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- PDB-5ha1: Crystal structure of human cellular retinol binding protein 1 in ... -

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Basic information

Entry
Database: PDB / ID: 5ha1
TitleCrystal structure of human cellular retinol binding protein 1 in complex with retinylamine
ComponentsRetinol-binding protein 1
KeywordsRETINOL-BINDING PROTEIN / retinylamine / retinol / binding protein
Function / homology
Function and homology information


all-trans-retinol binding / retinoic acid biosynthetic process / vitamin A metabolic process / retinoid binding / retinal binding / Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / lipid homeostasis / fatty acid transport / Retinoid metabolism and transport ...all-trans-retinol binding / retinoic acid biosynthetic process / vitamin A metabolic process / retinoid binding / retinal binding / Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / lipid homeostasis / fatty acid transport / Retinoid metabolism and transport / lipid droplet / fatty acid binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Retinol-binding protein 1 / 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
Chem-RNE / Retinol-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsGolczak, M. / Arne, J.M. / Silvaroli, J.A. / Kiser, P.D. / Banerjee, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)EY023948 United States
Department of Veterans AffairsIK2BX002683 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Ligand Binding Induces Conformational Changes in Human Cellular Retinol-binding Protein 1 (CRBP1) Revealed by Atomic Resolution Crystal Structures.
Authors: Silvaroli, J.A. / Arne, J.M. / Chelstowska, S. / Kiser, P.D. / Banerjee, S. / Golczak, M.
History
DepositionDec 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2May 11, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8542
Polymers16,5691
Non-polymers2851
Water5,134285
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.150, 49.570, 73.300
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 Retinol-binding protein 1 / Cellular retinol-binding protein / CRBP / Cellular retinol-binding protein I / CRBP-I


Mass: 16568.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP1, CRBP1 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: P09455
#2: Chemical ChemComp-RNE / (2~{E},4~{E},6~{E},8~{E})-3,7-dimethyl-9-(2,6,6-trimethylcyclohexen-1-yl)nona-2,4,6,8-tetraen-1-amine


Mass: 285.467 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H31N
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.04 Å3/Da / Density % sol: 39.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M Bis-Tris, 25% PEG 6000

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.35→27.55 Å / Num. obs: 30442 / % possible obs: 100 % / Redundancy: 5.9 % / Rsym value: 0.0103 / Net I/σ(I): 9.4
Reflection shellResolution: 1.32→1.35 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10pre_2138refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CRB

1crb


Resolution: 1.35→27.548 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1557 1548 5.09 %
Rwork0.122 --
obs0.1237 30442 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→27.548 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1159 0 21 285 1465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011250
X-RAY DIFFRACTIONf_angle_d1.1311690
X-RAY DIFFRACTIONf_dihedral_angle_d18.82480
X-RAY DIFFRACTIONf_chiral_restr0.087174
X-RAY DIFFRACTIONf_plane_restr0.007219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3501-1.39370.21841320.15432594X-RAY DIFFRACTION100
1.3937-1.44350.21071300.13582577X-RAY DIFFRACTION100
1.4435-1.50130.16231460.12052596X-RAY DIFFRACTION100
1.5013-1.56960.18491470.11282562X-RAY DIFFRACTION100
1.5696-1.65230.15191370.10742608X-RAY DIFFRACTION100
1.6523-1.75580.14711310.09832615X-RAY DIFFRACTION100
1.7558-1.89140.14281540.10092594X-RAY DIFFRACTION100
1.8914-2.08160.12041390.0972632X-RAY DIFFRACTION100
2.0816-2.38270.14821390.10662640X-RAY DIFFRACTION100
2.3827-3.00140.15641400.13112667X-RAY DIFFRACTION100

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