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- PDB-8d6n: Q108K:K40L:T53A:R58L:Q38F:Q4F mutant of hCRBPII bound to syntheti... -

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Basic information

Entry
Database: PDB / ID: 8d6n
TitleQ108K:K40L:T53A:R58L:Q38F:Q4F mutant of hCRBPII bound to synthetic fluorophore CM1V
ComponentsRetinol-binding protein 2
KeywordsTRANSPORT PROTEIN / hCRBPII
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 / MALONIC ACID / Chem-RH6 / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsBingham, C.R. / 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: Analyst / Year: 2023
Title: Light controlled reversible Michael addition of cysteine: a new tool for dynamic site-specific labeling of proteins.
Authors: Maity, S. / Bingham, C. / Sheng, W. / Ehyaei, N. / Chakraborty, D. / Tahmasebi-Nick, S. / Kimmel, T.E. / Vasileiou, C. / Geiger, J.H. / Borhan, B.
History
DepositionJun 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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
Revision 1.2Mar 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 16, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,83414
Polymers15,5471
Non-polymers1,28713
Water77543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.612, 67.106, 63.903
Angle α, β, γ (deg.)90.000, 90.108, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Retinol-binding protein 2 / Cellular retinol-binding protein II / CRBP-II


Mass: 15546.509 Da / Num. of mol.: 1 / Mutation: Q108K, K40L, T53A, R58L, Q38F, Q4F
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, 56 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-RH6 / (2E)-3-[7-(diethylamino)-2-oxo-2H-1-benzopyran-3-yl]prop-2-enal, bound form


Mass: 257.328 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19NO2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.04 Å3/Da / Density % sol: 39.77 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 4
Details: PEG 4000, Ammonium Acetate, Sodium Acetate, pH 4.0 - 4.8
PH range: pH 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: 1.1272 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1272 Å / Relative weight: 1
ReflectionResolution: 1.42→33.55 Å / Num. obs: 22948 / % possible obs: 97.28 % / Redundancy: 6.4 % / Biso Wilson estimate: 16.18 Å2 / Rpim(I) all: 0.014 / Rrim(I) all: 0.036 / Net I/σ(I): 22949
Reflection shellResolution: 1.42→1.47 Å / Num. unique obs: 2284 / CC1/2: 0.987 / Rpim(I) all: 0.079 / Rrim(I) all: 0.198 / % possible all: 96.21

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QYP

4qyp


Resolution: 1.42→33.55 Å / SU ML: 0.166 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 25.0478
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2326 1987 8.66 %
Rwork0.2127 20948 -
obs0.2145 22935 97.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.5 Å2
Refinement stepCycle: LAST / Resolution: 1.42→33.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1093 0 87 43 1223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00741195
X-RAY DIFFRACTIONf_angle_d0.84871594
X-RAY DIFFRACTIONf_chiral_restr0.0914164
X-RAY DIFFRACTIONf_plane_restr0.0037203
X-RAY DIFFRACTIONf_dihedral_angle_d24.2131436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.460.31611390.2561462X-RAY DIFFRACTION95.87
1.46-1.50.2951440.25661489X-RAY DIFFRACTION97.26
1.5-1.540.25381330.23551499X-RAY DIFFRACTION97.61
1.54-1.590.27011430.231491X-RAY DIFFRACTION97.38
1.59-1.650.26511420.21041479X-RAY DIFFRACTION95.47
1.65-1.710.22951290.2151423X-RAY DIFFRACTION94.81
1.71-1.790.21491480.21061517X-RAY DIFFRACTION98.64
1.79-1.880.2521450.20921517X-RAY DIFFRACTION98.4
1.88-20.24641430.20471512X-RAY DIFFRACTION98.63
2-2.160.21711450.20211532X-RAY DIFFRACTION98.47
2.16-2.370.2471470.20531496X-RAY DIFFRACTION98.5
2.37-2.720.2681430.21281526X-RAY DIFFRACTION98.41
2.72-3.420.21331370.20941436X-RAY DIFFRACTION93.52
3.42-33.550.20721490.21391569X-RAY DIFFRACTION99.02

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