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- PDB-2frs: Crystal structure of the f15w mutant of apo-cellular retinoic aci... -

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Basic information

Entry
Database: PDB / ID: 2frs
TitleCrystal structure of the f15w mutant of apo-cellular retinoic acid binding protein type ii at 1.51 angstroms resolution
ComponentsCellular retinoic acid-binding protein 2
KeywordsTRANSPORT PROTEIN / CRABPII / Retinoic Acid / Retinoids / Beta Barrel / High Resolution / Mutant
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
Cellular retinoic acid-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Rigid body refinement / Resolution: 1.51 Å
AuthorsVaezeslami, S. / Geiger, J.H.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: The structure of Apo-wild-type cellular retinoic acid binding protein II at 1.4 A and its relationship to ligand binding and nuclear translocation.
Authors: Vaezeslami, S. / Mathes, E. / 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
DepositionJan 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 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)31,3346
Polymers31,2422
Non-polymers924
Water7,855436
1
A: Cellular retinoic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7135
Polymers15,6211
Non-polymers924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cellular retinoic acid-binding protein 2


Theoretical massNumber of molelcules
Total (without water)15,6211
Polymers15,6211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.582, 37.030, 58.693
Angle α, β, γ (deg.)102.00, 106.12, 93.00
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: 15620.839 Da / Num. of mol.: 2 / Mutation: F15W
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% (w/v) PEG 4000, 0.2 M Bis-Tris-Propane pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 16, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.51→50 Å / Num. all: 42559 / Num. obs: 39496 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.032 / Χ2: 0.306 / Net I/σ(I): 14.38
Reflection shellResolution: 1.51→1.56 Å / % possible obs: 75 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 1.69 / Num. unique obs: 3188 / Χ2: 0.279 / % possible all: 75

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: Rigid body refinement / Resolution: 1.51→33.9 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.627 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24 3946 10 %RANDOM
Rwork0.174 ---
all0.18 35549 --
obs0.18 35549 92.7 %-
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: 18.305 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å2-0.11 Å20.2 Å2
2---1.14 Å2-0.11 Å2
3---1.73 Å2
Refinement stepCycle: LAST / Resolution: 1.51→33.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2047 0 4 468 2519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222079
X-RAY DIFFRACTIONr_bond_other_d0.0010.021910
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.9532815
X-RAY DIFFRACTIONr_angle_other_deg0.86234457
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6925253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.69125.05493
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.51315384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9071513
X-RAY DIFFRACTIONr_chiral_restr0.1020.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022258
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02395
X-RAY DIFFRACTIONr_nbd_refined0.2310.2392
X-RAY DIFFRACTIONr_nbd_other0.2040.21980
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2972
X-RAY DIFFRACTIONr_nbtor_other0.0870.21392
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.2265
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1980.21
X-RAY DIFFRACTIONr_metal_ion_refined0.2640.28
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2350.282
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.229
X-RAY DIFFRACTIONr_mcbond_it1.431.51282
X-RAY DIFFRACTIONr_mcbond_other0.561.5526
X-RAY DIFFRACTIONr_mcangle_it2.28722086
X-RAY DIFFRACTIONr_scbond_it3.0713836
X-RAY DIFFRACTIONr_scangle_it4.5574.5729
X-RAY DIFFRACTIONr_rigid_bond_restr1.71534194
X-RAY DIFFRACTIONr_sphericity_free5.6393472
X-RAY DIFFRACTIONr_sphericity_bonded2.93433957
LS refinement shellResolution: 1.51→1.55 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 250 -
Rwork0.196 2027 -
obs-2277 72.54 %

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