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- PDB-7aa0: Structural comparison of cellular retinoic acid binding protein I... -

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Basic information

Entry
Database: PDB / ID: 7aa0
TitleStructural comparison of cellular retinoic acid binding protein I and II in the presence and absence of natural and synthetic ligands
ComponentsCellular retinoic acid-binding protein 2
KeywordsSIGNALING PROTEIN / Retinoic Acid / Retinoid / CRABP
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 / Lipocalin/cytosolic fatty-acid binding domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin
Similarity search - Domain/homology
Chem-R6B / Cellular retinoic acid-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsTomlinson, C.W.E. / Cornish, K.A.S. / Pohl, E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Structure-functional relationship of cellular retinoic acid-binding proteins I and II interacting with natural and synthetic ligands.
Authors: Tomlinson, C.W.E. / Cornish, K.A.S. / Whiting, A. / Pohl, E.
History
DepositionSep 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
BBB: Cellular retinoic acid-binding protein 2
AAA: Cellular retinoic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1254
Polymers31,4262
Non-polymers6992
Water2,666148
1
BBB: Cellular retinoic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0622
Polymers15,7131
Non-polymers3491
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
AAA: Cellular retinoic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0622
Polymers15,7131
Non-polymers3491
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.550, 49.920, 67.380
Angle α, β, γ (deg.)90.000, 96.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cellular retinoic acid-binding protein 2 / Cellular retinoic acid-binding protein II / CRABP-II


Mass: 15713.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRABP2 / Production host: Escherichia coli (E. coli) / References: UniProt: P29373
#2: Chemical ChemComp-R6B / (~{E})-3-[4-(4,4-dimethyl-1-propan-2-yl-2,3-dihydroquinolin-6-yl)phenyl]prop-2-enoic acid


Mass: 349.466 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H27NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.1 Å3/Da / Density % sol: 41.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: PEG based

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.82→49.92 Å / Num. obs: 23023 / % possible obs: 97.6 % / Redundancy: 3.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.061 / Rrim(I) all: 0.089 / Net I/σ(I): 10.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9.1-49.922.90.0266040.9980.0260.037
1.82-1.863.70.73549180.4860.6781.003

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
REFMAC5.8.0266refinement
Aimless0.7.4data reduction
PHASERphasing
Cootmodel building
XDSdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OGB

5ogb


Resolution: 1.82→40.064 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.559 / SU ML: 0.133 / Cross valid method: FREE R-VALUE / ESU R: 0.162 / ESU R Free: 0.152
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2452 1125 4.888 %
Rwork0.1967 21891 -
all0.199 --
obs-23016 97.53 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 29.068 Å2
Baniso -1Baniso -2Baniso -3
1--0.042 Å2-0 Å20.705 Å2
2---1.062 Å2-0 Å2
3---0.934 Å2
Refinement stepCycle: LAST / Resolution: 1.82→40.064 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2178 0 52 148 2378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132290
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172235
X-RAY DIFFRACTIONr_angle_refined_deg1.551.6553098
X-RAY DIFFRACTIONr_angle_other_deg1.2811.5845148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9535277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.45422.414116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.03415431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0291516
X-RAY DIFFRACTIONr_chiral_restr0.0720.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022570
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02510
X-RAY DIFFRACTIONr_nbd_refined0.1860.2315
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.21981
X-RAY DIFFRACTIONr_nbtor_refined0.1630.21060
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.21252
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2118
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0150.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1990.222
X-RAY DIFFRACTIONr_nbd_other0.1910.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3080.219
X-RAY DIFFRACTIONr_mcbond_it2.2962.7791108
X-RAY DIFFRACTIONr_mcbond_other2.2922.7771107
X-RAY DIFFRACTIONr_mcangle_it3.34.1491385
X-RAY DIFFRACTIONr_mcangle_other3.3034.1511386
X-RAY DIFFRACTIONr_scbond_it3.2863.211182
X-RAY DIFFRACTIONr_scbond_other3.2873.211181
X-RAY DIFFRACTIONr_scangle_it5.2654.6271713
X-RAY DIFFRACTIONr_scangle_other5.2644.6271714
X-RAY DIFFRACTIONr_lrange_it6.65553.1878890
X-RAY DIFFRACTIONr_lrange_other6.63353.0618825
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.8670.391780.3051590X-RAY DIFFRACTION97.0896
1.867-1.9180.326750.2891564X-RAY DIFFRACTION96.9822
1.918-1.9740.319820.261508X-RAY DIFFRACTION97.2477
1.974-2.0350.3740.2411482X-RAY DIFFRACTION97.0075
2.035-2.1010.286720.2291429X-RAY DIFFRACTION97.0265
2.101-2.1750.316690.2271371X-RAY DIFFRACTION96.3211
2.175-2.2570.286630.2221349X-RAY DIFFRACTION97.9875
2.257-2.3490.286570.1981332X-RAY DIFFRACTION98.6506
2.349-2.4530.218900.1971229X-RAY DIFFRACTION98.4328
2.453-2.5730.266700.2041173X-RAY DIFFRACTION98.7291
2.573-2.7120.296610.2151122X-RAY DIFFRACTION98.0929
2.712-2.8760.249470.2031099X-RAY DIFFRACTION97.8651
2.876-3.0740.26560.1961007X-RAY DIFFRACTION97.5229
3.074-3.320.243370.185960X-RAY DIFFRACTION97.1735
3.32-3.6360.205420.174860X-RAY DIFFRACTION97.4082
3.636-4.0640.179520.184769X-RAY DIFFRACTION97.3903
4.064-4.6890.255300.151700X-RAY DIFFRACTION97.5936
4.689-5.7360.14250.156611X-RAY DIFFRACTION97.9969
5.736-8.0830.212290.175470X-RAY DIFFRACTION98.6166

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