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- PDB-4yh0: Crystal structure of the R111K:Y134F:T54V:R132Q:P39Y:R59Y mutant ... -

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Basic information

Entry
Database: PDB / ID: 4yh0
TitleCrystal structure of the R111K:Y134F:T54V:R132Q:P39Y:R59Y mutant of human Cellular Retinoic Acid Binding Protein II in complex with Retinal at 2.14 angstrom resolution - UV irradiated crystal - 3rd cycle
ComponentsCellular retinoic acid-binding protein 2
KeywordsTRANSPORT PROTEIN / 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 / 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 domain / Lipocalin / cytosolic fatty-acid binding protein family / 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: 2.144 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 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 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

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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)15,8632
Polymers15,5791
Non-polymers2841
Water1,65792
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)31,7264
Polymers31,1582
Non-polymers5692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465y-1,x+1,-z1
Buried area3220 Å2
ΔGint-24 kcal/mol
Surface area13860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.031, 59.031, 101.123
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: 15578.792 Da / Num. of mol.: 1 / Mutation: R111K, Y134F, T54V, R132Q, P39Y, 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.: 92 / 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: 3.26 Å3/Da / Density % sol: 62.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 12% 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-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 11730 / % possible obs: 100 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.075 / Rsym value: 0.06 / Net I/σ(I): 38.92
Reflection shellResolution: 2.14→2.18 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 4.1 / % possible all: 99.9

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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: 2.144→35.949 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 23.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2346 556 4.76 %
Rwork0.1987 --
obs0.2004 11692 99.97 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.103 Å2 / ksol: 0.32 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.6494 Å20 Å20 Å2
2---0.6494 Å2-0 Å2
3---1.2989 Å2
Refinement stepCycle: LAST / Resolution: 2.144→35.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1092 0 20 92 1204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091161
X-RAY DIFFRACTIONf_angle_d1.1671574
X-RAY DIFFRACTIONf_dihedral_angle_d16.569447
X-RAY DIFFRACTIONf_chiral_restr0.081179
X-RAY DIFFRACTIONf_plane_restr0.006203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1435-2.35920.29461290.23822749X-RAY DIFFRACTION100
2.3592-2.70050.29941410.23582723X-RAY DIFFRACTION100
2.7005-3.40190.29981470.20562758X-RAY DIFFRACTION100
3.4019-35.95410.17671390.17922906X-RAY DIFFRACTION100

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