETA-DIOL / Sex hormone-binding globulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsGrishkovskaya, I. / Avvakumov, G.V. / Hammond, G.L. / Catalano, M.G. / Muller, Y.A.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Steroid Ligands Bind Human Sex Hormone-binding Globulin in Specific Orientations and Produce Distinct Changes in Protein Conformation
Authors: Grishkovskaya, I. / Avvakumov, G.V. / Hammond, G.L. / Catalano, M.G. / Muller, Y.A.
History
DepositionApr 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 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 / pdbx_struct_conn_angle / struct_conn / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SEX HORMONE-BINDING GLOBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3053
Polymers20,9731
Non-polymers3332
Water1,67593
1
A: SEX HORMONE-BINDING GLOBULIN
hetero molecules

A: SEX HORMONE-BINDING GLOBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6116
Polymers41,9462
Non-polymers6654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+11
Unit cell
Length a, b, c (Å)103.892, 103.892, 84.579
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-480-

HOH

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Components

#1: Protein SEX HORMONE-BINDING GLOBULIN / SHBG / Sex steroid-binding protein / SBP / Testis-specific androgen-binding protein / ABP


Mass: 20972.832 Da / Num. of mol.: 1 / Fragment: LG-like 1 domain, Residues 30-218
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-AOM / 5-ALPHA-ANDROSTANE-3-BETA,17BETA-DIOL


Mass: 292.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H32O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.09 Å3/Da / Density % sol: 41.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES, Calcium chloride, 17b-DHA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 277 K
Details: Grishkovskaya, I., (1999) Acta Crystallogr., D55, 2053.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
113 mg/mlprotein1drop
280 mMimidazole-HCl1droppH7.5
31 mM1dropCaCl2
40.010 mMDHT1drop
510 %2-propanol1reservoir
620 %PEG40001reservoir
7100 mMsodium HEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 12, 2000
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 11464 / Num. obs: 11464 / % possible obs: 95.4 % / Rmerge(I) obs: 0.043
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.236 / % possible all: 93.7
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Num. measured all: 39305
Reflection shell
*PLUS
Highest resolution: 2 Å / % possible obs: 93.7 %

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Processing

Software
NameClassification
MAR345data collection
XDSdata reduction
CNSrefinement
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1D2S

1d2s


Resolution: 2→19.14 Å / Data cutoff high absF: 10000 / Data cutoff high rms absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.223 1114 RANDOM
Rwork0.187 --
all-11464 -
obs-10350 -
Refinement stepCycle: LAST / Resolution: 2→19.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1401 0 22 93 1516
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.01
X-RAY DIFFRACTIONc_bond_d1.55
Refinement
*PLUS
Highest resolution: 2.05 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.55

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