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- PDB-6e5s: Crystal structure of holo retinal-bound domain-swapped dimer Q108... -

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Basic information

Entry
Database: PDB / ID: 6e5s
TitleCrystal structure of holo retinal-bound 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 / 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
RETINAL / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.061 Å
AuthorsNosrati, M. / Ghanbarpour, 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 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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 1.5Nov 13, 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
B: Retinol-binding protein 2
C: Retinol-binding protein 2
D: Retinol-binding protein 2
E: Retinol-binding protein 2
F: Retinol-binding protein 2
G: Retinol-binding protein 2
H: Retinol-binding protein 2
I: Retinol-binding protein 2
J: Retinol-binding protein 2
K: Retinol-binding protein 2
L: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,34119
Polymers187,35012
Non-polymers1,9917
Water11,656647
1
A: Retinol-binding protein 2
C: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5093
Polymers31,2252
Non-polymers2841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8560 Å2
ΔGint-32 kcal/mol
Surface area13500 Å2
MethodPISA
2
B: Retinol-binding protein 2
J: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5093
Polymers31,2252
Non-polymers2841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8570 Å2
ΔGint-32 kcal/mol
Surface area13330 Å2
MethodPISA
3
D: Retinol-binding protein 2
K: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5093
Polymers31,2252
Non-polymers2841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8510 Å2
ΔGint-34 kcal/mol
Surface area13340 Å2
MethodPISA
4
E: Retinol-binding protein 2
L: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5093
Polymers31,2252
Non-polymers2841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-32 kcal/mol
Surface area13260 Å2
MethodPISA
5
F: Retinol-binding protein 2
H: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5093
Polymers31,2252
Non-polymers2841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8420 Å2
ΔGint-37 kcal/mol
Surface area13400 Å2
MethodPISA
6
G: Retinol-binding protein 2
I: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7944
Polymers31,2252
Non-polymers5692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9350 Å2
ΔGint-38 kcal/mol
Surface area12930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.199, 73.792, 353.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 12 / 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-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C20H28O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 647 / 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: 2.3 Å3/Da / Density % sol: 46.61 %
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-F / Wavelength: 1.0782 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Aug 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0782 Å / Relative weight: 1
ReflectionResolution: 2.061→45.46 Å / Num. obs: 108095 / % possible obs: 91.86 % / Redundancy: 5 % / Biso Wilson estimate: 35.24 Å2 / Rrim(I) all: 0.083 / Net I/σ(I): 22
Reflection shellResolution: 2.061→2.13 Å / Rrim(I) all: 0.939

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Processing

Software
NameVersionClassification
PHENIX1.7.2_869refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RCQ

2rcq


Resolution: 2.061→45.459 Å / SU ML: 0.71 / Cross valid method: FREE R-VALUE / σ(F): 0.16 / Phase error: 29.14
RfactorNum. reflection% reflection
Rfree0.2735 2000 2.01 %
Rwork0.2223 --
obs0.2234 99364 91.84 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Bsol: 41.723 Å2 / ksol: 0.343 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.0702 Å2-0 Å2-0 Å2
2---1.3815 Å20 Å2
3----2.6887 Å2
Refinement stepCycle: LAST / Resolution: 2.061→45.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13124 0 140 647 13911
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913562
X-RAY DIFFRACTIONf_angle_d1.13918273
X-RAY DIFFRACTIONf_dihedral_angle_d17.3415060
X-RAY DIFFRACTIONf_chiral_restr0.0771949
X-RAY DIFFRACTIONf_plane_restr0.0062371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.061-2.11250.31381250.27316103X-RAY DIFFRACTION82
2.1125-2.16960.33881320.26786401X-RAY DIFFRACTION86
2.1696-2.23350.37391370.26396666X-RAY DIFFRACTION89
2.2335-2.30560.31911380.27546722X-RAY DIFFRACTION89
2.3056-2.3880.30951400.2646836X-RAY DIFFRACTION92
2.388-2.48360.33721420.27036927X-RAY DIFFRACTION92
2.4836-2.59660.38111440.27296971X-RAY DIFFRACTION93
2.5966-2.73350.33571460.26157137X-RAY DIFFRACTION94
2.7335-2.90470.31731480.25597175X-RAY DIFFRACTION95
2.9047-3.12890.29721480.24537254X-RAY DIFFRACTION96
3.1289-3.44370.26711500.22287286X-RAY DIFFRACTION96
3.4437-3.94180.27221500.20367290X-RAY DIFFRACTION95
3.9418-4.96520.21131500.17187283X-RAY DIFFRACTION94
4.9652-45.47030.21721500.19817313X-RAY DIFFRACTION91

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