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- PDB-8db2: Q108K:K40L:T51C:T53A:R58L:Q38F mutant of hCRBPII bound to synthet... -

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Basic information

Entry
Database: PDB / ID: 8db2
TitleQ108K:K40L:T51C:T53A:R58L:Q38F mutant of hCRBPII bound to synthetic fluorophore CM1V
ComponentsRetinol-binding protein 2
KeywordsTRANSPORT PROTEIN / hCRBPII
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 / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBingham, C.R. / Geiger, J.H. / Borhan, B. / Staples, R.
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
DepositionJun 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 22, 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
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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)15,7872
Polymers15,5301
Non-polymers2571
Water1,15364
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)29.075, 66.292, 63.618
Angle α, β, γ (deg.)90.000, 90.000, 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-302-

HOH

21A-364-

HOH

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Components

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


Mass: 15529.503 Da / Num. of mol.: 1 / Mutation: Q108K,K40L,T51C,T53A,R58L,Q38F
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-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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.97 Å3/Da / Density % sol: 37.69 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-3000 / Detector: PIXEL / Date: Jan 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.5→17.59 Å / Num. obs: 18253 / % possible obs: 95.8 % / Redundancy: 2.3 % / Biso Wilson estimate: 18.9 Å2 / CC1/2: 0.843 / Net I/σ(I): 24.78
Reflection shellResolution: 1.5→1.56 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 0.76 / Num. unique obs: 1828 / % possible all: 83.9

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Processing

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

4qyn


Resolution: 1.5→17.59 Å / SU ML: 0.2449 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.0313
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2681 1807 9.91 %
Rwork0.225 16434 -
obs0.2292 18241 94.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.1 Å2
Refinement stepCycle: LAST / Resolution: 1.5→17.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1090 0 19 64 1173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00641135
X-RAY DIFFRACTIONf_angle_d0.88051530
X-RAY DIFFRACTIONf_chiral_restr0.0541163
X-RAY DIFFRACTIONf_plane_restr0.0043195
X-RAY DIFFRACTIONf_dihedral_angle_d7.0437929
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.40931140.39161069X-RAY DIFFRACTION79.72
1.54-1.590.40941370.38571231X-RAY DIFFRACTION93
1.59-1.640.3931410.35731258X-RAY DIFFRACTION94.21
1.64-1.70.34211470.31661270X-RAY DIFFRACTION95.29
1.7-1.760.32841370.28211264X-RAY DIFFRACTION96.22
1.76-1.840.30041390.24681314X-RAY DIFFRACTION96.61
1.84-1.940.29051430.24041290X-RAY DIFFRACTION96.24
1.94-2.060.22091420.21061278X-RAY DIFFRACTION96.27
2.06-2.220.24881430.19831290X-RAY DIFFRACTION95.98
2.22-2.440.25871380.20591300X-RAY DIFFRACTION96.12
2.44-2.80.27091460.22221295X-RAY DIFFRACTION96.71
2.8-3.520.25221400.20771307X-RAY DIFFRACTION96.85
3.52-17.590.23931400.19571268X-RAY DIFFRACTION92.15

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