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- PDB-6e51: Crystal structure of the apo domain-swapped dimer Q108K:K40L:T51W... -

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Basic information

Entry
Database: PDB / ID: 6.0E+51
TitleCrystal structure of the apo domain-swapped dimer Q108K:K40L:T51W mutant of human cellular retinol binding protein II
ComponentsRetinol-binding protein 2
KeywordsLIPID BINDING PROTEIN / Retinol / 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
Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.256 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 19, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Retinol-binding protein 2


Theoretical massNumber of molelcules
Total (without water)15,6681
Polymers15,6681
Non-polymers00
Water181
1
A: Retinol-binding protein 2

A: Retinol-binding protein 2


Theoretical massNumber of molelcules
Total (without water)31,3352
Polymers31,3352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
Buried area9130 Å2
ΔGint-40 kcal/mol
Surface area14000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.077, 60.828, 36.855
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: 15667.587 Da / Num. of mol.: 1 / Mutation: Q108K, K40L, T51W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2
Production host: Bacterial expression vector pBEN1-SGC (others)
References: UniProt: P50120
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, ammonium acetate, Sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.978 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.256→36.85 Å / Num. obs: 7191 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 43.08 Å2 / Rmerge(I) obs: 0.12 / Rrim(I) all: 0.128 / Net I/σ(I): 28.5
Reflection shellResolution: 2.26→2.3 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.2 / Mean I/σ(I) obs: 2.41 / Num. unique obs: 10581 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RCT

2rct


Resolution: 2.256→36.85 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.01
RfactorNum. reflection% reflection
Rfree0.2874 716 9.96 %
Rwork0.2081 --
obs0.216 7187 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.256→36.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1101 0 18 1 1120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091144
X-RAY DIFFRACTIONf_angle_d1.0761538
X-RAY DIFFRACTIONf_dihedral_angle_d16.884419
X-RAY DIFFRACTIONf_chiral_restr0.042163
X-RAY DIFFRACTIONf_plane_restr0.004198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2557-2.42980.3681420.25181246X-RAY DIFFRACTION99
2.4298-2.67430.33971410.26141272X-RAY DIFFRACTION100
2.6743-3.06110.33561370.25411287X-RAY DIFFRACTION100
3.0611-3.8560.29921470.20321288X-RAY DIFFRACTION100
3.856-36.85990.24161490.18031378X-RAY DIFFRACTION100

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