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- PDB-9dfb: Q108K:K40L:T51V:T53C:R58A:Y19W:Q38L:Q4A:T29L mutant of hCRBPII bo... -

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Basic information

Entry
Database: PDB / ID: 9dfb
TitleQ108K:K40L:T51V:T53C:R58A:Y19W:Q38L:Q4A:T29L mutant of hCRBPII bound to FR1V in the dark at pH 3.0
ComponentsRetinol-binding protein 2
KeywordsRETINOL BINDING PROTEIN / human cellular retinol binding protein II / hCRBPII / engineered protein / fluorescent 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
Chem-ZFJ / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.705 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. / Ehyaei, N. / Maity, S. / Cantrell, J. / Gwasdacus, J. / Sheng, W. / Vasileiou, C. / Borhan, B. / Geiger, J.H.
History
DepositionAug 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 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)31,5925
Polymers30,9192
Non-polymers6733
Water1,47782
1
B: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8273
Polymers15,4591
Non-polymers3682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7652
Polymers15,4591
Non-polymers3051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.964, 35.924, 63.938
Angle α, β, γ (deg.)85.701, 86.873, 65.217
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: 15459.499 Da / Num. of mol.: 2 / Mutation: Q108K:K40L:T51V:T53C:R58A: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-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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 40.92 %
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: 1.127 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.705→32.56 Å / Num. obs: 20907 / % possible obs: 76.81 % / Redundancy: 3.2 % / Rpim(I) all: 0.053 / Rrim(I) all: 0.095 / Net I/σ(I): 19.11
Reflection shellResolution: 1.705→1.765 Å / Num. unique obs: 2010 / Rpim(I) all: 0.369

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.705→32.56 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.5036
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2515 2019 9.67 %
Rwork0.2197 18855 -
obs0.2228 20874 76.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.19 Å2
Refinement stepCycle: LAST / Resolution: 1.705→32.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2130 0 50 82 2262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00842223
X-RAY DIFFRACTIONf_angle_d1.04693007
X-RAY DIFFRACTIONf_chiral_restr0.2927324
X-RAY DIFFRACTIONf_plane_restr0.0069375
X-RAY DIFFRACTIONf_dihedral_angle_d22.092786
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.705-1.750.34191190.33391200X-RAY DIFFRACTION69.35
1.75-1.790.34281660.28281515X-RAY DIFFRACTION86.34
1.79-1.850.35111650.26441486X-RAY DIFFRACTION84.58
1.85-1.910.25311590.23911499X-RAY DIFFRACTION83.61
1.91-1.970.27631430.2171417X-RAY DIFFRACTION81.85
1.97-2.050.29821570.22261433X-RAY DIFFRACTION81.08
2.05-2.150.27391410.23881415X-RAY DIFFRACTION80.83
2.15-2.260.28961520.22371437X-RAY DIFFRACTION80.66
2.26-2.40.26431380.23271342X-RAY DIFFRACTION75.74
2.4-2.590.2971320.24671276X-RAY DIFFRACTION72.32
2.59-2.850.27091210.23771040X-RAY DIFFRACTION60.47
2.85-3.260.29441150.2151076X-RAY DIFFRACTION60.92
3.26-4.10.22831490.20011264X-RAY DIFFRACTION72.91
4.11-32.560.18151620.19131455X-RAY DIFFRACTION83.22

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