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- PDB-1cbi: APO-CELLULAR RETINOIC ACID BINDING PROTEIN I -

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Basic information

Entry
Database: PDB / ID: 1cbi
TitleAPO-CELLULAR RETINOIC ACID BINDING PROTEIN I
ComponentsCELLULAR RETINOIC ACID BINDING PROTEIN I
KeywordsRETINOIC-ACID TRANSPORT
Function / homology
Function and homology information


RA biosynthesis pathway / retinoid binding / retinal binding / retinol binding / cytoplasm
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
Cellular retinoic acid-binding protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsThompson, J.R. / Bratt, J.M. / Banaszak, L.J.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Crystal structure of cellular retinoic acid binding protein I shows increased access to the binding cavity due to formation of an intermolecular beta-sheet.
Authors: Thompson, J.R. / Bratt, J.M. / Banaszak, L.J.
#1: Journal: Structure / Year: 1994
Title: Crystal Structures of Cellular Retinoic Acid Binding Proteins I and II in Complex with All-Trans-Retinoic Acid and a Synthetic Retinoid
Authors: Kleywegt, G.J. / Bergfors, T. / Senn, H. / Le Motte, P. / Gsell, B. / Shudo, K. / Jones, A.T.
History
DepositionJul 12, 1995Processing site: BNL
Revision 1.0Nov 14, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700SHEET CRABPI IS ACTUALLY A TEN-STRANDED BETA-BARREL. THIS IS REPRESENTED IN SHEET RECORDS BELOW BY ...SHEET CRABPI IS ACTUALLY A TEN-STRANDED BETA-BARREL. THIS IS REPRESENTED IN SHEET RECORDS BELOW BY AN ELEVEN-STRANDED SHEET.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CELLULAR RETINOIC ACID BINDING PROTEIN I
B: CELLULAR RETINOIC ACID BINDING PROTEIN I


Theoretical massNumber of molelcules
Total (without water)30,9612
Polymers30,9612
Non-polymers00
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-12 kcal/mol
Surface area14130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.450, 127.450, 53.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.8722, -0.4867, 0.0495), (-0.4889, -0.8709, 0.0501), (0.0187, -0.0679, -0.9975)
Vector: 34.0471, 134.78799, 55.7298)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD

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Components

#1: Protein CELLULAR RETINOIC ACID BINDING PROTEIN I


Mass: 15480.392 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: APO FORM / Source: (gene. exp.) Mus musculus (house mouse) / Gene: MOUSE CRABPI / Plasmid: PMON2670 / Gene (production host): MOUSE CRABPI / Production host: Escherichia coli (E. coli) / References: UniProt: P62965
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 4.06 Å3/Da / Density % sol: 69.69 %
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-14 mg/mlprotein 1drop
216 %PEG40001reservoir
30.1 mM1reservoirMgCl2
40.1 mMcitrate1reservoir

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Nov 16, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 12365 / % possible obs: 90.9 % / Observed criterion σ(I): 0 / Redundancy: 23 % / Rmerge(I) obs: 0.109
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 13 Å / Rmerge(I) obs: 0.109
Reflection shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.9 Å / % possible obs: 51 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 1.69

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.7→13 Å / σ(F): 2
RfactorNum. reflection
Rfree0.233 -
Rwork0.196 -
obs0.196 11857
Displacement parametersBiso mean: 14 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.7→13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2672 0 0 71 2743
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.56
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_d1.21
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
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.21

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