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- PDB-1cbq: CRYSTAL STRUCTURE OF CELLULAR RETINOIC-ACID-BINDING PROTEINS I AN... -

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Basic information

Entry
Database: PDB / ID: 1cbq
TitleCRYSTAL STRUCTURE OF CELLULAR RETINOIC-ACID-BINDING PROTEINS I AND II IN COMPLEX WITH ALL-TRANS-RETINOIC ACID AND A SYNTHETIC RETINOID
ComponentsCELLULAR RETINOIC ACID BINDING PROTEIN TYPE II
KeywordsRETINOIC-ACID TRANSPORT
Function / homology
Function and homology information


positive regulation of collateral sprouting / retinoid binding / retinal binding / retinoic acid binding / embryonic forelimb morphogenesis / retinoic acid metabolic process / retinol binding / Signaling by Retinoic Acid / epidermis development / fatty acid transport ...positive regulation of collateral sprouting / retinoid binding / retinal binding / retinoic acid binding / embryonic forelimb morphogenesis / retinoic acid metabolic process / retinol binding / Signaling by Retinoic Acid / epidermis development / fatty acid transport / cyclin binding / fatty acid binding / regulation of DNA-templated transcription / endoplasmic reticulum / signal transduction / extracellular exosome / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Chem-RE9 / Cellular retinoic acid-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsKleywegt, G.J. / Bergfors, T. / Jones, T.A.
Citation
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, 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.W. / Jones, T.A.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Crystallisation and Preliminary X-Ray Analysis of Recombinant Bovine Cellular Retinoic Acid-Binding Protein
Authors: Bergfors, T. / Kleywegt, G.J. / Jones, T.A.
#3: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallographic Studies on a Family of Lipophilic Transport Proteins. Refinement of P2 Myelin Protein and the Structure Determination and Refinement of Cellular Retinol-Binding Protein in ...Title: Crystallographic Studies on a Family of 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.
#4: Journal: Embo J. / Year: 1988
Title: The Three-Dimensional Structure of P2 Myelin Protein
Authors: Jones, T.A. / Bergfors, T. / Sedzik, J. / Unge, T.
History
DepositionSep 28, 1994Processing site: BNL
Revision 1.0Jan 26, 1995Provider: 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: CELLULAR RETINOIC ACID BINDING PROTEIN TYPE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9773
Polymers15,5821
Non-polymers3952
Water95553
1
A: CELLULAR RETINOIC ACID BINDING PROTEIN TYPE II
hetero molecules

A: CELLULAR RETINOIC ACID BINDING PROTEIN TYPE II
hetero molecules

A: CELLULAR RETINOIC ACID BINDING PROTEIN TYPE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9329
Polymers46,7453
Non-polymers1,1866
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_566z+1/2,-x+3/2,-y+11
crystal symmetry operation12_664-y+3/2,-z+1,x-1/21
Unit cell
Length a, b, c (Å)81.040, 81.040, 81.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-901-

PO4

21A-901-

PO4

31A-900-

HOH

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Components

#1: Protein CELLULAR RETINOIC ACID BINDING PROTEIN TYPE II


Mass: 15581.802 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Gene: HUMAN CRABP-II / Plasmid: PET-3A GENE: HUMAN CRABP-II / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P29373
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-RE9 / 6-(2,3,4,5,6,7-HEXAHYDRO-2,4,4-TRIMETHYL-1-METYLENEINDEN-2-YL)-3-METHYLHEXA-2,4-DIENOIC ACID


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


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.85 Å3/Da / Density % sol: 56.78 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mMTris-HCl1drop
210 %(v/v)mPEG50001reservoir
30.1 Msodium citrate1reservoir
45 %dimethyl sulphoxide1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 9011 / Observed criterion σ(I): 3
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 29 Å / % possible obs: 97.4 % / Num. measured all: 46981 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 77.8 % / Rmerge(I) obs: 0.268

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.264 --
Rwork0.21 --
obs0.21 8597 97.4 %
Displacement parametersBiso mean: 34 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1091 0 25 53 1169
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.62
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.31
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
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.31

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