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- PDB-5f6b: Crystal structure of the Q108K:K40L:T51V:R58Y:Y19W mutant of huma... -

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Basic information

Entry
Database: PDB / ID: 5f6b
TitleCrystal structure of the Q108K:K40L:T51V:R58Y:Y19W mutant of human Cellular Retinol Binding Protein II in complex with All-trans-Retinal at 1.3 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 / 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 / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding 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: 1.31 Å
AuthorsNosrati, M. / Nossoni, Z. / Geiger, J.H.
CitationJournal: To Be Published
Title: Crystal structure of the Q108K:K40L:T51V:R58Y:Y19W mutant of human Cellular Retinol Binding ProteinII in complex with All-trans-Retinal at 1.31 Angstrom Resolution
Authors: Nossoni, Z. / Nosrati, M. / Wang, W. / Berbasova, T. / Vasileiou, C. / Borhan, B. / Geiger, J.H.
History
DepositionDec 5, 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

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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)31,9066
Polymers31,2192
Non-polymers6874
Water6,251347
1
A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9533
Polymers15,6101
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)15,9533
Polymers15,6101
Non-polymers3432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.953, 35.721, 64.937
Angle α, β, γ (deg.)90.85, 88.45, 65.68
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: 15609.524 Da / Num. of mol.: 2 / Mutation: Q108K, K40L, T51V, R58Y, 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-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.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O

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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: 39.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 25 %PEG 4000, 0.1 M Ammonium Acetate, 0.1 M 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-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.31→50 Å / Num. all: 184981 / Num. obs: 59171 / % possible obs: 94.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 38.98
Reflection shellResolution: 1.31→1.33 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.9 / % possible all: 89.2

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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: 1.31→28.76 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 24.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.235 2843 5.08 %
Rwork0.2014 --
obs0.2031 55972 94.47 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.875 Å2 / ksol: 0.431 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.4462 Å2-0.3679 Å2-0.035 Å2
2--0.7365 Å2-0.0906 Å2
3----1.1828 Å2
Refinement stepCycle: LAST / Resolution: 1.31→28.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2195 0 48 347 2590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072289
X-RAY DIFFRACTIONf_angle_d1.1463087
X-RAY DIFFRACTIONf_dihedral_angle_d15.194840
X-RAY DIFFRACTIONf_chiral_restr0.073327
X-RAY DIFFRACTIONf_plane_restr0.005401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3079-1.33040.37921110.32872492X-RAY DIFFRACTION87
1.3304-1.35460.3671070.31032618X-RAY DIFFRACTION92
1.3546-1.38070.33431470.2972614X-RAY DIFFRACTION93
1.3807-1.40890.34891530.28812588X-RAY DIFFRACTION94
1.4089-1.43950.27411500.25912678X-RAY DIFFRACTION94
1.4395-1.4730.26291610.25452591X-RAY DIFFRACTION94
1.473-1.50980.26851450.23732666X-RAY DIFFRACTION95
1.5098-1.55060.26211430.22872635X-RAY DIFFRACTION94
1.5506-1.59630.25571380.21852690X-RAY DIFFRACTION96
1.5963-1.64780.27211310.2112693X-RAY DIFFRACTION95
1.6478-1.70670.21921360.21192692X-RAY DIFFRACTION95
1.7067-1.7750.22571490.21552707X-RAY DIFFRACTION96
1.775-1.85580.23851440.20812717X-RAY DIFFRACTION97
1.8558-1.95360.22081340.19212675X-RAY DIFFRACTION97
1.9536-2.0760.19061650.19312717X-RAY DIFFRACTION97
2.076-2.23620.24541470.19542736X-RAY DIFFRACTION97
2.2362-2.46110.24721620.19512696X-RAY DIFFRACTION98
2.4611-2.8170.23881350.1952769X-RAY DIFFRACTION97
2.817-3.54810.19741640.17292728X-RAY DIFFRACTION98
3.5481-28.7670.24731210.19852427X-RAY DIFFRACTION86
Refinement TLS params.Method: refined / Origin x: -1.5966 Å / Origin y: -1.9457 Å / Origin z: 15.4886 Å
111213212223313233
T0.158 Å2-0.0099 Å20.0004 Å2-0.1353 Å2-0.0011 Å2--0.1544 Å2
L0.0419 °2-0.0803 °2-0.0017 °2--0.1787 °2-0.1023 °2--1.1197 °2
S0.0031 Å °-0.012 Å °-0.0161 Å °0.0069 Å °-0.039 Å °-0.013 Å °-0.0382 Å °0.0071 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

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