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- PDB-4yko: Crystal structure of the R111K:Y134F:T54V:R132Q:P39Q:R59Y:A32Y:F3... -

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Basic information

Entry
Database: PDB / ID: 4yko
TitleCrystal structure of the R111K:Y134F:T54V:R132Q:P39Q:R59Y:A32Y: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 / Rhodopsin mimic / Photoswitchable protein / Retinal isomerization / Retinal PSB / Protein engineering / Retinal iminium pKa change by isomerization
Function / homology
Function and homology information


positive regulation of collateral sprouting / retinoid binding / retinoic acid binding / retinal 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 / retinoic acid binding / retinal 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 / cytoplasm / 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
RETINAL / Cellular retinoic acid-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsNosrati, M. / Geiger, J.
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 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Oct 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: Cellular retinoic acid-binding protein 2
B: Cellular retinoic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8024
Polymers31,2342
Non-polymers5692
Water5,386299
1
A: Cellular retinoic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9012
Polymers15,6171
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)15,9012
Polymers15,6171
Non-polymers2841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.737, 39.210, 58.402
Angle α, β, γ (deg.)86.78, 79.88, 70.83
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: 15616.798 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


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


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 20% PEG3350, 0.1M Malonate pH=6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1.0781 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 42116 / % possible obs: 93.3 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.069 / Rsym value: 0.062 / Net I/σ(I): 31
Reflection shellResolution: 1.57→1.6 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 2.55 / % possible all: 70.2

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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: 1.57→34.214 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 0.11 / Phase error: 23.55 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2236 2000 5.27 %
Rwork0.1958 --
obs0.1973 37981 89.3 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.154 Å2 / ksol: 0.384 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.4097 Å20.0871 Å2-3.5429 Å2
2---1.4669 Å2-0.9643 Å2
3---2.8766 Å2
Refinement stepCycle: LAST / Resolution: 1.57→34.214 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2188 0 40 299 2527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062275
X-RAY DIFFRACTIONf_angle_d1.1063075
X-RAY DIFFRACTIONf_dihedral_angle_d16.093865
X-RAY DIFFRACTIONf_chiral_restr0.073352
X-RAY DIFFRACTIONf_plane_restr0.005397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5674-1.60660.2824850.25591533X-RAY DIFFRACTION54
1.6066-1.65010.28741200.24062170X-RAY DIFFRACTION75
1.6501-1.69860.22991350.22742419X-RAY DIFFRACTION83
1.6986-1.75350.2481400.2212519X-RAY DIFFRACTION88
1.7535-1.81610.25451440.21412596X-RAY DIFFRACTION90
1.8161-1.88880.26571470.21972625X-RAY DIFFRACTION92
1.8888-1.97480.23011490.20792682X-RAY DIFFRACTION93
1.9748-2.07890.24311540.20142775X-RAY DIFFRACTION95
2.0789-2.20910.24271520.19632733X-RAY DIFFRACTION96
2.2091-2.37960.22741530.20012755X-RAY DIFFRACTION97
2.3796-2.6190.25341570.21612831X-RAY DIFFRACTION97
2.619-2.99780.23351550.20662783X-RAY DIFFRACTION98
2.9978-3.77620.20971560.17982808X-RAY DIFFRACTION97
3.7762-34.22260.1841530.1722752X-RAY DIFFRACTION95

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