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- PDB-5f58: Crystal structure of the Q108K:K40L:T51V:R58F mutant of human Cel... -

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Basic information

Entry
Database: PDB / ID: 5f58
TitleCrystal structure of the Q108K:K40L:T51V:R58F mutant of human Cellular Retinol Binding Protein II in complex with All-trans-Retinal after 24 hours of incubation at 1.54 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 / 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
ACETATE ION / RETINAL / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsNosrati, M. / Nossoni, Z. / Geiger, J.H.
CitationJournal: To Be Published
Title: Crystal structure of the Q108K:K40L:T51V:R58F mutant of human Cellular Retinol Binding Protein II in complex with All-trans-Retinal after 24 hours of incubation at 1.54 Angstrom Resolution
Authors: Nossoni, Z. / Nosrati, M. / Wang, W. / Berbasova, T. / Vasileiou, C. / Borhan, B. / Geiger, J.H.
History
DepositionDec 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 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 16, 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)31,8877
Polymers31,1412
Non-polymers7465
Water4,270237
1
A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9734
Polymers15,5701
Non-polymers4033
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9143
Polymers15,5701
Non-polymers3432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.234, 35.704, 64.104
Angle α, β, γ (deg.)91.28, 90.91, 114.19
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: 15570.489 Da / Num. of mol.: 2 / Mutation: Q108K, K40L, T51V, R58F
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-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 237 / 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: 39.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 30% PEG 4000, 0.1M Ammonium Acetate, 0.1M Sodium Acetate pH = 4.5
PH range: 4-4.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0781 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 1.54→50 Å / Num. all: 136653 / Num. obs: 36188 / % possible obs: 96.1 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 31.67
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 2.17 / % possible all: 94

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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: 4EXZ

4exz


Resolution: 1.54→32.553 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 24.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2288 1734 4.99 %
Rwork0.1934 --
obs0.1951 34777 96.07 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.517 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.4245 Å2-0.0902 Å2-0.1853 Å2
2--0.5531 Å2-0.0686 Å2
3----0.9776 Å2
Refinement stepCycle: LAST / Resolution: 1.54→32.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2188 0 52 237 2477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072333
X-RAY DIFFRACTIONf_angle_d1.0813164
X-RAY DIFFRACTIONf_dihedral_angle_d15.815871
X-RAY DIFFRACTIONf_chiral_restr0.073342
X-RAY DIFFRACTIONf_plane_restr0.005412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5399-1.58520.30291280.24212705X-RAY DIFFRACTION93
1.5852-1.63640.25331410.23112703X-RAY DIFFRACTION94
1.6364-1.69490.26641300.21732726X-RAY DIFFRACTION94
1.6949-1.76270.23071330.20382711X-RAY DIFFRACTION95
1.7627-1.84290.24071380.20872700X-RAY DIFFRACTION95
1.8429-1.94010.25531520.2032755X-RAY DIFFRACTION96
1.9401-2.06160.27031520.20352764X-RAY DIFFRACTION96
2.0616-2.22080.23741390.19772775X-RAY DIFFRACTION97
2.2208-2.44420.22171720.18962746X-RAY DIFFRACTION97
2.4442-2.79770.23551470.2012832X-RAY DIFFRACTION98
2.7977-3.52410.20741550.17432791X-RAY DIFFRACTION98
3.5241-32.55980.21021470.18422835X-RAY DIFFRACTION99

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