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- PDB-6on8: Crystal Structure of the Reduced Form of Apo Domain-Swapped Dimer... -

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Basic information

Entry
Database: PDB / ID: 6on8
TitleCrystal Structure of the Reduced Form of Apo Domain-Swapped Dimer Q108K:T51D:A28C:L36C:F57H 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 / 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: 2.395 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
DepositionApr 20, 2019Deposition 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)15,6261
Polymers15,6261
Non-polymers00
Water1267
1
A: Retinol-binding protein 2

A: Retinol-binding protein 2


Theoretical massNumber of molelcules
Total (without water)31,2512
Polymers31,2512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7570 Å2
ΔGint-36 kcal/mol
Surface area14230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.551, 63.782, 36.966
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: 15625.511 Da / Num. of mol.: 1 / Mutation: Q108K,T51D,A28C,L36C,F57H
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.: 7 / 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: 46.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Bis-Tris:HCl, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97623 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.395→31.983 Å / Num. obs: 5892 / % possible obs: 98.15 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.087 / Net I/av σ(I): 22.64 / Net I/σ(I): 22.6
Reflection shellResolution: 2.397→2.483 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 2.31 / Num. unique obs: 501 / Rrim(I) all: 0.6 / % possible all: 85.81

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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: 2.395→31.983 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 26.33
RfactorNum. reflection% reflection
Rfree0.2577 595 10.1 %
Rwork0.183 --
obs0.1902 5892 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.395→31.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1094 0 0 7 1101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091132
X-RAY DIFFRACTIONf_angle_d0.9851528
X-RAY DIFFRACTIONf_dihedral_angle_d3.43949
X-RAY DIFFRACTIONf_chiral_restr0.058165
X-RAY DIFFRACTIONf_plane_restr0.005197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3946-2.63540.31951450.21561236X-RAY DIFFRACTION94
2.6354-3.01660.29231390.21921313X-RAY DIFFRACTION100
3.0166-3.79960.28721520.18251341X-RAY DIFFRACTION100
3.7996-31.98560.22581590.17011407X-RAY DIFFRACTION99

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