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- PDB-3fa6: Crystal structure of the R132K:Y134F:R111L:L121D:T54V mutant of c... -

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Basic information

Entry
Database: PDB / ID: 3fa6
TitleCrystal structure of the R132K:Y134F:R111L:L121D:T54V mutant of cellular retinoic acid-binding protein II complexed with C15-aldehyde (a retinal analog) at 1.54 angstrom resolution
ComponentsCellular retinoic acid-binding protein 2
KeywordsTRANSPORT PROTEIN / CRABPII / retinal / protonated Schiff base / PSB / C15-aldehyde / retinoic acid / retinoid / Cytoplasm / 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 / 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
Chem-LSR / Cellular retinoic acid-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.54 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
DepositionNov 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 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 1.3Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.4Oct 30, 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
B: Cellular retinoic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3964
Polymers30,9872
Non-polymers4092
Water6,575365
1
A: Cellular retinoic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6982
Polymers15,4941
Non-polymers2041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cellular retinoic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6982
Polymers15,4941
Non-polymers2041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.261, 89.634, 90.621
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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, R111L, 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-LSR / 1,3,3-trimethyl-2-[(1E,3E)-3-methylpenta-1,3-dien-1-yl]cyclohexene


Mass: 204.351 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.44 Å3/Da / Density % sol: 49.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 0.1M sodium acetate, 18% PEG6000, pH 5.8, 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: Aug 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: 1.54→63.76 Å / Num. obs: 45260 / % possible obs: 98.7 % / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 31.3
Reflection shellResolution: 1.54→1.6 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 2.5 / % possible all: 96.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 1.54→32.16 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.08 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22055 2279 5 %RANDOM
Rwork0.17142 ---
obs0.17388 42922 98.72 %-
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: 25.613 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20 Å2
2--0.13 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.54→32.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2170 0 30 365 2565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222337
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.9863176
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1285304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93425.842101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4915456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8091511
X-RAY DIFFRACTIONr_chiral_restr0.1080.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021709
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2880.31081
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3240.51596
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2290.5501
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.337
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2490.540
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.55821463
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.06332322
X-RAY DIFFRACTIONr_scbond_it2.3592988
X-RAY DIFFRACTIONr_scangle_it2.9623836
X-RAY DIFFRACTIONr_rigid_bond_restr2.82932451
X-RAY DIFFRACTIONr_sphericity_free5.5833394
X-RAY DIFFRACTIONr_sphericity_bonded5.17232289
LS refinement shellResolution: 1.54→1.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 178 -
Rwork0.217 3001 -
obs--95.75 %

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