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- PDB-4m6s: Crystal structure of the R111K:R132Y:Y134F:T54V:R59W:A32W mutant ... -

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Basic information

Entry
Database: PDB / ID: 4m6s
TitleCrystal structure of the R111K:R132Y:Y134F:T54V:R59W:A32W mutant of the Cellular Retinoic Acid Binding Protein Type II in complex with All-Trans Retinal at 2.38 Angstrom Resolution
ComponentsCellular retinoic acid-binding protein 2
KeywordsTRANSPORT PROTEIN / protein engineering / wavelength regulation / pH-sensing / Retinylidene PSB / 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 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: 2.47 Å
AuthorsNosrati, M. / Geiger, J.H.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Rational Design of a Colorimetric pH Sensor from a Soluble Retinoic Acid Chaperone.
Authors: Berbasova, T. / Nosrati, M. / Vasileiou, C. / Wang, W. / Lee, K.S. / Yapici, I. / Geiger, J.H. / Borhan, B.
History
DepositionAug 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references
Revision 1.2Sep 20, 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 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1.3Oct 30, 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)15,9702
Polymers15,6861
Non-polymers2841
Water43224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.629, 56.629, 111.318
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: 15685.946 Da / Num. of mol.: 1 / Mutation: R111K:R132Y:Y134F:T54V:R59W:A32W
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-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.: 24 / 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: 3.28 Å3/Da / Density % sol: 62.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M malonate, pH 6.0, 12% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0782 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0782 Å / Relative weight: 1
ReflectionResolution: 2.38→44.88 Å / Num. obs: 8713
Reflection shellHighest resolution: 2.38 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2G7B

2g7b


Resolution: 2.47→44.88 Å / SU ML: 0.77 / σ(F): 0.28 / Phase error: 22.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2354 361 4.62 %
Rwork0.2045 --
obs0.2058 7810 99.54 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.24 Å2 / ksol: 0.331 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.996 Å2-0 Å20 Å2
2---0.996 Å2-0 Å2
3---1.9919 Å2
Refinement stepCycle: LAST / Resolution: 2.47→44.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1085 0 20 24 1129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081151
X-RAY DIFFRACTIONf_angle_d1.1281582
X-RAY DIFFRACTIONf_dihedral_angle_d17.949427
X-RAY DIFFRACTIONf_chiral_restr0.076177
X-RAY DIFFRACTIONf_plane_restr0.01203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.47-2.82790.42861390.30922406X-RAY DIFFRACTION99
2.8279-3.56270.27421060.1962461X-RAY DIFFRACTION100
3.5627-44.88720.19321160.19172582X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 30.167 Å / Origin y: -22.4683 Å / Origin z: -13.3425 Å
111213212223313233
T0.164 Å20.0365 Å20.0006 Å2-0.3972 Å20.072 Å2--0.3296 Å2
L5.657 °2-0.9216 °22.9878 °2-3.5336 °20.4263 °2--6.0262 °2
S-0.1846 Å °0.3792 Å °0.5011 Å °-0.1378 Å °-0.0844 Å °-0.2126 Å °-0.1063 Å °0.3288 Å °0.2312 Å °
Refinement TLS groupSelection details: all

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