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- PDB-4ygg: CRYSTAL STRUCTURE OF R111K:Y134F:T54V:R132Q:P39Y:R59Y MUTANT OF H... -

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Basic information

Entry
Database: PDB / ID: 4ygg
TitleCRYSTAL STRUCTURE OF R111K:Y134F:T54V:R132Q:P39Y:R59Y MUTANT OF HUMAN CELLULAR RETINOIC ACID BINDING PROTEIN II WITH RETINAL AT 1.9 ANGSTROM RESOLUTION - VISIBLE LIGHT IRRADIATED CRYSTAL - 2ND CYCLE
ComponentsCellular retinoic acid-binding protein 2
KeywordsTRANSPORT PROTEIN / Photo switchable protein / Retinal isomerization / Retinal Protonated Schiff Base 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: 1.9 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 1.1Jun 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

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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
Water2,432135
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 operation5_554x-y,-y,-z-1/31
Buried area3200 Å2
ΔGint-24 kcal/mol
Surface area13860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.199, 59.199, 100.038
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 / Retinal


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 3.25 Å3/Da / Density % sol: 62.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / 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: 1.9→50 Å / Num. obs: 16619 / % possible obs: 99.8 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.059 / Rsym value: 0.046 / Net I/σ(I): 48.04
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 11 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 4.53 / % possible all: 99.2

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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: 1.9→35.802 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 23.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2381 835 5.04 %
Rwork0.2043 --
obs0.206 16570 99.8 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.055 Å2 / ksol: 0.318 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0443 Å2-0 Å2-0 Å2
2---0.0443 Å20 Å2
3---0.0885 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35.802 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1092 0 20 135 1247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071154
X-RAY DIFFRACTIONf_angle_d1.1231564
X-RAY DIFFRACTIONf_dihedral_angle_d16.989441
X-RAY DIFFRACTIONf_chiral_restr0.085180
X-RAY DIFFRACTIONf_plane_restr0.003199
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.898-2.01690.32111410.24812555X-RAY DIFFRACTION99
2.0169-2.17260.25921520.22972562X-RAY DIFFRACTION100
2.1726-2.39120.26171180.22532600X-RAY DIFFRACTION100
2.3912-2.73720.24851510.23062597X-RAY DIFFRACTION100
2.7372-3.44810.20261330.20512658X-RAY DIFFRACTION100
3.4481-35.80850.23461400.18132763X-RAY DIFFRACTION100

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