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- PDB-7x68: CYS179 and CYS504 of CRMP2 were covalently binded by a Sesquiterp... -

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Basic information

Entry
Database: PDB / ID: 7x68
TitleCYS179 and CYS504 of CRMP2 were covalently binded by a Sesquiterpene lactone
ComponentsDihydropyrimidinase-related protein 2
KeywordsPROTEIN BINDING / inhibitor / covalent binding / ENDOCYTOSIS
Function / homology
Function and homology information


dihydropyrimidinase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / CRMPs in Sema3A signaling / nucleobase-containing compound metabolic process / Recycling pathway of L1 / cytoskeleton organization / endocytosis / nervous system development / cell differentiation / cytoskeleton ...dihydropyrimidinase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / CRMPs in Sema3A signaling / nucleobase-containing compound metabolic process / Recycling pathway of L1 / cytoskeleton organization / endocytosis / nervous system development / cell differentiation / cytoskeleton / signal transduction / extracellular exosome / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Hydantoinase/dihydropyrimidinase / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolase
Similarity search - Domain/homology
Chem-BX0 / Dihydropyrimidinase-related protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZhang, S.D. / Ma, Y.F. / Zhang, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81302651 China
CitationJournal: To Be Published
Title: CYS179 and CYS504 of CRMP2 were covalently binded by a Sesquiterpene lactone
Authors: Zhang, S.D. / Ma, Y.F. / Zhang, J.
History
DepositionMar 6, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydropyrimidinase-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9034
Polymers57,3841
Non-polymers5203
Water4,792266
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint-4 kcal/mol
Surface area19880 Å2
Unit cell
Length a, b, c (Å)113.649, 113.649, 196.585
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-763-

HOH

21A-915-

HOH

31A-930-

HOH

41A-943-

HOH

51A-948-

HOH

61A-965-

HOH

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Components

#1: Protein Dihydropyrimidinase-related protein 2 / DRP-2 / Collapsin response mediator protein 2 / CRMP-2 / N2A3 / Unc-33-like phosphoprotein 2 / ULIP-2


Mass: 57383.848 Da / Num. of mol.: 1 / Fragment: UNP residues 1-525
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPYSL2, CRMP2, ULIP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16555
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-BX0 / (3aR,5S,8R,8aR,9aR)-5,8a-dimethyl-3-methylidene-8-oxidanyl-5,6,7,8,9,9a-hexahydro-3aH-benzo[f][1]benzofuran-2-one / 1beta-Hydroxyalantolactone


Mass: 248.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H20O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 Sodium chloride, 0.1 M Bis-tris Ph5.5; 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.97677 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97677 Å / Relative weight: 1
ReflectionResolution: 1.8→98.42 Å / Num. obs: 59704 / % possible obs: 100 % / Redundancy: 1 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 23.75
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.436 / Num. unique obs: 6750 / CC1/2: 0.763

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2gse

2gse


Resolution: 1.8→29.027 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.205 / WRfactor Rwork: 0.169 / SU B: 3.197 / SU ML: 0.092 / Average fsc free: 0.8778 / Average fsc work: 0.8915 / Cross valid method: FREE R-VALUE / ESU R: 0.104 / ESU R Free: 0.106 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2135 3113 5.217 %
Rwork0.1762 56556 -
all0.178 --
obs-59669 99.925 %
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: 35.477 Å2
Baniso -1Baniso -2Baniso -3
1-1.473 Å2-0 Å20 Å2
2--1.473 Å2-0 Å2
3----2.945 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3779 0 37 266 4082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0123969
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.6385402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7915504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45522.75200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.39815665
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8181523
X-RAY DIFFRACTIONr_chiral_restr0.1210.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023016
X-RAY DIFFRACTIONr_nbd_refined0.2210.21823
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22749
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2256
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2570.279
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2060.220
X-RAY DIFFRACTIONr_mcbond_it3.0733.2461996
X-RAY DIFFRACTIONr_mcangle_it4.0434.8482507
X-RAY DIFFRACTIONr_scbond_it4.5683.7111971
X-RAY DIFFRACTIONr_scangle_it6.2685.4072894
X-RAY DIFFRACTIONr_lrange_it7.21746.1426072
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.3362340.3254109X-RAY DIFFRACTION99.908
1.847-1.8970.3312100.2934051X-RAY DIFFRACTION100
1.897-1.9520.3062260.2763894X-RAY DIFFRACTION100
1.952-2.0120.2671910.2433804X-RAY DIFFRACTION100
2.012-2.0780.2521990.2193703X-RAY DIFFRACTION100
2.078-2.1510.2522240.2063559X-RAY DIFFRACTION100
2.151-2.2320.2291820.1923465X-RAY DIFFRACTION99.9726
2.232-2.3230.2312000.1853309X-RAY DIFFRACTION100
2.323-2.4270.2482010.1893172X-RAY DIFFRACTION100
2.427-2.5450.2571550.1783074X-RAY DIFFRACTION100
2.545-2.6830.2431560.1732925X-RAY DIFFRACTION100
2.683-2.8450.2231460.1722780X-RAY DIFFRACTION100
2.845-3.0420.2011380.1672613X-RAY DIFFRACTION100
3.042-3.2850.2391390.1772433X-RAY DIFFRACTION100
3.285-3.5980.1871250.1682257X-RAY DIFFRACTION100
3.598-4.0220.1761010.1482067X-RAY DIFFRACTION100
4.022-4.6430.156910.1241822X-RAY DIFFRACTION100
4.643-5.6830.1911140.1431547X-RAY DIFFRACTION100
5.683-8.0240.152400.151255X-RAY DIFFRACTION100
8.024-29.0270.136410.141717X-RAY DIFFRACTION97.3042

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