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- PDB-6hkr: Human Cellular Retinoic Acid Binding Protein II (CRABPII) with bo... -

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Basic information

Entry
Database: PDB / ID: 6hkr
TitleHuman Cellular Retinoic Acid Binding Protein II (CRABPII) with bound synthetic retinoid DC271.
ComponentsCellular retinoic acid-binding protein 2
KeywordsSIGNALING PROTEIN / Retinoid / Fluorescent / DC271 / CRABPII
Function / homology
Function and homology information


positive regulation of collateral sprouting / retinoid binding / retinoic acid binding / retinal 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 / retinoic acid binding / retinal 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 / cytosol / cytoplasm
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
Chem-G9Q / Cellular retinoic acid-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsTomlinson, C. / Chisholm, D. / Whiting, A. / Pohl, E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
CitationJournal: ACS Med Chem Lett / Year: 2018
Title: Novel Fluorescence Competition Assay for Retinoic Acid Binding Proteins.
Authors: Tomlinson, C.W.E. / Chisholm, D.R. / Valentine, R. / Whiting, A. / Pohl, E.
History
DepositionSep 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 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)16,5016
Polymers15,7131
Non-polymers7885
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint6 kcal/mol
Surface area8090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.689, 47.479, 77.733
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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 / Plasmid: pGEX4T1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P29373

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Non-polymers , 5 types, 136 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-G9Q / 4-[2-(4,4-dimethyl-1-propan-2-yl-2,3-dihydroquinolin-6-yl)ethynyl]benzoic acid


Mass: 347.450 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H25NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG5000, TRIS HCL, Sodium Acetate / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.5→40.55 Å / Num. obs: 27170 / % possible obs: 100 % / Redundancy: 6.3 % / Net I/σ(I): 2.3
Reflection shellResolution: 1.5→1.53 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FR3

2fr3


Resolution: 1.5→40.55 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.222 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.06 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17548 1374 5.1 %RANDOM
Rwork0.14292 ---
obs0.14462 25796 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.184 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å2-0 Å2
2---0.12 Å20 Å2
3---0.08 Å2
Refinement stepCycle: 1 / Resolution: 1.5→40.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1088 0 49 131 1268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0141166
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171089
X-RAY DIFFRACTIONr_angle_refined_deg1.9031.681573
X-RAY DIFFRACTIONr_angle_other_deg1.1331.6662554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8815141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.09322.75958
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.57415213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.656158
X-RAY DIFFRACTIONr_chiral_restr0.1020.2154
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021271
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02201
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_it1.5331.182555
X-RAY DIFFRACTIONr_mcbond_other1.5161.181554
X-RAY DIFFRACTIONr_mcangle_it21.783693
X-RAY DIFFRACTIONr_mcangle_other2.0061.784694
X-RAY DIFFRACTIONr_scbond_it2.7621.586611
X-RAY DIFFRACTIONr_scbond_other2.7621.587611
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3182.208879
X-RAY DIFFRACTIONr_long_range_B_refined3.17724.7674666
X-RAY DIFFRACTIONr_long_range_B_other3.17724.7634666
X-RAY DIFFRACTIONr_rigid_bond_restr2.28132254
X-RAY DIFFRACTIONr_sphericity_free23.255542
X-RAY DIFFRACTIONr_sphericity_bonded11.35752327
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 83 -
Rwork0.165 1886 -
obs--99.95 %

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