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- PDB-8dn1: Q108K:K40L:T51C:T53A:R58L:Q38F:Q4F mutant of hCRBPII bound to syn... -

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Basic information

Entry
Database: PDB / ID: 8dn1
TitleQ108K:K40L:T51C:T53A:R58L:Q38F:Q4F mutant of hCRBPII bound to synthetic fluorophore CM1V at pH 7.2
ComponentsRetinol-binding protein 2
KeywordsTRANSPORT PROTEIN / hCRBPII / cellular retinol binding protein II / covalently bound fluorophore
Function / homology
Function and homology information


vitamin A metabolic process / molecular carrier activity / retinoid binding / retinal binding / retinol binding / epidermis development / fatty acid transport / Retinoid metabolism and 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
Chem-RH6 / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsBingham, C.R. / Borhan, B. / Geiger, J.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB) United States
CitationJournal: Analyst / Year: 2023
Title: Light controlled reversible Michael addition of cysteine: a new tool for dynamic site-specific labeling of proteins.
Authors: Maity, S. / Bingham, C. / Sheng, W. / Ehyaei, N. / Chakraborty, D. / Tahmasebi-Nick, S. / Kimmel, T.E. / Vasileiou, C. / Geiger, J.H. / Borhan, B.
History
DepositionJul 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9904
Polymers15,5491
Non-polymers4423
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.222, 66.833, 63.704
Angle α, β, γ (deg.)90.000, 91.926, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-538-

HOH

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Components

#1: Protein Retinol-binding protein 2 / Cellular retinol-binding protein II / CRBP-II


Mass: 15548.548 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2 / Production host: Escherichia coli (E. coli) / References: UniProt: P50120
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-RH6 / (2E)-3-[7-(diethylamino)-2-oxo-2H-1-benzopyran-3-yl]prop-2-enal, bound form


Mass: 257.328 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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 Å3/Da / Density % sol: 38.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 25% PEG 4000, ammonium acetate, sodium acetate pH 4.0 - 4.8
PH range: 4.0 - 4.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1272 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1272 Å / Relative weight: 1
ReflectionResolution: 1.32→29.59 Å / Num. obs: 28092 / % possible obs: 98.13 % / Redundancy: 11.9 % / Biso Wilson estimate: 14.43 Å2 / Rpim(I) all: 0.024 / Rrim(I) all: 0.087 / Net I/σ(I): 30.8
Reflection shellResolution: 1.32→1.369 Å / Num. unique obs: 2805 / Rpim(I) all: 0.134 / Rrim(I) all: 0.376

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QZT

4qzt


Resolution: 1.32→29.59 Å / SU ML: 0.1259 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 20.7834
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2174 2009 7.15 %
Rwork0.188 26083 -
obs0.19 28092 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.32 Å2
Refinement stepCycle: LAST / Resolution: 1.32→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1087 0 31 157 1275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00941177
X-RAY DIFFRACTIONf_angle_d1.15631591
X-RAY DIFFRACTIONf_chiral_restr0.0859167
X-RAY DIFFRACTIONf_plane_restr0.0052205
X-RAY DIFFRACTIONf_dihedral_angle_d24.1408432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.32-1.360.26231480.22521874X-RAY DIFFRACTION98.06
1.36-1.390.23791400.22521863X-RAY DIFFRACTION98.96
1.39-1.430.26361420.22241860X-RAY DIFFRACTION98.86
1.43-1.480.22581420.21391868X-RAY DIFFRACTION98.34
1.48-1.530.23121440.19881854X-RAY DIFFRACTION97.75
1.53-1.590.1941470.19151813X-RAY DIFFRACTION97.17
1.59-1.670.19371320.1891820X-RAY DIFFRACTION95.27
1.67-1.750.22691370.19711855X-RAY DIFFRACTION98.32
1.75-1.860.20871510.18731885X-RAY DIFFRACTION99.85
1.86-2.010.20881460.17631897X-RAY DIFFRACTION99.8
2.01-2.210.20231460.17331889X-RAY DIFFRACTION99.51
2.21-2.530.22631440.1891869X-RAY DIFFRACTION98.24
2.53-3.190.24551380.19131795X-RAY DIFFRACTION93.97
3.19-29.590.20211520.18091941X-RAY DIFFRACTION99.95

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