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- PDB-3cr6: Crystal Structure of the R132K:R111L:A32E Mutant of Cellular Reti... -

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Basic information

Entry
Database: PDB / ID: 3cr6
TitleCrystal Structure of the R132K:R111L:A32E Mutant of Cellular Retinoic Acid Binding Protein Type II Complexed with C15-aldehyde (a retinal analog) at 1.22 Angstrom resolution.
ComponentsCellular retinoic acid-binding protein 2
KeywordsTRANSPORT PROTEIN / CRABPII / retinal / schiff base / protonated schiff base / PSB / C15-aldehyde / retinoic acid / retinoid / Nucleus / Retinol-binding / Transport / Vitamin A
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-LSR / Cellular retinoic acid-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.22 Å
AuthorsJia, X. / Geiger, J.H.
Citation
Journal: To be Published
Title: Two distinctive orientations of binding determined by a single mutation in the CRABPII mutant-C15-aldehyde complexes
Authors: Jia, X. / Lee, K.S. / Vasileiou, C. / Borhan, B. / Geiger, J.H.
#1: Journal: To be Published
Title: Protein engineering: wavelength regulation mechanism investigated in a rhodopsin mimic
Authors: Lee, K.S. / Jia, X. / Vasileiou, C. / Geiger, J.H. / Borhan, B.
History
DepositionApr 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 28, 2016Group: Structure summary
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 13, 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)15,7722
Polymers15,5681
Non-polymers2041
Water5,585310
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.852, 46.347, 37.324
Angle α, β, γ (deg.)90.000, 92.530, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cellular retinoic acid-binding protein 2 / Cellular retinoic acid- binding protein II / CRABP-II / Retinoic acid-binding protein II / cellular


Mass: 15567.790 Da / Num. of mol.: 1 / Mutation: R132K, R111L, A32E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRABP2 / Plasmid: CRABPII-pET17b-KL-A32E / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P29373
#2: Chemical ChemComp-LSR / 1,3,3-trimethyl-2-[(1E,3E)-3-methylpenta-1,3-dien-1-yl]cyclohexene


Mass: 204.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 1.93 Å3/Da / Density % sol: 36.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M sodium citrate, 0.2M ammonium acetate, 26% PEG 4000, pH 7.5, 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: 0.97869 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 8, 2007
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97869 Å / Relative weight: 1
ReflectionResolution: 1.03→50 Å / Num. obs: 42691 / % possible obs: 72.4 % / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.046 / Χ2: 0.982 / Net I/σ(I): 9.5
Reflection shellResolution: 1.03→1.07 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.806 / Mean I/σ(I) obs: 0.759 / Num. unique all: 284 / Χ2: 0.687 / % possible all: 4.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.533 / Cor.coef. Fo:Fc: 0.457
Highest resolutionLowest resolution
Rotation1.8 Å23.17 Å
Translation1.8 Å23.17 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
SHELXrefinement
PDB_EXTRACT3.005data extraction
EMBLdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXLrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2G7B

2g7b


Resolution: 1.22→10 Å / σ(F): 4
RfactorNum. reflection% reflectionSelection details
Rfree0.1848 1417 -Random
Rwork0.1137 ---
all0.188 32033 --
obs0.124 26990 84.2 %-
Displacement parametersBiso mean: 20.928 Å2
Refinement stepCycle: LAST / Resolution: 1.22→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1090 0 15 310 1415
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.017
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.093
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_from_restr_planes0.425
LS refinement shellResolution: 1.22→1.252 Å
RfactorNum. reflection% reflection
Rfree0.259 --
Rwork0.236 --
obs-1986 79.82 %

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