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- PDB-4yda: Crystal structure of R111K:Y134F:T54V:R132Q:P39Q:R59Y mutant of h... -

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Basic information

Entry
Database: PDB / ID: 4yda
TitleCrystal structure of R111K:Y134F:T54V:R132Q:P39Q:R59Y mutant of human cellular retinoic acid binding proteinii with retinal at 1.95 angstrom - after 1hour visible light irradiation - 3rd cycle
ComponentsCellular retinoic acid-binding protein 2
KeywordsTRANSPORT PROTEIN / Photo switchable protein / retinal isomerization / pKa change of retinal PSB / protein engineering / rhodopsin mimic
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: 1.951 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
DepositionFeb 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Structure summary
Revision 1.2Jun 29, 2016Group: Database references
Revision 1.3Aug 3, 2016Group: Database references
Revision 1.4Sep 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 1.5Nov 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: Cellular retinoic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8282
Polymers15,5441
Non-polymers2841
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cellular retinoic acid-binding protein 2
hetero molecules

A: Cellular retinoic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6564
Polymers31,0872
Non-polymers5692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area3290 Å2
ΔGint-24 kcal/mol
Surface area13690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.509, 58.509, 99.688
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 15543.747 Da / Num. of mol.: 1 / Mutation: R111K, Y134F, T54V, R132Q, P39Q, R59Y
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.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 3.17 Å3/Da / Density % sol: 61.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 12% PEG3350, 8% Tacsimate pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 14966 / % possible obs: 99.4 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 26.69
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 2 / % possible all: 99

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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: 1.951→45.17 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 0.2 / Phase error: 21.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2405 750 5.05 %
Rwork0.1916 --
obs0.194 14837 99.38 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.867 Å2 / ksol: 0.346 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.638 Å2-0 Å2-0 Å2
2--0.638 Å20 Å2
3----1.2761 Å2
Refinement stepCycle: LAST / Resolution: 1.951→45.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1089 0 20 140 1249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081162
X-RAY DIFFRACTIONf_angle_d1.2011577
X-RAY DIFFRACTIONf_dihedral_angle_d15.428446
X-RAY DIFFRACTIONf_chiral_restr0.077182
X-RAY DIFFRACTIONf_plane_restr0.005203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9508-2.10140.28691530.24472750X-RAY DIFFRACTION99
2.1014-2.31290.24721510.20762756X-RAY DIFFRACTION99
2.3129-2.64750.26071510.2132780X-RAY DIFFRACTION99
2.6475-3.33540.25011560.19282814X-RAY DIFFRACTION99
3.3354-45.18220.21511390.17132987X-RAY DIFFRACTION100

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