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- PDB-4qgv: Crystal structure of the R132K:R111L mutant of Cellular Retinoic ... -

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Basic information

Entry
Database: PDB / ID: 4qgv
TitleCrystal structure of the R132K:R111L mutant of Cellular Retinoic Acid Binding ProteinII complexed with a synthetic ligand (Merocyanine) at 1.73 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 / 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
Chem-LMC / Cellular retinoic acid-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 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 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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 1.4Sep 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
Revision 1.5Nov 27, 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
B: Cellular retinoic acid-binding protein 2
A: Cellular retinoic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2873
Polymers31,0202
Non-polymers2671
Water3,819212
1
B: Cellular retinoic acid-binding protein 2


Theoretical massNumber of molelcules
Total (without water)15,5101
Polymers15,5101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cellular retinoic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7772
Polymers15,5101
Non-polymers2671
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)31,2873
Polymers31,0202
Non-polymers2671
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area1120 Å2
ΔGint-9 kcal/mol
Surface area14390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.785, 37.340, 60.091
Angle α, β, γ (deg.)104.53, 106.04, 90.87
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: 15509.753 Da / Num. of mol.: 2 / Mutation: R132K, R111L
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


Mass: 18.015 Da / Num. of mol.: 212 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis Tris Propane, 0.2 M Sodium Fluoride, 16% PEG 3350, 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-D / Wavelength: 1.1272 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1272 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. all: 134315 / Num. obs: 28219 / % possible obs: 95.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.045 / Rsym value: 0.035 / Net I/σ(I): 36.9
Reflection shellResolution: 1.73→1.77 Å / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 3.4 / % possible all: 94.6

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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: 1.73→35.997 Å / SU ML: 0.48 / σ(F): 2 / Phase error: 27.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2401 1423 5.04 %
Rwork0.1966 --
obs0.1989 28219 96.5 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.872 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.3485 Å2-0.1546 Å20.2293 Å2
2---0.4769 Å2-0.0802 Å2
3---0.1285 Å2
Refinement stepCycle: LAST / Resolution: 1.73→35.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2156 0 19 212 2387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072262
X-RAY DIFFRACTIONf_angle_d1.2853076
X-RAY DIFFRACTIONf_dihedral_angle_d17.076861
X-RAY DIFFRACTIONf_chiral_restr0.079364
X-RAY DIFFRACTIONf_plane_restr0.004387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7301-1.79190.37941290.28982621X-RAY DIFFRACTION95
1.7919-1.86360.30731150.25522669X-RAY DIFFRACTION95
1.8636-1.94850.3041250.23072701X-RAY DIFFRACTION95
1.9485-2.05120.28571420.21432636X-RAY DIFFRACTION96
2.0512-2.17970.27831380.20922676X-RAY DIFFRACTION96
2.1797-2.34790.27521720.21312649X-RAY DIFFRACTION97
2.3479-2.58420.26161410.21862690X-RAY DIFFRACTION97
2.5842-2.95790.25941550.19752722X-RAY DIFFRACTION98
2.9579-3.72610.21061500.17122733X-RAY DIFFRACTION98
3.7261-36.00490.20171560.18042699X-RAY DIFFRACTION98

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