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- PDB-4ykm: Crystal structure of the R111K:Y134F:T54V:R132Q:P39Q:R59Y:A32W:F3... -

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Basic information

Entry
Database: PDB / ID: 4ykm
TitleCrystal structure of the R111K:Y134F:T54V:R132Q:P39Q:R59Y:A32W:F3Q mutant of human Cellular Retinoic Acid Binding Protein II with Retinal at 1.58 angstrom resolution
ComponentsCellular retinoic acid-binding protein 2
KeywordsTRANSPORT PROTEIN / Photoswitchable protein / Rhodopsin mimic / Retinal isomerization / Retinal iminium pKa change / Protein engineering
Function / homology
Function and homology information


positive regulation of collateral sprouting / retinoid binding / retinal binding / retinoic acid binding / embryonic forelimb morphogenesis / retinoic acid metabolic process / retinol binding / Signaling by Retinoic Acid / epidermis development / fatty acid transport ...positive regulation of collateral sprouting / retinoid binding / retinal binding / retinoic acid binding / embryonic forelimb morphogenesis / retinoic acid metabolic process / retinol binding / Signaling by Retinoic Acid / epidermis development / fatty acid transport / cyclin binding / fatty acid binding / regulation of DNA-templated transcription / endoplasmic reticulum / signal transduction / extracellular exosome / nucleoplasm / nucleus / cytosol / cytoplasm
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
RETINAL / Cellular retinoic acid-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsNosrati, M. / Geiger, J.H.
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: A Photoisomerizing Rhodopsin Mimic Observed at Atomic Resolution.
Authors: Nosrati, M. / Berbasova, T. / Vasileiou, C. / Borhan, B. / Geiger, J.H.
History
DepositionMar 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Aug 3, 2016Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cellular retinoic acid-binding protein 2
B: Cellular retinoic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8494
Polymers31,2802
Non-polymers5692
Water6,774376
1
A: Cellular retinoic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9242
Polymers15,6401
Non-polymers2841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cellular retinoic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9242
Polymers15,6401
Non-polymers2841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.692, 39.296, 58.431
Angle α, β, γ (deg.)87.15, 80.00, 70.54
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Cellular retinoic acid-binding protein 2 / Cellular retinoic acid-binding protein II / CRABP-II


Mass: 15639.833 Da / Num. of mol.: 2 / Mutation: R111K, Y134F, T54V, R132Q, P39Q, R59Y, A32W, F3Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRABP2 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29373
#2: Chemical ChemComp-RET / RETINAL / Retinal


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


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.5 Å3/Da / Density % sol: 50.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 20% PEG3350, 0.1M Bis Tris Propane pH=6.0, 0.2M Sodium Floride

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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: 1.58→50 Å / Num. obs: 41716 / % possible obs: 95.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.064 / Rsym value: 0.048 / Net I/σ(I): 31.2
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 2.6 / % possible all: 88.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G7B

2g7b


Resolution: 1.58→31.758 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 21.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2162 2025 5.06 %
Rwork0.1819 --
obs0.1837 40016 95.73 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.327 Å2 / ksol: 0.38 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.5091 Å20.0956 Å2-0.3281 Å2
2--0.4971 Å2-0.3455 Å2
3---0.012 Å2
Refinement stepCycle: LAST / Resolution: 1.58→31.758 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2192 0 40 376 2608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072296
X-RAY DIFFRACTIONf_angle_d1.1293111
X-RAY DIFFRACTIONf_dihedral_angle_d15.402873
X-RAY DIFFRACTIONf_chiral_restr0.072356
X-RAY DIFFRACTIONf_plane_restr0.004402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5766-1.61610.29441390.24192451X-RAY DIFFRACTION87
1.6161-1.65970.25641570.21982655X-RAY DIFFRACTION95
1.6597-1.70860.24131360.21042693X-RAY DIFFRACTION94
1.7086-1.76370.25121290.19912749X-RAY DIFFRACTION96
1.7637-1.82680.25361550.19312684X-RAY DIFFRACTION96
1.8268-1.89990.2281340.19352701X-RAY DIFFRACTION95
1.8999-1.98630.23511630.19482691X-RAY DIFFRACTION96
1.9863-2.09110.23811300.19172757X-RAY DIFFRACTION96
2.0911-2.2220.2261550.18212706X-RAY DIFFRACTION97
2.222-2.39350.19641490.17732766X-RAY DIFFRACTION97
2.3935-2.63430.2181470.19342770X-RAY DIFFRACTION97
2.6343-3.01520.26091480.20082778X-RAY DIFFRACTION98
3.0152-3.79790.20111480.1642782X-RAY DIFFRACTION99
3.7979-31.76480.16651350.15692808X-RAY DIFFRACTION98

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