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

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Basic information

Entry
Database: PDB / ID: 9ddu
TitleQ108K:K40L:T51V:T53C:R58Y:Y19W:Q38L:Q4A:T29L mutant of hCRBPII bound to FR1V and irradiated with UV light at pH 3.0
ComponentsRetinol-binding protein 2
KeywordsRETINOL BINDING PROTEIN / human cellular retinol binding protein II / hCRBPII / protein engineering / fluorescent protein / FR1V
Function / homology
Function and homology information


vitamin A metabolic process / 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
ACETIC ACID / Chem-ZFJ / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.599 Å
AuthorsBingham, C. / Geiger, J.H.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)
CitationJournal: To Be Published
Title: Photoswitching fluorescence via a novel Trp-flap mechanism
Authors: Bingham, C. / Ehyeai, N. / Maity, S. / Cantrell, J. / Gwasdacus, J. / Sheng, W. / Vasileiou, C. / Borhan, B. / Geiger, J.H.
History
DepositionAug 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 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)32,63515
Polymers31,1072
Non-polymers1,52813
Water1,982110
1
B: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3808
Polymers15,5541
Non-polymers8267
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2557
Polymers15,5541
Non-polymers7026
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.021, 35.939, 64.043
Angle α, β, γ (deg.)86.010, 86.510, 65.280
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
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-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
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.08 Å3/Da / Density % sol: 40.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: PEG4000, ammonium acetate, sodium acetate, pH 4.0-4.8
PH range: 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: 1.272 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: 1.272 Å / Relative weight: 1
ReflectionResolution: 1.599→29.63 Å / Num. obs: 29102 / % possible obs: 87.82 % / Redundancy: 6.5 % / Rpim(I) all: 0.038 / Rrim(I) all: 0.097 / Net I/σ(I): 88.1
Reflection shellResolution: 1.599→1.657 Å / Num. unique obs: 2868 / CC1/2: 0.928 / CC star: 0.981 / Rpim(I) all: 0.192 / Rrim(I) all: 0.447 / % possible all: 85.63

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Processing

Software
NameVersionClassification
PHENIX1.16refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.599→29.63 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2179 --
Rwork0.1928 --
obs-29102 87.82 %
Displacement parametersBiso mean: 27.96 Å2
Refinement stepCycle: LAST / Resolution: 1.599→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2177 0 106 110 2393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01742337
X-RAY DIFFRACTIONf_angle_d1.1513147
X-RAY DIFFRACTIONf_chiral_restr0.0747329
X-RAY DIFFRACTIONf_plane_restr0.0089391
X-RAY DIFFRACTIONf_dihedral_angle_d19.7141346

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