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- PDB-2fs6: Crystal Structure of Apo-Cellular Retinoic Acid Binding Protein T... -

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Basic information

Entry
Database: PDB / ID: 2fs6
TitleCrystal Structure of Apo-Cellular Retinoic Acid Binding Protein Type II At 1.35 Angstroms Resolution
ComponentsCellular retinoic acid-binding protein 2
KeywordsTRANSPORT PROTEIN / CRABPII / Retinoic Acid / Retinoids / Beta Barrel / High Resolution
Function / homology
Function and homology information


positive regulation of collateral sprouting / retinoid binding / retinal binding / retinoic acid 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 / retinal binding / retinoic acid 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 / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding 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: 1.35 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 21, 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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)31,63511
Polymers31,1642
Non-polymers4729
Water7,044391
1
A: Cellular retinoic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9007
Polymers15,5821
Non-polymers3186
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cellular retinoic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7354
Polymers15,5821
Non-polymers1543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.449, 37.056, 56.527
Angle α, β, γ (deg.)72.68, 76.37, 87.28
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: 15581.802 Da / Num. of mol.: 2
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 / Acetate


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.15 Å3/Da / Density % sol: 42.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 30% (w/v) PEG 8000 (4000), 0.1 M TRIS-HCl pH 8.0 (8.5), and 0.2 M Sodium Acetate, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. all: 56961 / Num. obs: 50380 / % possible obs: 88.4 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.042 / Χ2: 0.591 / Net I/σ(I): 14.56
Reflection shellResolution: 1.35→1.4 Å / % possible obs: 56.5 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 1.77 / Num. unique obs: 3219 / Χ2: 0.517 / % possible all: 56.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: Rigid body refinement / Resolution: 1.35→17.24 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.636 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.204 5082 10.1 %RANDOM
Rwork0.148 ---
all0.154 50364 --
obs0.154 50364 88.4 %-
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: 16.794 Å2
Baniso -1Baniso -2Baniso -3
1--1.46 Å2-0.28 Å20.3 Å2
2---0.4 Å2-0.2 Å2
3---1.87 Å2
Refinement stepCycle: LAST / Resolution: 1.35→17.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2199 0 31 427 2657
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222251
X-RAY DIFFRACTIONr_bond_other_d0.0010.022109
X-RAY DIFFRACTIONr_angle_refined_deg1.7751.9643049
X-RAY DIFFRACTIONr_angle_other_deg0.89834915
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8185271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.19125.294102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74115421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1571514
X-RAY DIFFRACTIONr_chiral_restr0.1180.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022443
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02417
X-RAY DIFFRACTIONr_nbd_refined0.2210.2364
X-RAY DIFFRACTIONr_nbd_other0.1960.22083
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21080
X-RAY DIFFRACTIONr_nbtor_other0.0850.21503
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2279
X-RAY DIFFRACTIONr_metal_ion_refined0.1530.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.235
X-RAY DIFFRACTIONr_symmetry_vdw_other0.260.298
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.242
X-RAY DIFFRACTIONr_mcbond_it1.7741.51395
X-RAY DIFFRACTIONr_mcbond_other0.7481.5559
X-RAY DIFFRACTIONr_mcangle_it2.61922272
X-RAY DIFFRACTIONr_scbond_it3.3913884
X-RAY DIFFRACTIONr_scangle_it4.8464.5777
X-RAY DIFFRACTIONr_rigid_bond_restr1.99634527
X-RAY DIFFRACTIONr_sphericity_free7.2393429
X-RAY DIFFRACTIONr_sphericity_bonded3.35434336
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 260 -
Rwork0.233 2047 -
obs-2307 54.38 %

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