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- PDB-8vzx: Q108K:K40L:T53A:R58F mutant of hCRBPII bound to synthetic fluorop... -

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Basic information

Entry
Database: PDB / ID: 8vzx
TitleQ108K:K40L:T53A:R58F 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: 1.47 Å
AuthorsNossoni, Z. / Bingham, C.R. / 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: Acs Chem.Biol. / Year: 2024
Title: Regulation of Absorption and Emission in a Protein/Fluorophore Complex.
Authors: Santos, E.M. / Chandra, I. / Assar, Z. / Sheng, W. / Ghanbarpour, A. / Bingham, C. / 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
Revision 1.1Aug 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 28, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 4, 2024Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)62,94910
Polymers62,1704
Non-polymers7796
Water7,242402
1
A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6012
Polymers15,5421
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6012
Polymers15,5421
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8733
Polymers15,5421
Non-polymers3302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8733
Polymers15,5421
Non-polymers3302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.451, 55.167, 69.876
Angle α, β, γ (deg.)109.940, 98.490, 101.410
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: 15542.435 Da / Num. of mol.: 4 / Mutation: Q108K:K40L:T53A:R58F
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.: 4 / 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.: 2 / Source method: obtained synthetically / Formula: C16H17NOS / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 2.03 Å3/Da / Density % sol: 39.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: ammonium acetate, sodium acetate, PEG4000 / 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-F / Wavelength: 0.97872 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.47→27.4 Å / Num. obs: 82805 / % possible obs: 95.71 % / Redundancy: 2.9 % / CC1/2: 0.896 / Net I/σ(I): 32.9
Reflection shellResolution: 1.47→1.51 Å / Num. unique obs: 16538 / CC1/2: 0.912

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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: 1.47→27.4 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.263 --
Rwork0.233 --
obs-79203 95.71 %
Displacement parametersBiso mean: 26.56 Å2
Refinement stepCycle: LAST / Resolution: 1.47→27.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4364 0 52 402 4818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00734494
X-RAY DIFFRACTIONf_angle_d1.28346048
X-RAY DIFFRACTIONf_chiral_restr0.0511644
X-RAY DIFFRACTIONf_plane_restr0.0042780
X-RAY DIFFRACTIONf_dihedral_angle_d15.28582630

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