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- PDB-1crb: CRYSTALLOGRAPHIC STUDIES ON A FAMILY OF CELLULAR LIPOPHILIC TRANS... -

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Basic information

Entry
Database: PDB / ID: 1crb
TitleCRYSTALLOGRAPHIC STUDIES ON A FAMILY OF CELLULAR LIPOPHILIC TRANSPORT PROTEINS. REFINEMENT OF P2 MYELIN PROTEIN AND THE STRUCTURE DETERMINATION AND REFINEMENT OF CELLULAR RETINOL-BINDING PROTEIN IN COMPLEX WITH ALL-TRANS-RETINOL
ComponentsCELLULAR RETINOL BINDING PROTEIN
KeywordsCELLULAR LIPOPHILIC TRANSPORT PROTEIN
Function / homology
Function and homology information


regulation of granulocyte differentiation / response to benzoic acid / The canonical retinoid cycle in rods (twilight vision) / Retinoid metabolism and transport / all-trans-retinol binding / retinoic acid biosynthetic process / maintenance of location in cell / vitamin A metabolic process / lipid storage / retinal binding ...regulation of granulocyte differentiation / response to benzoic acid / The canonical retinoid cycle in rods (twilight vision) / Retinoid metabolism and transport / all-trans-retinol binding / retinoic acid biosynthetic process / maintenance of location in cell / vitamin A metabolic process / lipid storage / retinal binding / response to vitamin A / retinoic acid metabolic process / retinol metabolic process / retinol binding / lipid homeostasis / response to retinoic acid / fatty acid transport / retinoid metabolic process / lipid droplet / fatty acid binding / cell body / nucleus / cytosol
Similarity search - Function
Retinol-binding protein 1 / Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
: / RETINOL / Retinol-binding protein 1
Similarity search - Component
Biological speciesRattus rattus (black rat)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsCowan, S.W. / Jones, T.A.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Crystallographic studies on a family of cellular lipophilic transport proteins. Refinement of P2 myelin protein and the structure determination and refinement of cellular retinol-binding ...Title: Crystallographic studies on a family of cellular lipophilic transport proteins. Refinement of P2 myelin protein and the structure determination and refinement of cellular retinol-binding protein in complex with all-trans-retinol.
Authors: Cowan, S.W. / Newcomer, M.E. / Jones, T.A.
#1: Journal: Adv.Protein Chem. / Year: 1994
Title: Lipid-Binding Proteins: A Family of Fatty Acid and Retinoid Transport Proteins
Authors: Banaszak, L. / Winter, N. / Xu, Z. / Bernlohr, D.A. / Cowan, S. / Jones, T.A.
#2: Journal: Eur.J.Biochem. / Year: 1992
Title: The Primary Structure of Piscine (Oncorhynchus Mykiss) Retinol-Binding Protein and a Comparison with the Three-Dimensional Structure of Mammalian Retinol-Binding Protein
Authors: Zapponi, M.C. / Zanotti, G. / Stoppini, M. / Berni, R.
#3: Journal: Proteins / Year: 1990
Title: Crystallographic Refinement of Human Serum Retinol Binding Protein at 2 Angstroms Resolution
Authors: Cowan, S.W. / Newcomer, M.E. / Jones, T.A.
#4: Journal: J.Biol.Chem. / Year: 1981
Title: Crystallization of and Preliminary X-Ray Data for an Intracellular Vitamin A-Binding Protein from Rat Liver
Authors: Newcomer, M.E. / Liljas, A. / Eriksson, V. / Sundelin, J. / Rask, L. / Peterson, P.A.
History
DepositionFeb 10, 1993Processing site: BNL
Revision 1.0Dec 20, 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 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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: CELLULAR RETINOL BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2364
Polymers15,7251
Non-polymers5113
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.090, 47.390, 69.340
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 CELLULAR RETINOL BINDING PROTEIN


Mass: 15724.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus rattus (black rat) / References: UniProt: P02696
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-RTL / RETINOL


Mass: 286.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.09 Å3/Da / Density % sol: 41.26 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
275 mM1dropNaCl
330 mMTris-HCl1drop
420 %PEG60001reservoir
50.1-20 mM1reservoirCdCl2

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.1 Å / % possible obs: 80 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.1→8 Å / Rfactor Rfree: 0.248 / Rfactor Rwork: 0.188 / Rfactor obs: 0.188 / σ(F): 0
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1102 0 23 73 1198
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.31
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.99
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d1.31
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg0.99

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