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- PDB-7ry5: Cellular Retinoic Acid Binding Protein II with Bound Inhibitor 4-... -

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Basic information

Entry
Database: PDB / ID: 7ry5
TitleCellular Retinoic Acid Binding Protein II with Bound Inhibitor 4-[6-({4-[(fluorosulfonyl)oxy]phenyl}ethynyl)-4,4-dimethyl-3,4-dihydroquinolin-1(2H)-yl]-4-oxobutanoic acid
ComponentsCellular retinoic acid-binding protein 2
KeywordsSIGNALING PROTEIN/INHIBITOR / Inhibitor complex / SIGNALING PROTEIN-INHIBITOR complex
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 protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin
Similarity search - Domain/homology
Chem-80V / Cellular retinoic acid-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKimmel, B.R. / Mrksich, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DGE-1842165 United States
CitationJournal: Chemistry / Year: 2021
Title: Development of an Enzyme-Inhibitor Reaction Using Cellular Retinoic Acid Binding Protein II for One-Pot Megamolecule Assembly.
Authors: Kimmel, B.R. / Mrksich, M.
History
DepositionAug 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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 2
BBB: Cellular retinoic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7074
Polymers34,7882
Non-polymers9192
Water4,594255
1
AAA: Cellular retinoic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8532
Polymers17,3941
Non-polymers4591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Cellular retinoic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8532
Polymers17,3941
Non-polymers4591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.604, 69.655, 120.845
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 17393.787 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 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P29373
#2: Chemical ChemComp-80V / 4-[6-({4-[(fluorosulfonyl)oxy]phenyl}ethynyl)-4,4-dimethyl-3,4-dihydroquinolin-1(2H)-yl]-4-oxobutanoic acid


Mass: 459.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H22FNO6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.21 Å3/Da / Density % sol: 44.24 %
Description: Long thin needles growing in clusters, which had to be mechanically separated for data collection.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Sodium Acetate, 18% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 17, 2021
RadiationMonochromator: C(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 21965 / % possible obs: 99.7 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.055 / Rrim(I) all: 0.139 / Χ2: 1.621 / Net I/σ(I): 19.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 3.57 / Num. unique obs: 2169 / CC1/2: 0.877 / CC star: 0.967 / Rpim(I) all: 0.236 / Rrim(I) all: 0.602 / Χ2: 0.964 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000v714ndata reduction
HKL-2000v714ndata scaling
PHASERPhaser-2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6HKR

6hkr


Resolution: 2→35.057 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.214 / WRfactor Rwork: 0.159 / SU B: 4.204 / SU ML: 0.115 / Average fsc free: 0.9252 / Average fsc work: 0.9411 / Cross valid method: FREE R-VALUE / ESU R: 0.178 / ESU R Free: 0.168
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2333 1083 5.017 %Random
Rwork0.1754 20503 --
all0.178 ---
obs-21586 99.686 %-
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: 24.819 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.006 Å20 Å2
3----0.014 Å2
Refinement stepCycle: LAST / Resolution: 2→35.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2214 0 62 255 2531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132338
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152226
X-RAY DIFFRACTIONr_angle_refined_deg1.6681.6573167
X-RAY DIFFRACTIONr_angle_other_deg1.3481.6075126
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8475285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.37422.773119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27215423
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8511516
X-RAY DIFFRACTIONr_chiral_restr0.0740.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022779
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02521
X-RAY DIFFRACTIONr_nbd_refined0.1890.2328
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.21983
X-RAY DIFFRACTIONr_nbtor_refined0.1670.21098
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21155
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2216
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0850.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1230.29
X-RAY DIFFRACTIONr_nbd_other0.1440.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1930.228
X-RAY DIFFRACTIONr_mcbond_it2.0162.3541127
X-RAY DIFFRACTIONr_mcbond_other2.0152.3551128
X-RAY DIFFRACTIONr_mcangle_it2.9733.5191408
X-RAY DIFFRACTIONr_mcangle_other2.9733.521408
X-RAY DIFFRACTIONr_scbond_it3.2232.7871211
X-RAY DIFFRACTIONr_scbond_other3.1942.7841209
X-RAY DIFFRACTIONr_scangle_it5.0054.0271756
X-RAY DIFFRACTIONr_scangle_other4.9864.0261756
X-RAY DIFFRACTIONr_lrange_it6.48828.1092534
X-RAY DIFFRACTIONr_lrange_other6.37927.4882462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.27770.2161485X-RAY DIFFRACTION100
2.052-2.1080.267910.2091436X-RAY DIFFRACTION100
2.108-2.1690.253760.2091415X-RAY DIFFRACTION100
2.169-2.2360.282630.1981369X-RAY DIFFRACTION100
2.236-2.3090.277710.1891354X-RAY DIFFRACTION100
2.309-2.390.256690.1811281X-RAY DIFFRACTION99.926
2.39-2.480.214550.1721264X-RAY DIFFRACTION100
2.48-2.5810.269780.1941197X-RAY DIFFRACTION100
2.581-2.6960.227540.1781137X-RAY DIFFRACTION99.9161
2.696-2.8270.187660.1631139X-RAY DIFFRACTION99.9171
2.827-2.9790.286480.181050X-RAY DIFFRACTION99.7275
2.979-3.160.231650.184998X-RAY DIFFRACTION99.8122
3.16-3.3770.262470.179953X-RAY DIFFRACTION99.7009
3.377-3.6470.205510.158875X-RAY DIFFRACTION99.1435
3.647-3.9930.215370.167819X-RAY DIFFRACTION99.0741
3.993-4.4620.235390.145742X-RAY DIFFRACTION99.2376
4.462-5.1480.198320.139673X-RAY DIFFRACTION98.878
5.148-6.2940.166340.16578X-RAY DIFFRACTION99.3506
6.294-8.8530.224180.174460X-RAY DIFFRACTION98.152
8.853-35.0570.225120.223275X-RAY DIFFRACTION95.3488

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