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- PDB-3d96: Crystal Structure of the R132K:Y134F Mutant of Apo-Cellular Retin... -

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Basic information

Entry
Database: PDB / ID: 3d96
TitleCrystal Structure of the R132K:Y134F Mutant of Apo-Cellular Retinoic Acid Binding Protein Type II at 1.71 Angstroms Resolution
ComponentsCellular retinoic acid-binding protein 2
KeywordsTRANSPORT PROTEIN / CRABPII / RETINOIC ACID / RETINOIDS / BETA BARREL / HIGH RESOLUTION / MUTANT / 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 / Cellular retinoic acid-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / RIGID BODY REFINEMENT / Resolution: 1.71 Å
AuthorsVaezeslami, S. / Geiger, J.H.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structural analysis of site-directed mutants of cellular retinoic acid-binding protein II addresses the relationship between structural integrity and ligand binding.
Authors: Vaezeslami, S. / Jia, X. / Vasileiou, C. / Borhan, B. / Geiger, J.H.
#1: Journal: Thesis
Title: Determining Crystal Structures of Proteins and Protein Complexes by X-Ray Crystallography: X-Ray Crystallographic Studies of the Mutants of Cellular Retinoic Acid Binding Protein Type II ...Title: Determining Crystal Structures of Proteins and Protein Complexes by X-Ray Crystallography: X-Ray Crystallographic Studies of the Mutants of Cellular Retinoic Acid Binding Protein Type II Toward Designing a Mimic of Rhodopsin
Authors: Vaezeslami, S.
History
DepositionMay 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
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 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)31,1353
Polymers31,0762
Non-polymers591
Water6,521362
1
A: Cellular retinoic acid-binding protein 2


Theoretical massNumber of molelcules
Total (without water)15,5381
Polymers15,5381
Non-polymers00
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)15,5972
Polymers15,5381
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.590, 37.230, 58.770
Angle α, β, γ (deg.)73.900, 74.820, 87.900
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 / Retinoic acid-binding protein II / cellular


Mass: 15537.788 Da / Num. of mol.: 2 / Mutation: R132K, Y134F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRABP2 / Plasmid: PET17-B / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% (W/V) PEG 4000, 0.1 M TRIS-HCL, 0.2 M SODIUM ACETATE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 27, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 26617 / % possible obs: 89.7 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 20.44
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 1.55 / % possible all: 48.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005phasing
RefinementMethod to determine structure: RIGID BODY REFINEMENT / Resolution: 1.71→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 5.839 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.081 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2298 8.9 %RANDOM
Rwork0.153 25713 --
obs0.16 25713 86.9 %-
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 max: 73.29 Å2 / Biso mean: 28.7411 Å2 / Biso min: 11.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å2-0.55 Å20.25 Å2
2---1.29 Å2-0.25 Å2
3---2.27 Å2
Refinement stepCycle: LAST / Resolution: 1.71→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2122 0 4 362 2488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222225
X-RAY DIFFRACTIONr_bond_other_d0.0010.022085
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.9573015
X-RAY DIFFRACTIONr_angle_other_deg0.80734873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3845272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47425.30698
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01115421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.31513
X-RAY DIFFRACTIONr_chiral_restr0.0930.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022407
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02416
X-RAY DIFFRACTIONr_nbd_refined0.2060.2344
X-RAY DIFFRACTIONr_nbd_other0.1920.22048
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21046
X-RAY DIFFRACTIONr_nbtor_other0.0870.21474
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2216
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2290.286
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5421.51790
X-RAY DIFFRACTIONr_mcbond_other0.4651.5560
X-RAY DIFFRACTIONr_mcangle_it1.86822257
X-RAY DIFFRACTIONr_scbond_it2.713972
X-RAY DIFFRACTIONr_scangle_it3.6694.5758
X-RAY DIFFRACTIONr_rigid_bond_restr1.35235163
X-RAY DIFFRACTIONr_sphericity_free6.73388
X-RAY DIFFRACTIONr_sphericity_bonded2.19234279
LS refinement shellResolution: 1.71→1.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.177 923 -
obs--42.42 %

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