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- PDB-7a9z: Structural comparison of cellular retinoic acid binding protein I... -

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Basic information

Entry
Database: PDB / ID: 7a9z
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
Chem-R62 / Cellular retinoic acid-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 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 23, 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
AAA: Cellular retinoic acid-binding protein 1
BBB: Cellular retinoic acid-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4853
Polymers31,1512
Non-polymers3341
Water70339
1
AAA: Cellular retinoic acid-binding protein 1
hetero molecules

BBB: Cellular retinoic acid-binding protein 1


Theoretical massNumber of molelcules
Total (without water)31,4853
Polymers31,1512
Non-polymers3341
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z+1/31
2
BBB: Cellular retinoic acid-binding protein 1

AAA: Cellular retinoic acid-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4853
Polymers31,1512
Non-polymers3341
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+y+1,-x,z-1/31
Unit cell
Length a, b, c (Å)127.545, 127.545, 52.161
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 3 - 136 / Label seq-ID: 3 - 136

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AAAA
22BBBB

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 (E. coli) / References: UniProt: P29762
#2: Chemical ChemComp-R62 / 4-[2-(5,5,8,8-tetramethyl-6,7-dihydroquinoxalin-2-yl)ethynyl]benzoic acid


Mass: 334.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H22N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.93 Å3/Da / Density % sol: 68.72 %
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: I04 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.41→110.46 Å / Num. obs: 19102 / % possible obs: 99.9 % / Redundancy: 19.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.123 / Rrim(I) all: 0.392 / Net I/σ(I): 7.1
Reflection shellResolution: 2.41→2.5 Å / Redundancy: 16.8 % / Rmerge(I) obs: 6.347 / Num. unique obs: 33328 / CC1/2: 0.398 / Rpim(I) all: 2.287 / Rrim(I) all: 6.751

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
REFMAC5.8.0266refinement
XDS0.7.4data processing
XDSdata reduction
PHASERphasing
Cootmodel building
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CBR

1cbr


Resolution: 2.41→110.457 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.931 / SU B: 10.06 / SU ML: 0.202 / Cross valid method: FREE R-VALUE / ESU R: 0.244 / ESU R Free: 0.214
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.25 848 4.445 %
Rwork0.2047 18230 -
all0.207 --
obs-19078 99.806 %
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: 53.96 Å2
Baniso -1Baniso -2Baniso -3
1-1.143 Å20.572 Å20 Å2
2--1.143 Å2-0 Å2
3----3.709 Å2
Refinement stepCycle: LAST / Resolution: 2.41→110.457 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2141 0 25 39 2205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132225
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182061
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.6553016
X-RAY DIFFRACTIONr_angle_other_deg1.281.5864735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.065273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45222.381126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.66615382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6011517
X-RAY DIFFRACTIONr_chiral_restr0.0640.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022566
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02527
X-RAY DIFFRACTIONr_nbd_refined0.1950.2298
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.21842
X-RAY DIFFRACTIONr_nbtor_refined0.1640.21023
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21214
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.265
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3780.29
X-RAY DIFFRACTIONr_nbd_other0.2090.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1450.22
X-RAY DIFFRACTIONr_mcbond_it4.7645.4071092
X-RAY DIFFRACTIONr_mcbond_other4.7475.4021091
X-RAY DIFFRACTIONr_mcangle_it7.3328.1011365
X-RAY DIFFRACTIONr_mcangle_other7.3388.1051366
X-RAY DIFFRACTIONr_scbond_it5.1585.9271132
X-RAY DIFFRACTIONr_scbond_other5.1595.9191129
X-RAY DIFFRACTIONr_scangle_it8.2558.6391651
X-RAY DIFFRACTIONr_scangle_other8.2588.6351650
X-RAY DIFFRACTIONr_lrange_it11.718101.6598643
X-RAY DIFFRACTIONr_lrange_other11.723101.6928629
X-RAY DIFFRACTIONr_ncsr_local_group_10.1540.053746
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.154070.05008
12BBBX-RAY DIFFRACTIONLocal ncs0.154070.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.41-2.4730.347650.37413190.37314060.560.55998.43530.377
2.473-2.5410.358720.33412810.33513530.6330.6661000.334
2.541-2.6140.39620.31712700.3213320.6940.7251000.315
2.614-2.6950.351710.31412180.31612890.7270.7671000.301
2.695-2.7830.315380.29711950.29812340.7750.80999.9190.284
2.783-2.8810.351400.2811810.28212220.8050.84499.91820.269
2.881-2.9890.354680.25411000.2611680.8040.8571000.235
2.989-3.1110.376290.24710960.2511250.8440.8721000.229
3.111-3.2490.262540.2210370.22210910.8970.9091000.199
3.249-3.4080.314360.2129690.21510050.8650.9181000.194
3.408-3.5920.311530.1959390.2019920.9060.9331000.18
3.592-3.810.216380.1739040.1749420.9230.9431000.161
3.81-4.0720.218430.1668430.1698860.9470.9521000.152
4.072-4.3980.118370.1287810.1288180.980.9781000.124
4.398-4.8170.135350.117230.1117580.9810.9831000.113
4.817-5.3850.119310.1346500.1336810.9830.9791000.135
5.385-6.2150.166200.1486000.1496200.9690.9741000.148
6.215-7.6060.211250.1815060.1825310.9360.9491000.185
7.606-10.7310.319150.1893990.1944150.9270.95499.7590.204
10.731-110.4570.346160.2832180.2872440.8990.94195.90160.422

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