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- PDB-9pt0: Q108K:K40L:T51V:T53S:R58W:Y19W:L117E mutant of hCRBPII bound to f... -

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Basic information

Entry
Database: PDB / ID: 9pt0
TitleQ108K:K40L:T51V:T53S:R58W:Y19W:L117E mutant of hCRBPII bound to fluorophore TD-1V-8
ComponentsRetinol-binding protein 2
KeywordsRETINOL BINDING PROTEIN / human cellular retinol binding protein II / hCRBPII / fluorescent protein / engineered protein
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
Similarity search - Domain/homology
: / ACETATE ION / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsGhanbarpour, A. / Bingham, C. / 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: To Be Published
Title: Exploring the Structure-Property Relationships of Protein/Fluorophore Complex
Authors: Santos, E. / Ghanbarpour, A. / Chandra, I. / Bingham, C. / Vasileiou, C. / Geiger, J.H. / Borhan, B.
History
DepositionJul 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9713
Polymers15,6341
Non-polymers3362
Water1,11762
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)29.303, 66.469, 64.285
Angle α, β, γ (deg.)90.000, 90.375, 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

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Components

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


Mass: 15634.491 Da / Num. of mol.: 1 / Mutation: Q108K:K40L:T51V:T53S:R58W:Y19W:L117E
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-A1CKZ / (2E)-3-[5'-(dimethylamino)[2,2'-bithiophen]-5-yl]but-2-enal


Mass: 277.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15NOS2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2 Å3/Da / Density % sol: 38.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: PEG4000, ammonium acetate, 100 mM sodium acetate, pH 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 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.64→33.23 Å / Num. obs: 14611 / % possible obs: 97.2 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 28.6
Reflection shellResolution: 1.64→1.7 Å / Rmerge(I) obs: 0.99 / Num. unique obs: 1373

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
Cootmodel building
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→33.23 Å / SU ML: 0.1714 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 21.362
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2225 1438 9.85 %
Rwork0.1745 13167 -
obs0.1791 14605 97.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.13 Å2
Refinement stepCycle: LAST / Resolution: 1.64→33.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1099 0 21 62 1182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00921148
X-RAY DIFFRACTIONf_angle_d1.01741549
X-RAY DIFFRACTIONf_chiral_restr0.3996161
X-RAY DIFFRACTIONf_plane_restr0.0044200
X-RAY DIFFRACTIONf_dihedral_angle_d25.1492416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.70.23861340.19821228X-RAY DIFFRACTION91.96
1.7-1.770.26461470.20291306X-RAY DIFFRACTION97.65
1.77-1.850.23731390.20391264X-RAY DIFFRACTION93.22
1.85-1.950.2531500.1911325X-RAY DIFFRACTION98.79
1.95-2.070.22891400.1711351X-RAY DIFFRACTION99.2
2.07-2.230.22921470.17311349X-RAY DIFFRACTION98.94
2.23-2.450.2021420.18871338X-RAY DIFFRACTION98.47
2.46-2.810.26761460.1791331X-RAY DIFFRACTION98.73
2.81-3.540.19971420.17581291X-RAY DIFFRACTION94.46
3.54-33.230.20371510.15361384X-RAY DIFFRACTION99.87

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