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- PDB-4ybp: Crystal structure of the R111K:Y134F:T54V:R132Q:P39Q:R59Y mutant ... -

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Basic information

Entry
Database: PDB / ID: 4ybp
TitleCrystal structure of the R111K:Y134F:T54V:R132Q:P39Q:R59Y mutant of human cellular retinoic acid binding proteinii with retinal after 24 hour incubation at 1.83 angstrom resolution - thermodynamic product - 1st cycle
ComponentsCellular retinoic acid-binding protein 2
KeywordsTRANSPORT PROTEIN / Protein Engineering / Photo switchable proteins / Retinal isomerization / Retinal Protonated Schiff Base pKa change
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 / cytosol / cytoplasm
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
RETINAL / Cellular retinoic acid-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.831 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 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Oct 23, 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)15,8282
Polymers15,5441
Non-polymers2841
Water3,243180
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)31,6564
Polymers31,0872
Non-polymers5692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465y-1,x+1,-z1
Buried area3180 Å2
ΔGint-24 kcal/mol
Surface area13790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.552, 58.552, 99.392
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: 15543.747 Da / Num. of mol.: 1 / Mutation: R111K, Y134F, T54V, P39Q, R132Q, 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


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.: 180 / 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: 3.16 Å3/Da / Density % sol: 61.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6 / Details: 12% PEG3350, 8% Tacsimate 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: Feb 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 17982 / % possible obs: 100 % / Redundancy: 10.5 % / Biso Wilson estimate: 22.54 Å2 / Rmerge(I) obs: 0.071 / Χ2: 0.911 / Net I/av σ(I): 36.1 / Net I/σ(I): 8.1 / Num. measured all: 189007
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.83-1.8610.60.5233.88610.564100
1.86-1.910.60.4599020.558100
1.9-1.9310.70.3548470.587100
1.93-1.9710.60.3118990.611100
1.97-2.0110.70.2598910.61100
2.01-2.0610.70.2048770.615100
2.06-2.1110.60.1768930.622100
2.11-2.1710.80.1628870.646100
2.17-2.2310.60.1298680.638100
2.23-2.3110.70.1179060.672100
2.31-2.3910.70.1058790.658100
2.39-2.4810.60.0989020.68100
2.48-2.610.60.0798950.706100
2.6-2.7310.60.0728930.742100
2.73-2.910.60.0689020.918100
2.9-3.1310.50.0739071.513100
3.13-3.4410.30.079252.27799.9
3.44-3.9410.20.0639042.528100
3.94-4.9710.20.0399371.319100
4.97-509.50.02710070.78899.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G7B

2g7b


Resolution: 1.831→35.493 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 0.24 / Phase error: 20.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2384 912 5.1 %
Rwork0.1857 --
obs0.1882 17868 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.964 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.5702 Å20 Å2-0 Å2
2--0.5702 Å20 Å2
3----1.1404 Å2
Refinement stepCycle: LAST / Resolution: 1.831→35.493 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1089 0 20 180 1289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071189
X-RAY DIFFRACTIONf_angle_d1.2111623
X-RAY DIFFRACTIONf_dihedral_angle_d14.646464
X-RAY DIFFRACTIONf_chiral_restr0.082189
X-RAY DIFFRACTIONf_plane_restr0.005208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8307-1.92730.27471430.23612338X-RAY DIFFRACTION100
1.9273-2.0480.22021260.19942394X-RAY DIFFRACTION100
2.048-2.20610.24751250.18772387X-RAY DIFFRACTION100
2.2061-2.42810.2561240.19572420X-RAY DIFFRACTION100
2.4281-2.77930.25971430.20732398X-RAY DIFFRACTION100
2.7793-3.50110.25181200.18592447X-RAY DIFFRACTION99
3.5011-35.49930.21121310.16432572X-RAY DIFFRACTION100

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