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- PDB-4i9r: Crystal Structure of the R111K:R132L:Y134F:T54V:R59W:A32W Mutant ... -

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Basic information

Entry
Database: PDB / ID: 4i9r
TitleCrystal Structure of the R111K:R132L:Y134F:T54V:R59W:A32W Mutant of the Cellular Retinoic Acid Binding Protein Type II in Complex with All-Trans Retinal at 2.6 Angstrom Resolution
ComponentsCellular retinoic acid-binding protein 2
KeywordsTRANSPORT PROTEIN / protein engineering / wavelength regulation / pH sensing / pKa / 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 / signal transduction / endoplasmic reticulum / 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: 2.6 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
DepositionDec 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references
Revision 1.2Jan 31, 2018Group: Advisory / Experimental preparation / Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.3Sep 20, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / 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 1.4Nov 6, 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)15,9202
Polymers15,6361
Non-polymers2841
Water19811
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.483, 57.483, 109.799
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: 15635.931 Da / Num. of mol.: 1 / Mutation: R111K:R132L: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.: 11 / 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: 3.35 Å3/Da / Density % sol: 63.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 2% PEG400, 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: 1.0333 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: 1.0333 Å / Relative weight: 1
ReflectionResolution: 2.6→36.878 Å / Num. obs: 6726

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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: 2.6→36.878 Å / SU ML: 0.75 / σ(F): 1.37 / Phase error: 31.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2764 335 4.98 %
Rwork0.1949 --
obs0.199 6726 98.03 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.325 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.1926 Å2-0 Å20 Å2
2---1.1926 Å2-0 Å2
3---2.3851 Å2
Refinement stepCycle: LAST / Resolution: 2.6→36.878 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1073 0 20 11 1104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011143
X-RAY DIFFRACTIONf_angle_d1.2551581
X-RAY DIFFRACTIONf_dihedral_angle_d17.861417
X-RAY DIFFRACTIONf_chiral_restr0.374178
X-RAY DIFFRACTIONf_plane_restr0.011203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6002-3.27570.35131610.25393060X-RAY DIFFRACTION97
3.2757-36.88160.25551740.17993331X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -35.2991 Å / Origin y: 15.0502 Å / Origin z: 13.2069 Å
111213212223313233
T0.3966 Å20.1444 Å2-0.0586 Å2-0.2184 Å2-0.009 Å2--0.3179 Å2
L4.7725 °2-2.872 °20.3352 °2-4.378 °2-1.08 °2--3.283 °2
S-0.2884 Å °-0.0437 Å °0.5069 Å °0.4053 Å °0.0678 Å °-0.3931 Å °-0.4659 Å °-0.1445 Å °0.1443 Å °
Refinement TLS groupSelection details: all

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