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- PDB-1hbq: CRYSTAL STRUCTURE OF LIGANDED AND UNLIGANDED FORMS OF BOVINE PLAS... -

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Basic information

Entry
Database: PDB / ID: 1hbq
TitleCRYSTAL STRUCTURE OF LIGANDED AND UNLIGANDED FORMS OF BOVINE PLASMA RETINOL-BINDING PROTEIN
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
Retinol-binding protein 4
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsZanotti, G. / Monaco, H.L.
Citation
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.
#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: 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
DepositionFeb 5, 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 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RETINOL BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)21,0851
Polymers21,0851
Non-polymers00
Water2,990166
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.550, 48.970, 76.870
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: 21084.650 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P18902
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: RETB_BOVIN SWISS-PROT RESIDUE PDB ATOM RECORDS NAME NUMBER NAME CHAIN SEQ/INSERT CODE HIS 52 GLN 52 ASP 175 ASN 175

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.79 %
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: 2.2 Å / Lowest resolution: 2.7 Å / Num. obs: 18382 / % possible obs: 94 % / Observed criterion σ(I): 1 / Num. measured all: 70544 / Rmerge(I) obs: 0.059

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementHighest resolution: 1.7 Å /
RfactorNum. reflection
Rwork0.196 -
obs0.196 18110
Refinement stepCycle: LAST / Highest resolution: 1.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1422 0 0 166 1588
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 9 Å / Rfactor obs: 0.196 / Num. reflection obs: 18110
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d2.9
X-RAY DIFFRACTIONx_dihedral_angle_d25.3
X-RAY DIFFRACTIONx_dihedral_angle_deg
X-RAY DIFFRACTIONx_plane_restr0.009

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