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- PDB-9pt3: Q108K:K40L:T51V:T53S:R58W:Y19W:L117E mutant of hCRBPII bound to f... -

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Basic information

Entry
Database: PDB / ID: 9pt3
TitleQ108K:K40L:T51V:T53S:R58W:Y19W:L117E mutant of hCRBPII bound to fluorophore TD-1V-9
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: 1.79 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 29, 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
C: Retinol-binding protein 2
D: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,83612
Polymers62,5384
Non-polymers1,2988
Water5,945330
1
A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9593
Polymers15,6341
Non-polymers3242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9593
Polymers15,6341
Non-polymers3242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9593
Polymers15,6341
Non-polymers3242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9593
Polymers15,6341
Non-polymers3242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.405, 66.742, 64.217
Angle α, β, γ (deg.)89.730, 90.282, 90.101
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,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.: 4 / 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-A1CK1 / (2E)-3-[4'-(dimethylamino)[1,1'-biphenyl]-4-yl]but-2-enal


Mass: 265.350 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H19NO / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 38.45 %
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: 1.79→33.37 Å / Num. obs: 44915 / % possible obs: 96.48 % / Redundancy: 2.8 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 24.07
Reflection shellResolution: 1.79→1.84 Å / Rmerge(I) obs: 0.614 / Num. unique obs: 4209

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
Cootmodel building
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→33.37 Å / SU ML: 0.186 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 42.7768
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2552 2013 4.52 %
Rwork0.2184 42556 -
obs0.2201 44569 96.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.64 Å2
Refinement stepCycle: LAST / Resolution: 1.79→33.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4392 0 92 330 4814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00674580
X-RAY DIFFRACTIONf_angle_d0.88316173
X-RAY DIFFRACTIONf_chiral_restr0.059642
X-RAY DIFFRACTIONf_plane_restr0.006794
X-RAY DIFFRACTIONf_dihedral_angle_d16.34221647
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.830.44421160.35892807X-RAY DIFFRACTION86.66
1.83-1.880.35291560.3392974X-RAY DIFFRACTION95.87
1.88-1.940.35471590.31023034X-RAY DIFFRACTION96.09
1.94-20.34591400.28963017X-RAY DIFFRACTION96.4
2-2.070.271520.26913091X-RAY DIFFRACTION96.81
2.07-2.150.33141320.25113056X-RAY DIFFRACTION96.78
2.15-2.250.27771530.24283048X-RAY DIFFRACTION96.85
2.25-2.370.25571330.23263086X-RAY DIFFRACTION97.22
2.37-2.520.25471450.2343066X-RAY DIFFRACTION97.57
2.52-2.710.27481460.2123109X-RAY DIFFRACTION97.72
2.71-2.980.25861540.21023072X-RAY DIFFRACTION98.02
2.98-3.420.23221330.19373106X-RAY DIFFRACTION98.12
3.42-4.30.21121560.16573105X-RAY DIFFRACTION98.43
4.3-33.370.19061380.16692985X-RAY DIFFRACTION94.21

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