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- PDB-2cbr: CELLULAR RETINOIC ACID BINDING PROTEIN I IN COMPLEX WITH A RETINO... -

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Basic information

Entry
Database: PDB / ID: 2cbr
TitleCELLULAR RETINOIC ACID BINDING PROTEIN I IN COMPLEX WITH A RETINOBENZOIC ACID (AM80)
ComponentsPROTEIN (CRABP-I)
KeywordsTRANSPORT PROTEIN / RETINOIC-ACID TRANSPORT
Function / homology
Function and homology information


RA biosynthesis pathway / retinoic acid binding / retinal binding / retinol binding / fatty acid transport / fatty acid binding / protein-containing complex / identical protein 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
Chem-A80 / Cellular retinoic acid-binding protein 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 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: PDBE / Processing site: RCSB
Revision 1.0Dec 21, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 5, 2011Group: Non-polymer description
Revision 1.4Nov 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
Revision 1.5Aug 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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (CRABP-I)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8322
Polymers15,4801
Non-polymers3511
Water1448
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.500, 133.500, 40.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper: (Code: generate
Matrix: (0.231781, -0.961217, 0.149465), (0.959479, 0.25121, 0.127646), (-0.160243, 0.113823, 0.980493)
Vector: 138.2278, 20.6091, -7.306)

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Components

#1: Protein PROTEIN (CRABP-I)


Mass: 15480.392 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle)
Description: MUS MUSCULUS (IDENTICAL WITH BOVINE PROTEIN) RECOMBINANT GENE
Gene: MOUSE / Plasmid: PT7-1-3 / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62964
#2: Chemical ChemComp-A80 / 4-[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbamoyl]benzoic acid


Mass: 351.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H25NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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

Crystal growpH: 8
Details: IN 30% PEG4000, 0.2M LI2SO4 AND 0.1 M TRIS-HCL, PH 8.0
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop
Details: drop contained equal volume of protein and reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
119 mg/mlprotein1drop
250 mMTris-HCl1drop
30.1 %beta-octyl glucoside1drop
41 mMbeta-mercaptoethanol1drop
530 %PEG40001reservoir
60.2 M1reservoirLi2SO4
70.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 277 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: 2.8→38.3 Å / Num. obs: 10128 / % possible obs: 97.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 20.2
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 5.2 / % possible all: 95.7
Reflection
*PLUS
Lowest resolution: 38 Å
Reflection shell
*PLUS
% possible obs: 95.7 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNS0.3refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CBR

1cbr


Resolution: 2.8→30 Å / Rfactor Rfree error: 0.009 / Data cutoff high rms absF: 1543984.01 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED THE STRUCTURE WAS REFINED WITH NCS CONSTRAINTS IN CNS (I.E., THE TWO MOLECULES ARE IDENTICAL).
RfactorNum. reflection% reflectionSelection details
Rfree0.268 820 8.1 %RANDOM
Rwork0.23 ---
obs-10125 97 %-
Displacement parametersBiso mean: 37.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.39 Å2-4.92 Å20 Å2
2--1.39 Å20 Å2
3----2.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1087 0 26 8 1121
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.71
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
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.355 123 7.5 %
Rwork0.31 1517 -
obs--95.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3AM8.PARAM8.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 9305 / Rfactor Rfree: 0.266 / Rfactor Rwork: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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