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- PDB-5ffh: Crystal structure of the Q108K:K40L:T51V:R58W:Y19W mutant of huma... -

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Basic information

Entry
Database: PDB / ID: 5ffh
TitleCrystal structure of the Q108K:K40L:T51V:R58W:Y19W mutant of human Cellular Retinol Binding Protein II in complex with All-trans-Retinal at 1.68 Angstrom Resolution
ComponentsRetinol-binding protein 2
KeywordsTRANSPORT PROTEIN / all-trans retinal / retinal light absorbing pigment / wavelength regulation
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 / RETINAL / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsNossoni, Z. / Nosrati, M. / Geiger, J.H.
CitationJournal: To Be Published
Title: Crystal structure of the Q108K:K40L:T51V:R58W:Y19W mutant of human Cellular Retinol Binding ProteinII in complex with All-trans-Retinal at 1.68 Angstrom Resolution
Authors: Nossoni, Z. / Nosrati, M. / Wang, W. / Berbasova, T. / Vasileiou, C. / Borhan, B. / Geiger, J.H.
History
DepositionDec 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 1.2Oct 23, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9526
Polymers31,2652
Non-polymers6874
Water3,621201
1
A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9763
Polymers15,6331
Non-polymers3432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9763
Polymers15,6331
Non-polymers3432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.964, 35.914, 64.568
Angle α, β, γ (deg.)90.63, 91.28, 113.89
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 15632.562 Da / Num. of mol.: 2 / Mutation: Q108K, K40L, T51V, R58W, Y19W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P50120
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 25% PEG4000, 0.1M Ammonium Acetate, 0.1M Sodium Acetate
PH range: 4.0-4.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 25558 / % possible obs: 91 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 20.43
Reflection shellResolution: 1.68→1.75 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.486 / % possible all: 70

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Processing

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

2rct


Resolution: 1.68→32.828 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 29.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2671 1304 5.1 %
Rwork0.2159 --
obs0.2185 25558 91.12 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.227 Å2 / ksol: 0.358 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.4491 Å20.239 Å2-0.1618 Å2
2--0.2008 Å20.0903 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 1.68→32.828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2200 0 33 201 2434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082276
X-RAY DIFFRACTIONf_angle_d1.23069
X-RAY DIFFRACTIONf_dihedral_angle_d16.583828
X-RAY DIFFRACTIONf_chiral_restr0.084325
X-RAY DIFFRACTIONf_plane_restr0.008398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.74730.36821100.33072067X-RAY DIFFRACTION70
1.7473-1.82680.33761460.29182387X-RAY DIFFRACTION81
1.8268-1.92310.3021320.24872601X-RAY DIFFRACTION88
1.9231-2.04350.29351380.23792740X-RAY DIFFRACTION93
2.0435-2.20130.32271610.23492825X-RAY DIFFRACTION96
2.2013-2.42280.31081460.23622920X-RAY DIFFRACTION98
2.4228-2.77320.2891600.23452892X-RAY DIFFRACTION98
2.7732-3.49330.281580.20812904X-RAY DIFFRACTION99
3.4933-32.83440.20451530.18032918X-RAY DIFFRACTION98

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