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- PDB-3cwk: Crystal Structure of the R132K:Y134F:R111L:T54V:L121E Mutant of C... -

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Basic information

Entry
Database: PDB / ID: 3cwk
TitleCrystal Structure of the R132K:Y134F:R111L:T54V:L121E Mutant of Cellular Retinoic Acid Binding Protein Type II in Complex with All-trans-Retinoic Acid at 1.57 Angstroms Resolution
ComponentsCellular retinoic acid-binding protein 2
KeywordsTRANSPORT PROTEIN / CRABPII / RETINOIC ACID / RETINOIDS / BETA BARREL / HIGH RESOLUTION / 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 / 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
RETINOIC ACID / Cellular retinoic acid-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / RIGID BODY REFINEMENT / Resolution: 1.6 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
DepositionApr 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9043
Polymers15,5081
Non-polymers3962
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.787, 44.860, 77.865
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 / Retinoic acid-binding protein II / cellular


Mass: 15507.735 Da / Num. of mol.: 1 / Mutation: T54V, R111L, L121E, 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-REA / RETINOIC ACID


Mass: 300.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.58 Å3/Da / Density % sol: 52.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES, 30% (W/V) PEG 5000, 0.2 M AMMONIUM SULFATE, pH 6.50, 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: Mar 13, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 21826 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.05 / Net I/σ(I): 27.28
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.157 / % possible all: 100

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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: 1.6→39.47 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.15 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.167 2110 9.9 %RANDOM
Rwork0.12 ---
obs0.125 19203 97.7 %-
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: 14.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2--0.13 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.6→39.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1146 0 27 238 1411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221190
X-RAY DIFFRACTIONr_bond_other_d0.0020.021122
X-RAY DIFFRACTIONr_angle_refined_deg1.8811.9841615
X-RAY DIFFRACTIONr_angle_other_deg0.96532635
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2315140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.9792655
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.33215238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.868156
X-RAY DIFFRACTIONr_chiral_restr0.1250.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021259
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02208
X-RAY DIFFRACTIONr_nbd_refined0.2120.2202
X-RAY DIFFRACTIONr_nbd_other0.2010.21141
X-RAY DIFFRACTIONr_nbtor_refined0.180.2578
X-RAY DIFFRACTIONr_nbtor_other0.0860.2792
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2174
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3140.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2471.5907
X-RAY DIFFRACTIONr_mcbond_other0.8111.5282
X-RAY DIFFRACTIONr_mcangle_it2.5721164
X-RAY DIFFRACTIONr_scbond_it3.9093558
X-RAY DIFFRACTIONr_scangle_it5.1274.5449
X-RAY DIFFRACTIONr_rigid_bond_restr2.30532743
X-RAY DIFFRACTIONr_sphericity_free9.1163238
X-RAY DIFFRACTIONr_sphericity_bonded3.68632295
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.193 113 -
Rwork0.115 1139 -
obs--79.09 %

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