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- PDB-3i17: Crystal structure of the apo R132K:L121E mutant of cellular retin... -

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Basic information

Entry
Database: PDB / ID: 3i17
TitleCrystal structure of the apo R132K:L121E mutant of cellular retinoic acid-binding protein II at 1.68 angstrom resolution
ComponentsCellular retinoic acid-binding protein 2
Keywordslipid binding / retinal binding / CRABPII / retinoic acid / retinoid / Nucleus / Retinol-binding / Transport / Vitamin A
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 / cytoplasm / cytosol
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
Cellular retinoic acid-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsJia, X. / Watson, C.T. / Geiger, J.H.
CitationJournal: Proteins / Year: 2009
Title: Elucidating the exact role of engineered CRABPII residues for the formation of a retinal protonated Schiff base.
Authors: Vasileiou, C. / Wang, W. / Jia, X. / Lee, K.S. / Watson, C.T. / Geiger, J.H. / Borhan, B.
History
DepositionJun 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 28, 2016Group: Structure summary
Revision 1.3Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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


Theoretical massNumber of molelcules
Total (without water)31,1392
Polymers31,1392
Non-polymers00
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-10 kcal/mol
Surface area15000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.699, 37.271, 60.371
Angle α, β, γ (deg.)105.80, 106.44, 89.97
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: 15569.745 Da / Num. of mol.: 2 / Mutation: R132K, L121E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRABP2 / Plasmid: CRABPII-pET17b-KE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P29373
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.31 Å3/Da / Density % sol: 46.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 0.1 M Bis-tris-propane, pH 9.5, 30% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.99999 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 9, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.68→55.56 Å / Num. obs: 30624 / % possible obs: 94.5 % / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 20.8
Reflection shellResolution: 1.68→1.724 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 4 / Num. unique all: 2025 / % possible all: 90.95

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2G7B

2g7b


Resolution: 1.68→35.74 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.704 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23095 1536 5 %RANDOM
Rwork0.18001 ---
all0.18259 ---
obs0.18259 29087 96.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.287 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.14 Å21.74 Å2
2---0.9 Å2-0.11 Å2
3---1.6 Å2
Refinement stepCycle: LAST / Resolution: 1.68→35.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2180 0 0 224 2404
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222212
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.963007
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8955289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.98725.62596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13815410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.3731511
X-RAY DIFFRACTIONr_chiral_restr0.0910.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021633
X-RAY DIFFRACTIONr_nbd_refined0.2150.3916
X-RAY DIFFRACTIONr_nbtor_refined0.3230.51518
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.5303
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.356
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2430.526
X-RAY DIFFRACTIONr_mcbond_it1.421437
X-RAY DIFFRACTIONr_mcangle_it2.18232262
X-RAY DIFFRACTIONr_scbond_it1.3412891
X-RAY DIFFRACTIONr_scangle_it2.0563736
LS refinement shellResolution: 1.68→1.724 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 86 -
Rwork0.251 2025 -
obs-2025 90.95 %

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