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- PDB-1opb: THE CRYSTAL STRUCTURES OF HOLO-AND APO-CELLULAR RETINOL BINDING P... -

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Basic information

Entry
Database: PDB / ID: 1opb
TitleTHE CRYSTAL STRUCTURES OF HOLO-AND APO-CELLULAR RETINOL BINDING PROTEIN II
ComponentsCELLULAR RETINOL BINDING PROTEIN II
KeywordsRETINOL TRANSPORT
Function / homology
Function and homology information


Retinoid metabolism and transport / retinal binding / retinol metabolic process / retinol binding / fatty acid transport / retinoid metabolic process / fatty acid binding / lipid binding / nucleus / cytosol
Similarity search - Function
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
RETINAL / Retinol-binding protein 2
Similarity search - Component
Biological speciesRattus rattus (black rat)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsWinter, N. / Banaszak, L.
CitationJournal: J.Mol.Biol. / Year: 1993
Title: Crystal structures of holo and apo-cellular retinol-binding protein II.
Authors: Winter, N.S. / Bratt, J.M. / Banaszak, L.J.
History
DepositionDec 9, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: 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 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Remark 700SHEET THE SHEET PRESENTED AS *S1* ON SHEET RECORDS BELOW IS ACTUALLY A TEN-STRANDED BETA-BARREL. ...SHEET THE SHEET PRESENTED AS *S1* ON SHEET RECORDS BELOW IS ACTUALLY A TEN-STRANDED BETA-BARREL. THIS IS REPRESENTED BY AN ELEVEN-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CELLULAR RETINOL BINDING PROTEIN II
B: CELLULAR RETINOL BINDING PROTEIN II
C: CELLULAR RETINOL BINDING PROTEIN II
D: CELLULAR RETINOL BINDING PROTEIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5648
Polymers62,4264
Non-polymers1,1384
Water2,828157
1
A: CELLULAR RETINOL BINDING PROTEIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8912
Polymers15,6071
Non-polymers2841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CELLULAR RETINOL BINDING PROTEIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8912
Polymers15,6071
Non-polymers2841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CELLULAR RETINOL BINDING PROTEIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8912
Polymers15,6071
Non-polymers2841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: CELLULAR RETINOL BINDING PROTEIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8912
Polymers15,6071
Non-polymers2841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.000, 64.600, 56.000
Angle α, β, γ (deg.)92.60, 102.90, 92.50
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
CELLULAR RETINOL BINDING PROTEIN II


Mass: 15606.570 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus rattus (black rat) / References: UniProt: P06768
#2: Chemical
ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H28O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.08 Å3/Da / Density % sol: 40.96 %
Crystal grow
*PLUS
Temperature: 17.5 ℃ / pH: 4.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
20.10 Msodium acetate1drop
315 %(w/v)PEG1drop
40.10 Msodium acetate1reservoir
530 %(w/v)PEG1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 23764 / % possible obs: 75 % / Num. measured all: 57160 / Rmerge(I) obs: 0.0642

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.173 / Rfactor obs: 0.173 / Highest resolution: 1.9 Å
Details: DATA WAS COLLECTED TO 2.1 ANGSTROMS RESOLUTION ON SIEMENS AREA DETECTOR. THE STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT USING THE COORDINATES OF CELLULAR RETINOL BINDING PROTEIN AS A MODEL.
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4348 0 84 157 4589
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg2.336
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: 2.1 Å / Rfactor obs: 0.173 / Num. reflection obs: 52976 / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.3 Å2
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.336

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