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

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Basic information

Entry
Database: PDB / ID: 1cbr
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 I
KeywordsRETINOIC-ACID TRANSPORT
Function / homology
Function and homology information


RA biosynthesis pathway / retinoid binding / retinal binding / retinoic acid binding / retinol binding / fatty acid transport / fatty acid binding / nucleus / cytosol / cytoplasm
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
RETINOIC ACID / Cellular retinoic acid-binding protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.9 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.
#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

Downloads & links

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Assembly

Deposited unit
A: CELLULAR RETINOIC ACID BINDING PROTEIN TYPE I
B: CELLULAR RETINOIC ACID BINDING PROTEIN TYPE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5624
Polymers30,9612
Non-polymers6012
Water50428
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.440, 41.440, 202.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.781496, -0.392775, -0.484758), (-0.489669, -0.867614, -0.086429), (-0.386636, 0.304915, -0.870367)
Vector: -0.36603, 0.05477, -26.27855)
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 M1 A 1 .. A 136 B 1 .. B 136 0.0 BECAUSE OF THE STRICT NON-CRYSTALLOGRAPHIC SYMMETRY USED IN REFINEMENT, THE TRANSFORMATION DESCRIBED, IN FACT, YIELDS EXACT COORDINATES FOR CHAIN B WHEN APPLIED TO CHAIN A.

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Components

#1: Protein CELLULAR RETINOIC ACID BINDING PROTEIN TYPE I


Mass: 15480.392 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: BL21 / Gene: MOUSE CRABP / Plasmid: PT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P62965
#2: Chemical ChemComp-REA / RETINOIC ACID / Retinoic acid


Mass: 300.435 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.81 Å3/Da / Density % sol: 56.25 %
Crystal grow
*PLUS
Temperature: 277 K / pH: 8 / Method: vapor diffusion, sitting drop
Details: Bergfors, T., (1994) Acta Crystallogr.,Sect.D, 50, 370.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
250 mMTris-HCl1drop
31-2 mMbeta-mercaptoethanol1drop
40.1-0.2 %beta-octylglucoside1drop
530-37.5 %PEG80001reservoir
60.1 MHEPES1reservoir
70.2 Msodium acetate1reservoirunbuffered
85 %isopropanol1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 7118 / Observed criterion σ(I): 3
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 30 Å / % possible obs: 94.2 % / Num. measured all: 16898 / Rmerge(I) obs: 0.086
Reflection shell
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 2.98 Å

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.9→8 Å / σ(F): 2
Details: THE LIGAND FOR THIS ENTRY WAS TAKEN FROM ENTRY 1CBS AND ADJUSTED TO THE DENSITY AS A RIGID BODY BY X-PLOR. THIS HAS INTRODUCED A SHORT CONTACT (2.2 A) BETWEEN AN OXYGEN OF THE LIGAND AND THE ...Details: THE LIGAND FOR THIS ENTRY WAS TAKEN FROM ENTRY 1CBS AND ADJUSTED TO THE DENSITY AS A RIGID BODY BY X-PLOR. THIS HAS INTRODUCED A SHORT CONTACT (2.2 A) BETWEEN AN OXYGEN OF THE LIGAND AND THE HYDROXYL OXYGEN OF TYR 133. THE STRUCTURE WAS REFINED WITH NCS CONSTRAINTS IN X-PLOR (I.E., THE TWO MOLECULES ARE IDENTICAL). SINCE CONTACTS DUE TO CRYSTALLOGRAPHIC SYMMETRY ARE NOT EVALUATED IN X-PLOR IF STRICT NCS IS USED, THIS HAS INTRODUCED THREE SHORT CONTACTS.
RfactorNum. reflection% reflection
Rfree0.32 --
Rwork0.251 --
obs0.251 6743 94.2 %
Displacement parametersBiso mean: 49.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.55 Å
Refinement stepCycle: LAST / Resolution: 2.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2174 0 44 28 2246
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_d26.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.25
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
Rfactor obs: 0.251 / Rfactor Rfree: 0.32 / Rfactor Rwork: 0.251
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.56

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