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- PDB-5ogb: Human Cellular Retinoic Acid Binding Protein II (CRABPII) with bo... -

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Basic information

Entry
Database: PDB / ID: 5ogb
TitleHuman Cellular Retinoic Acid Binding Protein II (CRABPII) with bound synthetic retinoid DC360.
ComponentsCellular retinoic acid-binding protein 2
KeywordsSIGNALING PROTEIN / Retinoid / Fluorescent / DC360 / CRABPII
Function / homology
Function and homology information


positive regulation of collateral sprouting / retinoid binding / retinal binding / retinoic acid binding / embryonic forelimb morphogenesis / retinoic acid metabolic process / retinol binding / Signaling by Retinoic Acid / epidermis development / fatty acid transport ...positive regulation of collateral sprouting / retinoid binding / retinal binding / retinoic acid binding / embryonic forelimb morphogenesis / retinoic acid metabolic process / retinol binding / Signaling by Retinoic Acid / epidermis development / fatty acid transport / cyclin binding / fatty acid binding / regulation of DNA-templated transcription / endoplasmic reticulum / signal transduction / extracellular exosome / nucleoplasm / nucleus / cytoplasm / cytosol
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
Chem-9U5 / Cellular retinoic acid-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChisholm, D. / Tomlinson, C. / Whiting, A. / Pohl, E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: Fluorescent Retinoic Acid Analogues as Probes for Biochemical and Intracellular Characterization of Retinoid Signaling Pathways.
Authors: Chisholm, D.R. / Tomlinson, C.W.E. / Zhou, G.L. / Holden, C. / Affleck, V. / Lamb, R. / Newling, K. / Ashton, P. / Valentine, R. / Redfern, C. / Erostyak, J. / Makkai, G. / Ambler, C.A. / Whiting, A. / Pohl, E.
History
DepositionJul 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 17, 2024Group: 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: Cellular retinoic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0582
Polymers15,7131
Non-polymers3451
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.050, 45.580, 36.670
Angle α, β, γ (deg.)90.00, 102.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cellular retinoic acid-binding protein 2 / Cellular retinoic acid-binding protein II / CRABP-II


Mass: 15713.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRABP2 / Production host: Escherichia coli (E. coli) / References: UniProt: P29373
#2: Chemical ChemComp-9U5 / 4-[2-(4,4-dimethyl-1-propan-2-yl-quinolin-6-yl)ethynyl]benzoic acid


Mass: 345.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H23NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 1.71 Å3/Da / Density % sol: 28.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, Na Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.0388 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0388 Å / Relative weight: 1
ReflectionResolution: 1.8→35.77 Å / Num. obs: 9030 / % possible obs: 91.1 % / Redundancy: 2.6 % / Net I/σ(I): 6.2

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
Aimlessdata scaling
BUCCANEERmodel building
Cootmodel building
REFMAC5.8.0158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FR3

2fr3


Resolution: 1.8→35.77 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.635 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.165 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23582 468 5.2 %RANDOM
Rwork0.17341 ---
obs0.17675 8554 90.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.969 Å2
Baniso -1Baniso -2Baniso -3
1-3.98 Å2-0 Å20.13 Å2
2---1.57 Å2-0 Å2
3----2.23 Å2
Refinement stepCycle: 1 / Resolution: 1.8→35.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1078 0 26 62 1166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191128
X-RAY DIFFRACTIONr_bond_other_d0.0020.021079
X-RAY DIFFRACTIONr_angle_refined_deg1.6811.9561525
X-RAY DIFFRACTIONr_angle_other_deg0.9622.9732504
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3935135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.92725.10249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.02515215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.446157
X-RAY DIFFRACTIONr_chiral_restr0.0970.2173
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021220
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02219
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7512.087540
X-RAY DIFFRACTIONr_mcbond_other1.7452.085539
X-RAY DIFFRACTIONr_mcangle_it2.793.109672
X-RAY DIFFRACTIONr_mcangle_other2.7923.111673
X-RAY DIFFRACTIONr_scbond_it2.3572.408588
X-RAY DIFFRACTIONr_scbond_other2.3592.41587
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8463.477853
X-RAY DIFFRACTIONr_long_range_B_refined7.56923.9821176
X-RAY DIFFRACTIONr_long_range_B_other7.54123.7961168
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 31 -
Rwork0.277 462 -
obs--67.81 %

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