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- PDB-9d8o: Q108K:K40L:T51V:T53C:R58Y:Y19W:Q38L:Q4A:T29L mutant of hCRBPII in... -

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Basic information

Entry
Database: PDB / ID: 9d8o
TitleQ108K:K40L:T51V:T53C:R58Y:Y19W:Q38L:Q4A:T29L mutant of hCRBPII in complex with FR1V in the dark state at pH 3.0
ComponentsRetinol-binding protein 2
KeywordsRETINOL BINDING PROTEIN / human cellular retinol binding protein II / hCRBPII / transport protein / fluorescent protein / protein engineering
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 / Chem-ZFJ / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsBingham, 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: Photoswitching fluorescence via a novel Trp-flap mechanism
Authors: Bingham, C. / Ehyaei, N. / Maity, S. / Cantrell, J. / Gwasdacus, J. / Sheng, W. / Vasileiou, C. / Babak, B. / Geiger, J.H.
History
DepositionAug 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Retinol-binding protein 2
A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,20510
Polymers31,1072
Non-polymers1,0978
Water3,585199
1
B: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1946
Polymers15,5541
Non-polymers6415
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0104
Polymers15,5541
Non-polymers4573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.031, 35.866, 63.915
Angle α, β, γ (deg.)85.840, 86.520, 65.300
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: 15553.569 Da / Num. of mol.: 2 / Mutation: Q108K:K40L:T51V:T53C:R58Y:Y19W:Q38L:Q4A:T29L
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.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ZFJ / (4aP)-N,N-diethyl-9,9-dimethyl-7-[(1E)-prop-1-en-1-yl]-9H-fluoren-2-amine


Mass: 305.456 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H27N / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.07 Å3/Da / Density % sol: 40.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: PEG4000, ammonium acetate, 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: Apr 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.32→32.54 Å / Num. obs: 49318 / % possible obs: 84.04 % / Redundancy: 9.8 % / CC1/2: 0.93 / CC star: 0.982 / Rpim(I) all: 0.015 / Rrim(I) all: 0.049 / Net I/σ(I): 84.2
Reflection shellResolution: 1.32→1.34 Å / Num. unique obs: 3896 / CC1/2: 0.93 / Rpim(I) all: 0.146 / Rrim(I) all: 0.37

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.32→32.54 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2368 --
Rwork0.2 --
obs-49318 84.04 %
Displacement parametersBiso mean: 23.76 Å2
Refinement stepCycle: LAST / Resolution: 1.32→32.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2180 0 78 199 2457
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00692317
X-RAY DIFFRACTIONf_angle_d0.85893128
X-RAY DIFFRACTIONf_chiral_restr0.0782329
X-RAY DIFFRACTIONf_plane_restr0.0069391
X-RAY DIFFRACTIONf_dihedral_angle_d19.34011340

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