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- PDB-9de1: Q108K:K40L:T51V:T53C:R58Y:Y19W:Q38L:Q4A:T29L mutant of hCRBPII bo... -

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Basic information

Entry
Database: PDB / ID: 9de1
TitleQ108K:K40L:T51V:T53C:R58Y:Y19W:Q38L:Q4A:T29L mutant of hCRBPII bound to FR1V in the dark at pH 6.0
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 / MALONATE ION / Chem-ZFJ / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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. / Borhan, B. / Geiger, J.H.
History
DepositionAug 28, 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

Downloads & links

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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)32,1659
Polymers31,1072
Non-polymers1,0587
Water3,855214
1
B: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2046
Polymers15,5541
Non-polymers6515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9613
Polymers15,5541
Non-polymers4082
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.032, 35.790, 63.770
Angle α, β, γ (deg.)85.897, 85.870, 65.291
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 2 molecules BA

#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

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Non-polymers , 5 types, 221 molecules

#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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.06 Å3/Da / Density % sol: 40.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 25% PEG4000, 100 mM ammonium acetate, 100 mM 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: 1.121 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: 1.121 Å / Relative weight: 1
ReflectionResolution: 1.4→32.48 Å / Num. obs: 46852 / % possible obs: 95.63 % / Redundancy: 3.1 % / Rpim(I) all: 0.053 / Rrim(I) all: 0.096 / Net I/σ(I): 32.23
Reflection shellResolution: 1.4→1.45 Å / Num. unique obs: 4549 / Rpim(I) all: 0.053 / Rrim(I) all: 0.452

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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: 1.4→32.48 Å / SU ML: 0.1534 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 23.6194
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2086 2007 4.29 %
Rwork0.1946 44787 -
obs0.1952 46794 95.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.05 Å2
Refinement stepCycle: LAST / Resolution: 1.4→32.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2184 0 76 214 2474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162320
X-RAY DIFFRACTIONf_angle_d1.15613133
X-RAY DIFFRACTIONf_chiral_restr0.0813329
X-RAY DIFFRACTIONf_plane_restr0.0065394
X-RAY DIFFRACTIONf_dihedral_angle_d23.8399842
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.440.27771440.2613076X-RAY DIFFRACTION91.4
1.44-1.470.2551290.24213138X-RAY DIFFRACTION93.72
1.47-1.520.23871510.22113120X-RAY DIFFRACTION94.27
1.52-1.570.2761530.21373197X-RAY DIFFRACTION94.71
1.57-1.620.24041290.20163189X-RAY DIFFRACTION94.94
1.62-1.690.22331420.20623148X-RAY DIFFRACTION95.2
1.69-1.760.21761490.20893184X-RAY DIFFRACTION95.5
1.76-1.860.22541380.19873233X-RAY DIFFRACTION96.07
1.86-1.970.20481390.19183251X-RAY DIFFRACTION96.64
1.97-2.130.20981400.19413222X-RAY DIFFRACTION96.75
2.13-2.340.20381500.19263246X-RAY DIFFRACTION97.11
2.34-2.680.23411470.2073263X-RAY DIFFRACTION97.68
2.68-3.370.19511460.19063282X-RAY DIFFRACTION97.91
3.37-32.480.18581500.17753238X-RAY DIFFRACTION96.66

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