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- PDB-8w02: Q108K:K40L:T51V:T53S:R58W mutant of hCRBPII bound to synthetic fl... -

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Basic information

Entry
Database: PDB / ID: 8w02
TitleQ108K:K40L:T51V:T53S:R58W mutant of hCRBPII bound to synthetic fluorophore TD-1V
ComponentsRetinol-binding protein 2
KeywordsRETINOL BINDING PROTEIN / human cellular retinol binding protein II / hCRBPII / TD-1V / engineered protein / fluorescent protein
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
: / ACETATE ION / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.499 Å
AuthorsGhanbarpour, A. / Geiger, J.H. / Borhan, B.
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: Regulation of Emission via a Protein-Bound Fluorophore
Authors: Santos, E.M. / Chandra, I. / Assar, Z. / Sheng, W. / Ghanbarpour, A. / Bingham, C.R. / Vasileiou, C. / Geiger, J.H. / Borhan, B.
History
DepositionFeb 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2024Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5805
Polymers31,1912
Non-polymers3893
Water2,684149
1
A: Retinol-binding protein 2
hetero molecules


  • defined by author&software
  • 15.7 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)15,6552
Polymers15,5951
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Retinol-binding protein 2
hetero molecules


  • defined by author
  • 15.9 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)15,9263
Polymers15,5951
Non-polymers3302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.889, 36.209, 64.081
Angle α, β, γ (deg.)90.320, 91.860, 113.620
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: 15595.499 Da / Num. of mol.: 2 / Mutation: Q108K:K40L:T51V:T53S:R58W
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 / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-A1AEQ / (2E)-3-{5-[4-(dimethylamino)phenyl]thiophen-2-yl}but-2-enal


Mass: 271.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17NOS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.04 Å3/Da / Density % sol: 39.58 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: ammonium acetate, PEG 4000, sodium acetate / PH range: 4.0 - 4.8 / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.499→27.36 Å / Num. obs: 39448 / % possible obs: 96.4 % / Redundancy: 3.9 % / Biso Wilson estimate: 21.22 Å2 / CC1/2: 0.882 / Rpim(I) all: 0.027 / Rrim(I) all: 0.052 / Net I/av σ(I): 41.07 / Net I/σ(I): 20.8
Reflection shellResolution: 1.499→1.553 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.24 / Num. unique obs: 11993 / CC1/2: 0.89 / CC star: 0.97 / Rpim(I) all: 0.281 / Rrim(I) all: 0.555 / % possible all: 94.4

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Processing

Software
NameVersionClassification
PHENIX1.16refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4QYN

4qyn


Resolution: 1.499→27.36 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2375 --
Rwork0.2071 --
obs-38091 96.33 %
Displacement parametersBiso mean: 32.33 Å2
Refinement stepCycle: LAST / Resolution: 1.499→27.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2090 0 26 149 2265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01682177
X-RAY DIFFRACTIONf_angle_d1.77552963
X-RAY DIFFRACTIONf_chiral_restr0.0876330
X-RAY DIFFRACTIONf_plane_restr0.009383
X-RAY DIFFRACTIONf_dihedral_angle_d14.21231258

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