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

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Basic information

Entry
Database: PDB / ID: 9psy
TitleQ108K:K40L:T51V:T53S:R58W:Y19W:L117E mutant of hCRBPII bound to fluorophore TD-1V-1
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: 1.62 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
B: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9037
Polymers31,2692
Non-polymers6345
Water2,360131
1
A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9223
Polymers15,6341
Non-polymers2872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9814
Polymers15,6341
Non-polymers3463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.297, 66.840, 64.068
Angle α, β, γ (deg.)90.000, 90.752, 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:L117
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-A1CKX / (2E)-3-(5-phenylthiophen-2-yl)but-2-enal


Mass: 228.309 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.01 Å3/Da / Density % sol: 38.68 %
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: 1.62→33.42 Å / Num. obs: 30514 / % possible obs: 96.47 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 37.8
Reflection shellResolution: 1.62→1.68 Å / Rmerge(I) obs: 0.679 / Num. unique obs: 2883

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
Cootmodel building
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→33.42 Å / SU ML: 0.2009 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.9829
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2452 1984 6.55 %
Rwork0.2206 28307 -
obs0.2223 30291 96.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.41 Å2
Refinement stepCycle: LAST / Resolution: 1.62→33.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2195 0 42 131 2368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00592298
X-RAY DIFFRACTIONf_angle_d0.86853099
X-RAY DIFFRACTIONf_chiral_restr0.0568324
X-RAY DIFFRACTIONf_plane_restr0.0044399
X-RAY DIFFRACTIONf_dihedral_angle_d23.2506834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.660.33941250.32011902X-RAY DIFFRACTION91.31
1.66-1.70.33511510.29311973X-RAY DIFFRACTION94.86
1.7-1.750.29251350.2671997X-RAY DIFFRACTION95.39
1.75-1.810.2691390.24652012X-RAY DIFFRACTION96.03
1.81-1.880.3441400.23812002X-RAY DIFFRACTION96.1
1.88-1.950.27321450.21632036X-RAY DIFFRACTION96.21
1.95-2.040.25181290.20912005X-RAY DIFFRACTION96.34
2.04-2.150.22851460.21452039X-RAY DIFFRACTION96.47
2.15-2.280.27511380.21932044X-RAY DIFFRACTION97.15
2.28-2.460.241410.23142058X-RAY DIFFRACTION97.73
2.46-2.710.33091390.2392057X-RAY DIFFRACTION97.73
2.71-3.10.25481510.23512039X-RAY DIFFRACTION97.77
3.1-3.90.22791540.20342073X-RAY DIFFRACTION97.76
3.9-33.420.18581510.19362070X-RAY DIFFRACTION96.31

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