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- PDB-6e6l: Crystal structure of the holo retinal-bound domain-swapped dimer ... -

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Basic information

Entry
Database: PDB / ID: 6e6l
TitleCrystal structure of the holo retinal-bound domain-swapped dimer Q108K:K40L:T51F:Y60A mutant of human cellular retinol binding protein II
ComponentsRetinol-binding protein 2
KeywordsLIPID BINDING PROTEIN / iLBP / Protein Switch
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 beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / RETINAL / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsGhanbarpour, A. / Geiger, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Engineering the hCRBPII Domain-Swapped Dimer into a New Class of Protein Switches.
Authors: Ghanbarpour, A. / Pinger, C. / Esmatpour Salmani, R. / Assar, Z. / Santos, E.M. / Nosrati, M. / Pawlowski, K. / Spence, D. / Vasileiou, C. / Jin, X. / Borhan, B. / Geiger, J.H.
History
DepositionJul 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)15,8803
Polymers15,5361
Non-polymers3432
Water79344
1
A: Retinol-binding protein 2
hetero molecules

A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7606
Polymers31,0732
Non-polymers6874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
Buried area8330 Å2
ΔGint-46 kcal/mol
Surface area14010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.765, 60.554, 36.573
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 15536.456 Da / Num. of mol.: 1 / Mutation: Q108K, K40L, T51F, Y60A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P50120
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
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: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, sodium acetate, Ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.08→43.909 Å / Num. obs: 8971 / % possible obs: 99.9 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.094 / Net I/σ(I): 34.2
Reflection shellResolution: 2.08→2.154 Å / Rmerge(I) obs: 1.2 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 442 / CC1/2: 0.787 / Rpim(I) all: 0.336 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RCT

2rct


Resolution: 2.08→43.909 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.77
RfactorNum. reflection% reflection
Rfree0.2479 893 9.97 %
Rwork0.1979 --
obs0.2029 8955 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.08→43.909 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1091 0 9 44 1144
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071128
X-RAY DIFFRACTIONf_angle_d0.8141520
X-RAY DIFFRACTIONf_dihedral_angle_d6.431935
X-RAY DIFFRACTIONf_chiral_restr0.051165
X-RAY DIFFRACTIONf_plane_restr0.004197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0801-2.21040.28721500.23121316X-RAY DIFFRACTION100
2.2104-2.38110.28031470.21311310X-RAY DIFFRACTION100
2.3811-2.62060.30761390.22031329X-RAY DIFFRACTION100
2.6206-2.99980.30291530.22841322X-RAY DIFFRACTION100
2.9998-3.77910.24271500.19041353X-RAY DIFFRACTION100
3.7791-43.91920.20981540.18051432X-RAY DIFFRACTION99

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