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

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Basic information

Entry
Database: PDB / ID: 9psv
TitleQ108K:K40L:T51V:T53S:R58W:Y19W:L117E mutant of hCRBPII bound to fluorophore TD-1V-7
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: 1.51 Å
AuthorsGhanbarpour, A. / Bingam, 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. / Bingam, 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
B: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7786
Polymers31,2692
Non-polymers5094
Water4,432246
1
A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8893
Polymers15,6341
Non-polymers2542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8893
Polymers15,6341
Non-polymers2542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.259, 66.723, 63.954
Angle α, β, γ (deg.)90.000, 90.783, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,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.: 2 / 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-A1CKU / (2E)-3-[5-(dimethylamino)thiophen-2-yl]but-2-enal


Mass: 195.281 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13NOS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 38.38 %
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: 1.127 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: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.507→26.74 Å / Num. obs: 37540 / % possible obs: 96.34 % / Redundancy: 4 % / Biso Wilson estimate: 18.01 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 37.3
Reflection shellResolution: 1.51→1.56 Å / Rmerge(I) obs: 0.95 / Num. unique obs: 3548

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→26.74 Å / SU ML: 0.1595 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.9605
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.231 1999 5.35 %
Rwork0.2104 35399 -
obs0.2115 37398 96.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.2 Å2
Refinement stepCycle: LAST / Resolution: 1.51→26.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2188 0 32 246 2466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00952283
X-RAY DIFFRACTIONf_angle_d1.11443083
X-RAY DIFFRACTIONf_chiral_restr0.0687326
X-RAY DIFFRACTIONf_plane_restr0.0052396
X-RAY DIFFRACTIONf_dihedral_angle_d24.5376829
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.540.29751230.30532359X-RAY DIFFRACTION88.08
1.54-1.590.26231470.26642462X-RAY DIFFRACTION95.32
1.59-1.630.29121430.24762512X-RAY DIFFRACTION95.61
1.63-1.690.27071490.24432481X-RAY DIFFRACTION95.95
1.69-1.750.29131320.23022521X-RAY DIFFRACTION96.09
1.75-1.820.19271520.22352546X-RAY DIFFRACTION96.32
1.82-1.90.29441390.21412507X-RAY DIFFRACTION96.43
1.9-20.21871420.19852534X-RAY DIFFRACTION96.61
2-2.120.22451470.19882558X-RAY DIFFRACTION97.34
2.12-2.290.22221560.21172545X-RAY DIFFRACTION97.37
2.29-2.520.26661380.21432566X-RAY DIFFRACTION97.79
2.52-2.880.26291420.21992604X-RAY DIFFRACTION98.25
2.88-3.630.23431460.19562615X-RAY DIFFRACTION98.5
3.63-26.740.18361430.19342589X-RAY DIFFRACTION96.33

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