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- PDB-2cbs: CELLULAR RETINOIC ACID BINDING PROTEIN II IN COMPLEX WITH A SYNTH... -

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Basic information

Entry
Database: PDB / ID: 2cbs
TitleCELLULAR RETINOIC ACID BINDING PROTEIN II IN COMPLEX WITH A SYNTHETIC RETINOIC ACID (RO-13 6307)
ComponentsPROTEIN (CRABP-II)
KeywordsTRANSPORT PROTEIN / RETINOIC-ACID TRANSPORT
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
Chem-R13 / Cellular retinoic acid-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.1 Å
AuthorsChaudhuri, B. / Kleywegt, G.J. / Bergfors, T. / Jones, T.A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Structures of cellular retinoic acid binding proteins I and II in complex with synthetic retinoids.
Authors: Chaudhuri, B.N. / Kleywegt, G.J. / Broutin-L'Hermite, I. / Bergfors, T. / Senn, H. / Le Motte, P. / Partouche, O. / Jones, T.A.
#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, T.A.
#2: 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.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Crystallization and preliminary X-ray analysis of recombinant bovine cellular retinoic acid-binding protein.
Authors: Bergfors, T. / Kleywegt, G.J. / Jones, T.A.
History
DepositionFeb 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: PROTEIN (CRABP-II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9202
Polymers15,5821
Non-polymers3381
Water95553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.250, 47.640, 74.830
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 PROTEIN (CRABP-II)


Mass: 15581.802 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Plasmid: PET-1A / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P29373
#2: Chemical ChemComp-R13 / 3-METHYL-7-(5,5,8,8-TETRAMETHYL-5,6,7,8-TETRAHYDRO-NAPHTHALEN-2-YL) -OCTA-2,4,6-TRIENOIC ACID


Mass: 338.483 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H30O2
#3: 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.46 %
Crystal growpH: 5.5
Details: 20% MONOMETHYL PEG 5000 0.1 M SODIUM ACETATE PH 5.5
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Details: drop contained equal volume of protein and reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
124.6 mg/mlprotein1drop
250 mMTris-HCl1drop
320 %mPEG50001reservoir
40.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→45.2 Å / Num. obs: 9683 / % possible obs: 97.7 % / Redundancy: 4.3 % / Biso Wilson estimate: 11.3 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 25.9
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 11.6 / % possible all: 97.7
Reflection
*PLUS
Lowest resolution: 45 Å
Reflection shell
*PLUS
% possible obs: 97.7 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
CNS0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: OTHER
Starting model: 1CBS

1cbs


Resolution: 2.1→8 Å / Rfactor Rfree error: 0.008 / Data cutoff high rms absF: 1271032.11 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.233 780 8.3 %RANDOM
Rwork0.2 ---
obs-9453 97.2 %-
Displacement parametersBiso mean: 22.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.29 Å20 Å20 Å2
2---0.64 Å20 Å2
3---3.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1091 0 25 53 1169
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.69
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.41.5
X-RAY DIFFRACTIONx_mcangle_it2.192
X-RAY DIFFRACTIONx_scbond_it2.632
X-RAY DIFFRACTIONx_scangle_it4.052.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.272 117 7.7 %
Rwork0.212 1396 -
obs--95.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3R13.PARR13.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 8770 / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.69
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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