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- PDB-5f7g: Crystal structure of the Q108K:K40L:T51V:R58Y:Y19W:Q38L mutant of... -

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Basic information

Entry
Database: PDB / ID: 5f7g
TitleCrystal structure of the Q108K:K40L:T51V:R58Y:Y19W:Q38L mutant of human Cellular Retinol Binding Protein II in complex with All-trans-Retinal at 1.48 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: 1.48 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 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 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 1.2Nov 20, 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)31,9357
Polymers31,1892
Non-polymers7465
Water3,945219
1
A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9383
Polymers15,5951
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)15,9974
Polymers15,5951
Non-polymers4033
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.970, 35.722, 64.455
Angle α, β, γ (deg.)90.87, 91.33, 114.36
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: 15594.554 Da / Num. of mol.: 2 / Mutation: Q108K, K40L, T51V, R58Y, Y19W, Q38L
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.: 219 / 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: 2.01 Å3/Da / Density % sol: 38.93 %
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-D / Wavelength: 1.0781 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. all: 160420 / Num. obs: 43022 / % possible obs: 95.5 % / Redundancy: 3.9 % / Net I/σ(I): 37.3
Reflection shellResolution: 1.48→1.5 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 2.37 / % possible all: 93.6

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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: 1.48→27.288 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 24.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2519 1955 5.04 %
Rwork0.2038 --
obs0.2062 38828 95.63 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.769 Å2 / ksol: 0.408 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0121 Å2-0.1265 Å2-0.0349 Å2
2--0.133 Å20.2447 Å2
3----0.1451 Å2
Refinement stepCycle: LAST / Resolution: 1.48→27.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2192 0 52 219 2463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072351
X-RAY DIFFRACTIONf_angle_d1.1833191
X-RAY DIFFRACTIONf_dihedral_angle_d15.947877
X-RAY DIFFRACTIONf_chiral_restr0.074345
X-RAY DIFFRACTIONf_plane_restr0.012418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.5170.29741240.28052573X-RAY DIFFRACTION93
1.517-1.55810.29361610.2482589X-RAY DIFFRACTION94
1.5581-1.60390.24641360.23672545X-RAY DIFFRACTION94
1.6039-1.65570.29281460.22542601X-RAY DIFFRACTION94
1.6557-1.71480.27311210.23152635X-RAY DIFFRACTION95
1.7148-1.78350.26251500.22262623X-RAY DIFFRACTION95
1.7835-1.86460.26841340.2242624X-RAY DIFFRACTION95
1.8646-1.96290.24381430.2042626X-RAY DIFFRACTION96
1.9629-2.08580.24361390.20182633X-RAY DIFFRACTION96
2.0858-2.24680.22971430.2082689X-RAY DIFFRACTION97
2.2468-2.47280.27991330.2052674X-RAY DIFFRACTION97
2.4728-2.83030.27021330.21642689X-RAY DIFFRACTION98
2.8303-3.56460.24271430.19282726X-RAY DIFFRACTION98
3.5646-27.29220.2381490.18532646X-RAY DIFFRACTION96

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