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- PDB-2fr3: Crystal Structure of Cellular Retinoic Acid Binding Protein Type ... -

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Basic information

Entry
Database: PDB / ID: 2fr3
TitleCrystal Structure of Cellular Retinoic Acid Binding Protein Type II in Complex with All-Trans-Retinoic Acid at 1.48 Angstroms Resolution
ComponentsCellular retinoic acid binding protein 2
KeywordsTRANSPORT PROTEIN / CRABPII / Retinoic Acid / Retinoids / Beta Barrel / High Resolution
Function / homology
Function and homology information


positive regulation of collateral sprouting / retinoid binding / retinoic acid binding / retinal 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 / retinoic acid binding / retinal 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 / 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
ACETATE ION / RETINOIC ACID / Cellular retinoic acid-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Rigid Body Refinement / Resolution: 1.48 Å
AuthorsVaezeslami, S. / Geiger, J.H.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: The structure of Apo-wild-type cellular retinoic acid binding protein II at 1.4 A and its relationship to ligand binding and nuclear translocation.
Authors: Vaezeslami, S. / Mathes, E. / Vasileiou, C. / Borhan, B. / Geiger, J.H.
#1: Journal: Thesis
Title: Determining crystal structures of proteins and protein complexes by X-ray crystallography: X-ray crystallographic studies of the mutants of cellular retinoic acid binding protein type II ...Title: Determining crystal structures of proteins and protein complexes by X-ray crystallography: X-ray crystallographic studies of the mutants of cellular retinoic acid binding protein type II toward designing a mimic of rhodopsin
Authors: Vaezeslami, S.
History
DepositionJan 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cellular retinoic acid binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9413
Polymers15,5821
Non-polymers3592
Water3,819212
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.287, 46.464, 77.261
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 retinoic acid binding protein 2 / Cellular retinoic acid binding protein II / CRABP-II / Retinoic acid-binding protein II /


Mass: 15581.802 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRABP2 / Plasmid: pET17-b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P29373
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-REA / RETINOIC 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.: 212 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 30% (w/v) PEG 4000, 0.1 M sodium citrate/citric acid pH 5.4, and 0.2 ammonium acetate (crystallization performed in dark room and under red light), VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1771
21
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 23, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.48→39.81 Å / Num. all: 27332 / Num. obs: 26090 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.044 / Χ2: 2.781 / Net I/σ(I): 28.19
Reflection shellResolution: 1.48→1.53 Å / % possible obs: 96.4 % / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 5.08 / Num. unique obs: 2590 / Χ2: 0.777 / % possible all: 96.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: Rigid Body Refinement / Resolution: 1.48→39.81 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.952 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.174 2622 10 %RANDOM
Rwork0.126 ---
all0.131 23523 --
obs0.131 23523 95.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.735 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20 Å2
2--0.37 Å20 Å2
3----0.81 Å2
Refinement stepCycle: LAST / Resolution: 1.48→39.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1101 0 26 228 1355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221143
X-RAY DIFFRACTIONr_bond_other_d0.0010.021069
X-RAY DIFFRACTIONr_angle_refined_deg1.8151.9791552
X-RAY DIFFRACTIONr_angle_other_deg1.06332486
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3745138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.6532552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.91115207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.076158
X-RAY DIFFRACTIONr_chiral_restr0.1310.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021247
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02214
X-RAY DIFFRACTIONr_nbd_refined0.2160.2170
X-RAY DIFFRACTIONr_nbd_other0.2030.21105
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2546
X-RAY DIFFRACTIONr_nbtor_other0.0830.2779
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2147
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2550.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.227
X-RAY DIFFRACTIONr_mcbond_it2.3551.5899
X-RAY DIFFRACTIONr_mcbond_other0.9541.5281
X-RAY DIFFRACTIONr_mcangle_it2.87521132
X-RAY DIFFRACTIONr_scbond_it3.8623514
X-RAY DIFFRACTIONr_scangle_it5.0014.5419
X-RAY DIFFRACTIONr_rigid_bond_restr1.93232644
X-RAY DIFFRACTIONr_sphericity_free9.0573228
X-RAY DIFFRACTIONr_sphericity_bonded4.39432196
LS refinement shellResolution: 1.48→1.515 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 178 -
Rwork0.15 1593 -
obs-1771 88.73 %

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