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- PDB-3fek: Crystal structure of the R132K:Y134F:R111L:L121D:T54V mutant of c... -

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Basic information

Entry
Database: PDB / ID: 3fek
TitleCrystal structure of the R132K:Y134F:R111L:L121D:T54V mutant of cellular retinoic acid-binding protein II at 1.51 angstrom resolution
ComponentsCellular retinoic acid-binding protein 2
KeywordsTRANSPORT PROTEIN / CRABPII / 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
ACETATE ION / DI(HYDROXYETHYL)ETHER / Cellular retinoic acid-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsJia, X. / Geiger, J.H.
CitationJournal: To be Published
Title: Crystal structures of apo cellular retinoic acid-binding protein II mutants: Structural integrity investigated through multiple site mutations
Authors: Jia, X. / Lee, K.S. / Vasileiou, C. / Borhan, B. / Geiger, J.H.
History
DepositionNov 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 28, 2016Group: Structure summary
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2595
Polymers30,9872
Non-polymers2713
Water5,729318
1
A: Cellular retinoic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7654
Polymers15,4941
Non-polymers2713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cellular retinoic acid-binding protein 2


Theoretical massNumber of molelcules
Total (without water)15,4941
Polymers15,4941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.601, 37.189, 57.056
Angle α, β, γ (deg.)73.64, 76.67, 87.70
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: 15493.708 Da / Num. of mol.: 2 / Mutation: R132K, Y134F, R111, L121D, T54V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRABP2 / Plasmid: CRABPII-pET17b-KFLDV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P29373
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.21 Å3/Da / Density % sol: 44.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Tris, 0.2M NaOAc, 24% PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 13, 2007
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.51→53.5 Å / Num. obs: 39062 / % possible obs: 93.3 % / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Biso Wilson estimate: 29.6 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 46.2
Reflection shellResolution: 1.51→1.56 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 4.5 / Num. unique all: 2938 / % possible all: 70.5

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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: 1.51→33.66 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / SU B: 3.527 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21028 1961 5 %RANDOM
Rwork0.17385 ---
all0.17579 ---
obs0.17579 37100 94.25 %-
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: 29.467 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å2-0.57 Å20.36 Å2
2---2.68 Å20.57 Å2
3---2.9 Å2
Refinement stepCycle: LAST / Resolution: 1.51→33.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2170 0 15 318 2503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222304
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.973125
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.745299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.54925.6100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.85615456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3871512
X-RAY DIFFRACTIONr_chiral_restr0.0930.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021676
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.3963
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3230.51577
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.5401
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.393
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.545
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.14121468
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.91332319
X-RAY DIFFRACTIONr_scbond_it2.3342956
X-RAY DIFFRACTIONr_scangle_it3.0063791
X-RAY DIFFRACTIONr_rigid_bond_restr2.31632424
X-RAY DIFFRACTIONr_sphericity_free5.8853330
X-RAY DIFFRACTIONr_sphericity_bonded5.06932260
LS refinement shellResolution: 1.51→1.552 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 112 -
Rwork0.193 2260 -
obs-2260 77.04 %

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