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- PDB-1kqw: Crystal structure of holo-CRBP from zebrafish -

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Basic information

Entry
Database: PDB / ID: 1kqw
TitleCrystal structure of holo-CRBP from zebrafish
ComponentsCellular retinol-binding protein
KeywordsTRANSPORT PROTEIN / retinol / vitamin A / retinol-binding
Function / homology
Function and homology information


Retinoid metabolism and transport / fatty acid transport / fatty acid 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
RETINOL / Cellular retinol-binding protein type II
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsCalderone, V. / Folli, C. / Marchesani, A. / Berni, R. / Zanotti, G.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Identification and structural analysis of a zebrafish apo and holo cellular retinol-binding protein.
Authors: Calderone, V. / Folli, C. / Marchesani, A. / Berni, R. / Zanotti, G.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallographic Studies on a Family of Cellular Lipophilic Transport Proteins. Refinement of P2 Myelin Protein and the Structure Determination and Refinement of Cellular Retinol-binding ...Title: Crystallographic Studies on a Family of Cellular 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.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Crystal structures of holo and apo-cellular retinol-binding protein II
Authors: Winter, N.S. / Bratt, J.M. / Banaszak, L.J.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Identification, retinoid binding and X-ray analysis of a human retinol-binding protein
Authors: Folli, C. / Calderone, V. / Ottonello, S. / Bolchi, A. / Zanotti, G. / Stoppini, M. / Berni, R.
History
DepositionJan 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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: Cellular retinol-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9862
Polymers15,7001
Non-polymers2861
Water3,495194
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.018, 89.018, 38.271
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Cellular retinol-binding protein / CRBP


Mass: 15699.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8UVG6
#2: Chemical ChemComp-RTL / RETINOL


Mass: 286.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.1 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: PEG 4000, Ammonium acetate, sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 %(w/v)PEG40001reservoir
20.1 Msodium citrate1reservoir
30.2 Mammonium acetate1reservoirpH5.6
48.0 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.38→40 Å / Num. all: 22343 / Num. obs: 22343 / % possible obs: 72.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 8.1
Reflection shellResolution: 1.38→1.46 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 2.9 / Num. unique all: 581 / Rsym value: 0.234 / % possible all: 13.2
Reflection
*PLUS
Lowest resolution: 21 Å / Num. obs: 22248 / % possible obs: 82.4 % / Num. measured all: 144066 / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
Lowest resolution: 1.45 Å / % possible obs: 72.3 % / Rmerge(I) obs: 0.234

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Processing

Software
NameVersionClassification
AMoREphasing
SHELXL-97refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OPB

1opb


Resolution: 1.38→20.989 Å / Num. parameters: 11921 / Num. restraintsaints: 14123 / Isotropic thermal model: anisotropic / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2326 1103 5.2 %RANDOM
Rwork0.1588 ---
all0.1654 22198 --
obs0.1654 22198 71 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 4 / Occupancy sum non hydrogen: 1319.21
Refinement stepCycle: LAST / Resolution: 1.38→20.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1103 0 23 194 1320
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.025
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0261
X-RAY DIFFRACTIONs_zero_chiral_vol0.04
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.049
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.01
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.049
X-RAY DIFFRACTIONs_approx_iso_adps0.062
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Num. reflection all: 22198 / Rfactor all: 0.1654 / Rfactor Rfree: 0.227 / Rfactor Rwork: 0.154
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2
LS refinement shell
*PLUS
Rfactor Rwork: 0.299

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