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- PDB-1fem: CRYSTALLOGRAPHIC STUDIES ON COMPLEXES BETWEEN RETINOIDS AND PLASM... -

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Basic information

Entry
Database: PDB / ID: 1fem
TitleCRYSTALLOGRAPHIC STUDIES ON COMPLEXES BETWEEN RETINOIDS AND PLASMA RETINOL-BINDING PROTEIN
ComponentsRETINOL BINDING PROTEIN
KeywordsTRANSPORT PROTEIN
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
RETINOIC ACID / Retinol-binding protein 4
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsZanotti, G. / Marcello, M. / Malpeli, G. / Sartori, G. / Berni, R.
Citation
Journal: J.Biol.Chem. / Year: 1994
Title: Crystallographic studies on complexes between retinoids and plasma retinol-binding protein.
Authors: Zanotti, G. / Marcello, M. / Malpeli, G. / Folli, C. / Sartori, G. / Berni, R.
#1: 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 Angstroms Resolution
Authors: Zanotti, G. / Malpeli, G. / Berni, R.
#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: 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.
History
DepositionAug 29, 1994Processing site: BNL
Revision 1.0Nov 1, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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)21,3962
Polymers21,0961
Non-polymers3001
Water2,954164
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.210, 48.810, 75.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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-REA / RETINOIC ACID


Mass: 300.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.29 %
Crystal
*PLUS
Density % sol: 43 %
Crystal grow
*PLUS
Method: microdialysis / 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: 7294 / % possible obs: 43 % / Observed criterion σ(I): 0 / Num. measured all: 16527 / Rmerge(I) obs: 0.105

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 1.9→9 Å / σ(F): 0 /
RfactorNum. reflection
obs0.184 7294
Refinement stepCycle: LAST / Resolution: 1.9→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1423 0 22 164 1609
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Num. reflection all: 7294 / Rfactor all: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONt_bond_d0.0080.02
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg2.83
X-RAY DIFFRACTIONt_dihedral_angle_d19.810
X-RAY DIFFRACTIONt_dihedral_angle_deg
X-RAY DIFFRACTIONt_plane_restr0.0060.02

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