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- PDB-1erb: THE INTERACTION OF N-ETHYL RETINAMIDE WITH PLASMA RETINOL-BINDING... -

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Basic information

Entry
Database: PDB / ID: 1erb
TitleTHE INTERACTION OF N-ETHYL RETINAMIDE WITH PLASMA RETINOL-BINDING PROTEIN (RBP) AND THE CRYSTAL STRUCTURE OF THE RETINOID-RBP COMPLEX AT 1.9 ANGSTROMS RESOLUTION
ComponentsRETINOL BINDING PROTEIN
KeywordsRETINOL TRANSPORT
Function / homology
Function and homology information


retinol transport / retinol transmembrane transporter activity / retinal binding / retinol binding / extracellular space
Similarity search - Function
Retinol binding protein/Purpurin / Lipocalin, ApoD type / Lipocalin family conserved site / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
N-ETHYL RETINAMIDE / Retinol-binding protein 4
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsZanotti, G. / Berni, R.
Citation
Journal: J.Biol.Chem. / Year: 1993
Title: The interaction of N-ethyl retinamide with plasma retinol-binding protein (RBP) and the crystal structure of the retinoid-RBP complex at 1.9-A resolution.
Authors: Zanotti, G. / Malpeli, G. / Berni, R.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystal Structure of the Trigonal Form of Human Plasma Retinol-Binding Protein at 2.5 Angstroms Resolution
Authors: Zanotti, G. / Ottonello, S. / Berni, R. / Monaco, H.L.
#2: Journal: J.Biol.Chem. / Year: 1993
Title: Crystal Structure of Liganded and Unliganded Forms of Bovine Plasma Retinol-Binding Protein
Authors: Zanotti, G. / Berni, R. / Monaco, H.L.
#3: Journal: Eur.J.Biochem. / Year: 1990
Title: The Bovine Plasma Retinol-Binding Protein. Amino Acid Sequence, Interaction with Transthyretin, Crystallization and Preliminary X-Ray Data
Authors: Berni, R. / Stoppini, M. / Zapponi, C.M. / Meloni, M.L. / Monaco, H.L. / Zanotti, G.
History
DepositionOct 1, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 9, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: RETINOL BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4232
Polymers21,0961
Non-polymers3281
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.270, 49.110, 76.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CYS 174 - ASP 175 OMEGA = 0.02 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein RETINOL BINDING PROTEIN


Mass: 21095.654 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P18902
#2: Chemical ChemComp-ETR / N-ETHYL RETINAMIDE


Mass: 327.504 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H33NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.21 %
Crystal grow
*PLUS
Method: microdialysis / Details: referred to 1hbq / PH range low: 5.3 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16-10 mg/mlbRBP11
20.1 Msodium chloride12
30.01-1. mMcadmium acetate12
40.1 Msodium acetate12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 9999 Å / Num. obs: 11262 / % possible obs: 79 % / Observed criterion σ(I): 1 / Num. measured all: 37176 / Rmerge(I) obs: 0.038
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 2 Å / % possible obs: 59 % / Num. unique obs: 1645

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Processing

SoftwareName: TNT / Classification: refinement
RefinementRfactor obs: 0.172 / Highest resolution: 1.9 Å
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1401 0 24 160 1585
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.009
X-RAY DIFFRACTIONt_angle_deg2.6
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 9 Å / Num. reflection obs: 11261 / σ(I): 1 / Rfactor obs: 0.172
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg
X-RAY DIFFRACTIONt_dihedral_angle_d26.6
X-RAY DIFFRACTIONt_dihedral_angle_deg
X-RAY DIFFRACTIONt_plane_restr0.005

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