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

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Basic information

Entry
Database: PDB / ID: 5mkv
TitleCrystal Structure of Human Dihydropyrimidinease-like 2 (DPYSL2A)/Collapsin Response Mediator Protein (CRMP2) residues 13-516
ComponentsDihydropyrimidinase-related protein 2
KeywordsHYDROLASE / CRMP2 / 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
Dihydropyrimidinase-related protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSethi, R. / Zheng, Y. / Krojer, T. / 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 5, 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
A: Dihydropyrimidinase-related protein 2
B: Dihydropyrimidinase-related protein 2
C: Dihydropyrimidinase-related protein 2
D: Dihydropyrimidinase-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,78226
Polymers220,4174
Non-polymers1,36522
Water10,737596
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17290 Å2
ΔGint21 kcal/mol
Surface area61640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.900, 157.510, 87.420
Angle α, β, γ (deg.)90.00, 93.61, 90.00
Int Tables number4
Space group name H-MP1211

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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: 55104.156 Da / Num. of mol.: 4
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 596 / 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: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M ammonium acetate, 30% PEG 4000 and 0.1M citrate buffer pH 5.5

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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: Feb 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.8→19.87 Å / Num. obs: 194435 / % possible obs: 97.71 % / Redundancy: 3.6 % / Net I/σ(I): 15.84

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GSE

2gse


Resolution: 1.8→19.87 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.434 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.107 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19963 9717 5 %RANDOM
Rwork0.16654 ---
obs0.1682 184609 97.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.454 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.8→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14957 0 88 596 15641
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01915335
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214548
X-RAY DIFFRACTIONr_angle_refined_deg1.9521.95220766
X-RAY DIFFRACTIONr_angle_other_deg1.107333537
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.22451946
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.45624.686668
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38152553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9561580
X-RAY DIFFRACTIONr_chiral_restr0.1250.22342
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02117377
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023359
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_it2.2832.3637793
X-RAY DIFFRACTIONr_mcbond_other2.2792.3627792
X-RAY DIFFRACTIONr_mcangle_it3.0463.5319733
X-RAY DIFFRACTIONr_mcangle_other3.0463.5329734
X-RAY DIFFRACTIONr_scbond_it3.1762.6747542
X-RAY DIFFRACTIONr_scbond_other3.1742.6747542
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5533.87711033
X-RAY DIFFRACTIONr_long_range_B_refined5.4728.13316825
X-RAY DIFFRACTIONr_long_range_B_other5.46928.13516826
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 711 -
Rwork0.228 13505 -
obs--97.67 %

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