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- PDB-4qgx: Crystal structure of the R132K:R111L:L121E mutant of Cellular Ret... -

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Basic information

Entry
Database: PDB / ID: 4qgx
TitleCrystal structure of the R132K:R111L:L121E mutant of Cellular Retinoic Acid Binding ProteinII complexed with a synthetic ligand (Merocyanine) at 1.47 angstrom resolution
ComponentsCellular retinoic acid-binding protein 2
KeywordsPROTEIN BINDING / Protein Engineering / Protein Fluorescence / Merocyanine dyes for fluorescent protein labeling / Fluorescent protein tag / Merocyanine Protonated Schiff Base Iminium
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
Chem-LMC / Cellular retinoic acid-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.471 Å
AuthorsNosrati, M. / Yapici, I. / Geiger, J.H.
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: "Turn-on" protein fluorescence: in situ formation of cyanine dyes.
Authors: Yapici, I. / Lee, K.S. / Berbasova, T. / Nosrati, M. / Jia, X. / Vasileiou, C. / Wang, W. / Santos, E.M. / Geiger, J.H. / Borhan, B.
History
DepositionMay 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Sep 9, 2020Group: Database references / Derived calculations / Structure summary
Category: struct / struct_conn ...struct / struct_conn / struct_ref_seq_dif / struct_site
Item: _struct.title / _struct_conn.pdbx_leaving_atom_flag ..._struct.title / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)31,3193
Polymers31,0512
Non-polymers2671
Water5,999333
1
A: Cellular retinoic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7932
Polymers15,5261
Non-polymers2671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cellular retinoic acid-binding protein 2


Theoretical massNumber of molelcules
Total (without water)15,5261
Polymers15,5261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Cellular retinoic acid-binding protein 2
hetero molecules

B: Cellular retinoic acid-binding protein 2


Theoretical massNumber of molelcules
Total (without water)31,3193
Polymers31,0512
Non-polymers2671
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area1200 Å2
ΔGint-8 kcal/mol
Surface area15090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.651, 36.964, 58.599
Angle α, β, γ (deg.)72.58, 76.35, 88.14
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: 15525.708 Da / Num. of mol.: 2 / Mutation: R132K, R111L, L121E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRABP2 / Plasmid: Pet17b / Production host: Escherichia coli (E. coli) / References: UniProt: P29373
#2: Chemical ChemComp-LMC / (2E,4E,6E)-3-methyl-6-(1,3,3-trimethyl-1,3-dihydro-2H-indol-2-ylidene)hexa-2,4-dienal / (2E,4E,6Z)-3-methyl-6-(1,3,3-trimethylindolin-2-ylidene)hexa-2,4-dienal


Mass: 267.365 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H21NO
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M bis Tris Propane, 0.2M Sodium Floride, 16% PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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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: Feb 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.47→50 Å / Num. all: 174571 / Num. obs: 45647 / % possible obs: 96.5 % / Redundancy: 4 % / Rmerge(I) obs: 0.045 / Rsym value: 0.034 / Net I/σ(I): 31.5
Reflection shellResolution: 1.47→1.5 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.371 / % possible all: 93.6

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Processing

Software
NameVersionClassification
HKL-3000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2G7B

2g7b


Resolution: 1.471→35.239 Å / SU ML: 0.44 / σ(F): 1.99 / Phase error: 22.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2204 2212 5.02 %
Rwork0.1887 --
obs0.1903 44036 96.29 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.962 Å2 / ksol: 0.375 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0184 Å2-0.0015 Å20.0959 Å2
2---0.0016 Å20.037 Å2
3---0.0201 Å2
Refinement stepCycle: LAST / Resolution: 1.471→35.239 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2174 0 19 333 2526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062284
X-RAY DIFFRACTIONf_angle_d1.2523105
X-RAY DIFFRACTIONf_dihedral_angle_d14.04879
X-RAY DIFFRACTIONf_chiral_restr0.073362
X-RAY DIFFRACTIONf_plane_restr0.004391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4711-1.50310.29391340.25342473X-RAY DIFFRACTION91
1.5031-1.5380.29151450.22952521X-RAY DIFFRACTION95
1.538-1.57650.22561200.21582604X-RAY DIFFRACTION95
1.5765-1.61910.2351230.19822614X-RAY DIFFRACTION95
1.6191-1.66680.25821360.1972599X-RAY DIFFRACTION95
1.6668-1.72060.26241300.19582618X-RAY DIFFRACTION96
1.7206-1.7820.23231350.19772581X-RAY DIFFRACTION96
1.782-1.85340.24451310.19532627X-RAY DIFFRACTION96
1.8534-1.93770.24811290.18792645X-RAY DIFFRACTION97
1.9377-2.03990.20631240.19592635X-RAY DIFFRACTION97
2.0399-2.16770.22851630.19232642X-RAY DIFFRACTION97
2.1677-2.3350.21931670.18962616X-RAY DIFFRACTION97
2.335-2.56990.24011230.20242649X-RAY DIFFRACTION98
2.5699-2.94160.2551420.20852679X-RAY DIFFRACTION98
2.9416-3.70550.19621690.17342660X-RAY DIFFRACTION99
3.7055-35.24950.17871410.16262661X-RAY DIFFRACTION98

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