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- PDB-7a9y: Structural comparison of cellular retinoic acid binding protein I... -

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Basic information

Entry
Database: PDB / ID: 7a9y
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 1
KeywordsSIGNALING PROTEIN / Retinoic Acid / Retinoid / CRABP
Function / homology
Function and homology information


RA biosynthesis pathway / retinoid binding / retinoic acid binding / retinal binding / retinol binding / fatty acid transport / fatty acid binding / signal transduction / nucleus / 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
Similarity search - Domain/homology
MYRISTIC ACID / N-TRIDECANOIC ACID / Cellular retinoic acid-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 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 / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
BBB: Cellular retinoic acid-binding protein 1
AAA: Cellular retinoic acid-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6865
Polymers31,1512
Non-polymers5353
Water2,774154
1
AAA: Cellular retinoic acid-binding protein 1
hetero molecules

BBB: Cellular retinoic acid-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6865
Polymers31,1512
Non-polymers5353
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
2
BBB: Cellular retinoic acid-binding protein 1
hetero molecules

AAA: Cellular retinoic acid-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6865
Polymers31,1512
Non-polymers5353
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Unit cell
Length a, b, c (Å)36.890, 109.980, 170.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11BBB-366-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11BBB
21AAA

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 2 - 136 / Label seq-ID: 2 - 136

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11BBBA
22AAAB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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


Mass: 15575.536 Da / Num. of mol.: 2 / Mutation: L29C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRABP1, RBP5 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P29762
#2: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-TDA / N-TRIDECANOIC ACID


Mass: 214.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H26O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.77 Å3/Da / Density % sol: 55.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: PEG mixture

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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 PILATUS 6M / Detector: PIXEL / Date: Oct 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.64→36.05 Å / Num. obs: 43110 / % possible obs: 99.9 % / Redundancy: 1.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.029 / Rpim(I) all: 0.029 / Rrim(I) all: 0.029 / Net I/σ(I): 9.8
Reflection shellResolution: 1.64→1.67 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.791 / Num. unique obs: 4050 / CC1/2: 0.48 / Rpim(I) all: 0.559 / Rrim(I) all: 0.559

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
REFMAC5.8.0266refinement
Aimless0.7.4data scaling
Cootmodel building
PHASERphasing
XDSdata processing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CBR

1cbr


Resolution: 1.64→36.05 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.249 / SU ML: 0.072 / Cross valid method: FREE R-VALUE / ESU R: 0.088 / ESU R Free: 0.088
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2184 2049 4.753 %
Rwork0.1914 41059 -
all0.193 --
obs-43108 99.861 %
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: 35.424 Å2
Baniso -1Baniso -2Baniso -3
1-0.028 Å20 Å2-0 Å2
2--0.248 Å20 Å2
3----0.277 Å2
Refinement stepCycle: LAST / Resolution: 1.64→36.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2171 0 37 154 2362
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132289
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182169
X-RAY DIFFRACTIONr_angle_refined_deg1.6991.663088
X-RAY DIFFRACTIONr_angle_other_deg1.4331.5864997
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.955281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.65721.704135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.00115401
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9561521
X-RAY DIFFRACTIONr_chiral_restr0.0870.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022626
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02549
X-RAY DIFFRACTIONr_nbd_refined0.1980.2310
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.21783
X-RAY DIFFRACTIONr_nbtor_refined0.1660.21036
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0950.21173
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.2116
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0820.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2850.215
X-RAY DIFFRACTIONr_nbd_other0.2080.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.6290.27
X-RAY DIFFRACTIONr_mcbond_it3.443.3171109
X-RAY DIFFRACTIONr_mcbond_other3.4393.3171108
X-RAY DIFFRACTIONr_mcangle_it4.6614.9671389
X-RAY DIFFRACTIONr_mcangle_other4.664.9671390
X-RAY DIFFRACTIONr_scbond_it5.0983.9541180
X-RAY DIFFRACTIONr_scbond_other5.0963.9561181
X-RAY DIFFRACTIONr_scangle_it7.7795.6881697
X-RAY DIFFRACTIONr_scangle_other7.7775.691698
X-RAY DIFFRACTIONr_lrange_it9.07338.3392379
X-RAY DIFFRACTIONr_lrange_other9.06737.9122344
X-RAY DIFFRACTIONr_ncsr_local_group_10.1150.054049
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11BBBX-RAY DIFFRACTIONLocal ncs0.114980.05008
12AAAX-RAY DIFFRACTIONLocal ncs0.114980.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.729-1.7790.3181600.3092855X-RAY DIFFRACTION99.7354
1.779-1.8340.3161570.2862745X-RAY DIFFRACTION99.828
1.834-1.8940.3051260.2522660X-RAY DIFFRACTION99.8566
1.894-1.960.241210.2182606X-RAY DIFFRACTION99.8535
1.96-2.0340.2461330.2152509X-RAY DIFFRACTION100
2.034-2.1170.2441070.2152415X-RAY DIFFRACTION100
2.117-2.2110.2411090.22329X-RAY DIFFRACTION100
2.211-2.3190.2371120.1872239X-RAY DIFFRACTION99.915
2.319-2.4440.2291050.1882124X-RAY DIFFRACTION100
2.444-2.5930.223910.1852009X-RAY DIFFRACTION100
2.593-2.7710.2311040.1841881X-RAY DIFFRACTION99.9496
2.771-2.9930.191700.1631785X-RAY DIFFRACTION99.9461
2.993-3.2790.177860.1711637X-RAY DIFFRACTION99.8841
3.279-3.6650.172830.1551482X-RAY DIFFRACTION99.6181
3.665-4.2310.197710.1651319X-RAY DIFFRACTION99.8563
4.231-5.1790.187610.1531127X-RAY DIFFRACTION99.4142

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