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- PDB-1lpj: Human cRBP IV -

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Basic information

Entry
Database: PDB / ID: 1lpj
TitleHuman cRBP IV
ComponentsRetinol-binding protein IV, cellular
KeywordsTRANSPORT PROTEIN / cellular retinol-binding protein / cRBP / retinol / vitamin A / iLBPs
Function / homology
Function and homology information


retinal binding / retinol binding / 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
Retinoid-binding protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCalderone, V. / Zanotti, G. / Berni, R. / Folli, C.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: Ligand binding and structural analysis of a human putative cellular retinol-binding protein
Authors: Folli, C. / Calderone, V. / Ramazzina, I. / Zanotti, G. / Berni, R.
#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
DepositionMay 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Retinol-binding protein IV, cellular


Theoretical massNumber of molelcules
Total (without water)15,4281
Polymers15,4281
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.053, 57.186, 67.939
Angle α, β, γ (deg.)90.00, 104.03, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-148-

HOH

21A-251-

HOH

31A-288-

HOH

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Components

#1: Protein Retinol-binding protein IV, cellular / CRBP-IV / Retinoid binding protein 7


Mass: 15427.511 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q96R05
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.08 Å3/Da / Density % sol: 40.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 10% PEG 4000, 10% isopropanol, 100 mM sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 %(w/v)PEG40001reservoir
210 %(v/v)2-propanol1reservoir
350 mMsodium citrate1reservoirpH5.6
48 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 14, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2→28.606 Å / Num. all: 7611 / Num. obs: 7611 / % possible obs: 89.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.124 / Rsym value: 0.124 / Net I/σ(I): 3.8
Reflection shellResolution: 2→2.1 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 1.3 / Num. unique all: 932 / Rsym value: 0.124 / % possible all: 87.8
Reflection
*PLUS
Lowest resolution: 28.6 Å / Num. measured all: 19128
Reflection shell
*PLUS
Lowest resolution: 2.11 Å / % possible obs: 91.4 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CRB

1crb


Resolution: 2→24.44 Å / Rfactor Rfree error: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 809 10.7 %RANDOM
Rwork0.23 ---
all-7579 --
obs-7579 87.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 112.525 Å2 / ksol: 0.422063 e/Å3
Displacement parametersBiso mean: 36.1 Å2
Baniso -1Baniso -2Baniso -3
1--4.32 Å20 Å2-2.88 Å2
2--5.57 Å20 Å2
3----1.25 Å2
Refine analyzeLuzzati coordinate error free: 0.35 Å / Luzzati sigma a free: 0.17 Å
Refinement stepCycle: LAST / Resolution: 2→24.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 0 0 150 1234
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d27.1
X-RAY DIFFRACTIONc_improper_angle_d0.7
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3 132 10.5 %
Rwork0.254 1126 -
obs--87.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
Refinement
*PLUS
Rfactor Rfree: 0.276 / Rfactor Rwork: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7
LS refinement shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.11 Å / Rfactor Rfree: 0.3 / Num. reflection Rfree: 136

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