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- PDB-6e5e: Crystal structure of the apo domain-swapped dimer Q108K:T51D muta... -

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Basic information

Entry
Database: PDB / ID: 6e5e
TitleCrystal structure of the apo domain-swapped dimer Q108K:T51D mutant of human cellular retinol binding protein II
ComponentsRetinol-binding protein 2
KeywordsLIPID BINDING PROTEIN / Retinol / iLBP / Protein Switch / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


vitamin A metabolic process / retinoid binding / retinal binding / retinol binding / epidermis development / Retinoid metabolism and transport / fatty acid transport / fatty acid binding / nucleus / cytosol
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Lipocalin/cytosolic fatty-acid binding domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.696 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 20, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8495
Polymers15,6121
Non-polymers2364
Water1,15364
1
A: Retinol-binding protein 2
hetero molecules

A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,69710
Polymers31,2252
Non-polymers4728
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area9300 Å2
ΔGint-39 kcal/mol
Surface area13290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.218, 63.757, 36.739
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: 15612.487 Da / Num. of mol.: 1 / Mutation: Q108K, T51D
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: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.26 Å3/Da / Density % sol: 45.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 4000 PEG, sodium acetate, ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.696→36.74 Å / Num. obs: 16292 / % possible obs: 99.71 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.22 / Rrim(I) all: 0.1 / Net I/σ(I): 10.6
Reflection shellResolution: 1.696→1.757 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.3

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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: 2RCQ

2rcq


Resolution: 1.696→36.739 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.33
RfactorNum. reflection% reflection
Rfree0.2424 1608 9.91 %
Rwork0.2042 --
obs0.2081 16228 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.696→36.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1086 0 16 65 1167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071127
X-RAY DIFFRACTIONf_angle_d0.8341517
X-RAY DIFFRACTIONf_dihedral_angle_d2.652933
X-RAY DIFFRACTIONf_chiral_restr0.055164
X-RAY DIFFRACTIONf_plane_restr0.004198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6959-1.75070.3041380.30911271X-RAY DIFFRACTION97
1.7507-1.81320.28181390.26581296X-RAY DIFFRACTION100
1.8132-1.88580.31481460.24571313X-RAY DIFFRACTION100
1.8858-1.97170.26021520.22651302X-RAY DIFFRACTION100
1.9717-2.07560.27581500.22091319X-RAY DIFFRACTION100
2.0756-2.20560.24351420.21951325X-RAY DIFFRACTION100
2.2056-2.37590.24481440.21471325X-RAY DIFFRACTION100
2.3759-2.61490.29111430.2191332X-RAY DIFFRACTION100
2.6149-2.99320.27331520.2141330X-RAY DIFFRACTION100
2.9932-3.77050.25391470.1921364X-RAY DIFFRACTION100
3.7705-36.74760.19051550.17971443X-RAY DIFFRACTION100

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