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- PDB-5mle: Crystal Structure of Human Dihydropyrimidinease-like 2 (DPYSL2A)/... -

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Basic information

Entry
Database: PDB / ID: 5mle
TitleCrystal Structure of Human Dihydropyrimidinease-like 2 (DPYSL2A)/Collapsin Response Mediator Protein (CRMP2 13-516) Mutant Y479E/Y499E
ComponentsDihydropyrimidinase-related protein 2
KeywordsHYDROLASE / CRMP2 / phospho-mutant / Ovarian cancer / Microtubule associated protein
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 / mitotic spindle / nervous system development / microtubule 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 / mitotic spindle / nervous system development / microtubule cytoskeleton / cell differentiation / cilium / signal transduction / extracellular exosome / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Hydantoinase/dihydropyrimidinase / : / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll ...Hydantoinase/dihydropyrimidinase / : / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / Dihydropyrimidinase-related protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsSethi, R. / Zheng, Y. / Talon, R. / Velupillai, S. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Ahmed, A.A. / von Delft, F.
CitationJournal: Nat Commun / Year: 2018
Title: Tuning microtubule dynamics to enhance cancer therapy by modulating FER-mediated CRMP2 phosphorylation.
Authors: Zheng, Y. / Sethi, R. / Mangala, L.S. / Taylor, C. / Goldsmith, J. / Wang, M. / Masuda, K. / Karaminejadranjbar, M. / Mannion, D. / Miranda, F. / Herrero-Gonzalez, S. / Hellner, K. / Chen, F. ...Authors: Zheng, Y. / Sethi, R. / Mangala, L.S. / Taylor, C. / Goldsmith, J. / Wang, M. / Masuda, K. / Karaminejadranjbar, M. / Mannion, D. / Miranda, F. / Herrero-Gonzalez, S. / Hellner, K. / Chen, F. / Alsaadi, A. / Albukhari, A. / Fotso, D.C. / Yau, C. / Jiang, D. / Pradeep, S. / Rodriguez-Aguayo, C. / Lopez-Berestein, G. / Knapp, S. / Gray, N.S. / Campo, L. / Myers, K.A. / Dhar, S. / Ferguson, D. / Bast, R.C. / Sood, A.K. / von Delft, F. / Ahmed, A.A.
History
DepositionDec 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 17, 2024Group: 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
C: Dihydropyrimidinase-related protein 2
A: Dihydropyrimidinase-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,12917
Polymers110,0722
Non-polymers1,05615
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint6 kcal/mol
Surface area33270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.900, 185.820, 196.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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: 55036.039 Da / Num. of mol.: 2 / Mutation: Y479E/Y499E
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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.94 Å3/Da / Density % sol: 58.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: (0.2M magnesium chloride, 25% PEG 3350 and 0.1M bis-tris buffer pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.48→83.98 Å / Num. obs: 46370 / % possible obs: 99.92 % / Redundancy: 6.8 % / CC1/2: 0.989 / Net I/σ(I): 6.21

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GSE

2gse


Resolution: 2.48→83.98 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.907 / SU B: 14.43 / SU ML: 0.278 / Cross valid method: THROUGHOUT / ESU R: 0.377 / ESU R Free: 0.264 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25408 2328 5 %RANDOM
Rwork0.20601 ---
obs0.20851 44041 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.954 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-0 Å2
2---0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.48→83.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7206 0 63 175 7444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0197418
X-RAY DIFFRACTIONr_bond_other_d0.0020.026865
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.95210039
X-RAY DIFFRACTIONr_angle_other_deg1.042315967
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4825943
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5824.984321
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.308151242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2981534
X-RAY DIFFRACTIONr_chiral_restr0.0850.21136
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218244
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021422
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_it2.3923.9183763
X-RAY DIFFRACTIONr_mcbond_other2.3693.9173762
X-RAY DIFFRACTIONr_mcangle_it3.7925.8664700
X-RAY DIFFRACTIONr_mcangle_other3.7955.8684701
X-RAY DIFFRACTIONr_scbond_it2.5914.2193655
X-RAY DIFFRACTIONr_scbond_other2.5894.2193655
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2346.1875337
X-RAY DIFFRACTIONr_long_range_B_refined7.87145.8127845
X-RAY DIFFRACTIONr_long_range_B_other7.87145.827846
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.48→2.544 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 175 -
Rwork0.38 3214 -
obs--99.97 %

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