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- PDB-1f5f: CRYSTAL STRUCTURE OF THE N-TERMINAL G-DOMAIN OF SHBG IN COMPLEX W... -

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Basic information

Entry
Database: PDB / ID: 1f5f
TitleCRYSTAL STRUCTURE OF THE N-TERMINAL G-DOMAIN OF SHBG IN COMPLEX WITH ZINC
ComponentsSEX HORMONE-BINDING GLOBULIN
KeywordsSIGNALING PROTEIN / Jellyroll
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 / ISOPROPYL ALCOHOL / Sex hormone-binding globulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsAvvakumov, V.A. / Muller, Y.A. / Hammond, G.L.
Citation
Journal: J.Biol.Chem. / Year: 2000
Title: Steroid-binding specificity of human sex hormone-binding globulin is influenced by occupancy of a zinc-binding site.
Authors: Avvakumov, G.V. / Muller, Y.A. / Hammond, G.L.
#1: Journal: 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
DepositionJun 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Nov 13, 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 / 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_asym_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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

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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)23,1326
Polymers22,6111
Non-polymers5215
Water2,342130
1
A: SEX HORMONE-BINDING GLOBULIN
hetero molecules

A: SEX HORMONE-BINDING GLOBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,26412
Polymers45,2212
Non-polymers1,04310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
Unit cell
Length a, b, c (Å)104.020, 104.020, 84.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsThe biological assembly is a dimer constructed from chain A and a symmetry partner generated by a two-fold.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein SEX HORMONE-BINDING GLOBULIN / SHBG


Mass: 22610.623 Da / Num. of mol.: 1 / Fragment: N-TERMINAL FRAGMENT OF SHBG (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

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Non-polymers , 5 types, 135 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-DHT / 5-ALPHA-DIHYDROTESTOSTERONE


Mass: 290.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H30O2 / Comment: hormone*YM
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.95 Å3/Da / Density % sol: 36.88 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Crystal growth: ISOPROPANOL, PEG400, HEPES-buffer, CaCl2, DHT Crystals were soaked with 2.5 mM ZnCl2 for three days, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal grow
*PLUS
Temperature: 293 K
Details: Grishkovskaya, I., (1999) Acta Crystallogr. Sec., D55, 2053
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
113 mg/mlprotein1drop
250 mMsodium HEPES1drop
32.5 mM1dropCaCl2
40.003 mMDHT1drop
520 %2-propanol1reservoir
610 %PEG4001reservoir
7100 mMsodium HEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 8, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 18785 / Num. obs: 18785 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 35.8 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.9
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.287 / Num. unique all: 2825 / % possible all: 90.7
Reflection
*PLUS
Num. measured all: 101085
Reflection shell
*PLUS
% possible obs: 93.3 % / Mean I/σ(I) obs: 2.8

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Processing

Software
NameClassification
XDSdata scaling
XDSdata reduction
REFMACrefinement
RefinementResolution: 1.7→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1867 -Random
Rwork0.197 ---
all-18785 --
obs-18785 96.3 %-
Displacement parametersBiso mean: 38.7 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1366 0 24 134 1524
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d0.035
X-RAY DIFFRACTIONp_mcbond_it3.832.5
X-RAY DIFFRACTIONp_mcangle_it5.285
X-RAY DIFFRACTIONp_scbond_it4.853
X-RAY DIFFRACTIONp_scangle_it6.96
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_mcbond_it3.832.5
X-RAY DIFFRACTIONp_scbond_it4.853
X-RAY DIFFRACTIONp_mcangle_it5.285
X-RAY DIFFRACTIONp_scangle_it6.96
LS refinement shell
*PLUS
Rfactor Rfree: 0.353 / Rfactor obs: 0.285

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