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- PDB-5hzq: Crystal structure of cellular retinoic acid binding protein 2 (CR... -

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Basic information

Entry
Database: PDB / ID: 5hzq
TitleCrystal structure of cellular retinoic acid binding protein 2 (CRABP2)-aryl fluorosulfate covalent conjugate
ComponentsCellular retinoic acid-binding protein 2
KeywordsLIPID BINDING PROTEIN / aryl fluorosulfate / retinoic acid
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 / cytoplasm / cytosol
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
Chem-YWZ / Cellular retinoic acid-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsChen, W. / Mortenson, D.E. / Wilson, I.A. / Kelly, J.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK106582 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: Arylfluorosulfates Inactivate Intracellular Lipid Binding Protein(s) through Chemoselective SuFEx Reaction with a Binding Site Tyr Residue.
Authors: Chen, W. / Dong, J. / Plate, L. / Mortenson, D.E. / Brighty, G.J. / Li, S. / Liu, Y. / Galmozzi, A. / Lee, P.S. / Hulce, J.J. / Cravatt, B.F. / Saez, E. / Powers, E.T. / Wilson, I.A. / ...Authors: Chen, W. / Dong, J. / Plate, L. / Mortenson, D.E. / Brighty, G.J. / Li, S. / Liu, Y. / Galmozzi, A. / Lee, P.S. / Hulce, J.J. / Cravatt, B.F. / Saez, E. / Powers, E.T. / Wilson, I.A. / Sharpless, K.B. / Kelly, J.W.
History
DepositionFeb 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)32,8745
Polymers31,8162
Non-polymers1,0573
Water3,045169
1
A: Cellular retinoic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3912
Polymers15,9081
Non-polymers4831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cellular retinoic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4833
Polymers15,9081
Non-polymers5752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.029, 89.732, 92.463
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 15908.198 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-YWZ / 4'-[(3,6,9,12-tetraoxapentadec-14-yn-1-yl)oxy][1,1'-biphenyl]-4-yl sulfurofluoridate


Mass: 482.519 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H27FO8S
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG3350 and 200 mM KH2PO4, cryoprotected using solution of same condition diluted with glycerol to 30% final glycerol concentration

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9784 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9784 Å / Relative weight: 1
ReflectionResolution: 1.75→37.03 Å / Num. obs: 31338 / % possible obs: 98.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 29.6 Å2 / Rsym value: 0.048 / Net I/σ(I): 17.5
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 5 % / Rmerge(I) obs: 0.979 / Mean I/σ(I) obs: 1.7 / % possible all: 92.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB: 2FS6

2fs6


Resolution: 1.75→34.37 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.427 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.117 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1569 5 %RANDOM
Rwork0.196 ---
obs0.197 29707 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20 Å2
2--0.98 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.75→34.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2151 0 48 169 2368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192332
X-RAY DIFFRACTIONr_bond_other_d0.0010.022213
X-RAY DIFFRACTIONr_angle_refined_deg1.3461.9023168
X-RAY DIFFRACTIONr_angle_other_deg0.7212.9165076
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8655275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44924.84295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82215405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8761515
X-RAY DIFFRACTIONr_chiral_restr0.0740.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0173042
X-RAY DIFFRACTIONr_gen_planes_other0.0010.018515
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.8 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 103 -
Rwork0.325 2015 -
obs--91.53 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.60650.05580.25690.28210.26170.3544-0.0449-0.04970.02570.00180.0175-0.00650.0429-0.00840.02750.0858-0.00550.01580.007-0.00260.08338.2721-12.7227-14.2452
20.69010.10430.02481.1438-1.20011.28640.0178-0.00380.0406-0.1326-0.0612-0.03110.14290.06150.04340.11170.01510.0420.0056-0.00350.05785.3271-6.2652-38.088
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 201
2X-RAY DIFFRACTION2B2 - 201

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