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- PDB-5nks: Human Dihydropyrimidinase-related Protein 4 (DPYSL4, CRMP3, ULIP-4) -

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Basic information

Entry
Database: PDB / ID: 5nks
TitleHuman Dihydropyrimidinase-related Protein 4 (DPYSL4, CRMP3, ULIP-4)
ComponentsDihydropyrimidinase-related protein 4
KeywordsHYDROLASE / Cytoskeleton / Neuroplasticity / Tetramerisation
Function / homology
Function and homology information


filamin binding / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / CRMPs in Sema3A signaling / nervous system development / 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 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsMathea, S. / Elkins, J.M. / Strain-Damerell, C. / Salah, E. / Borkowska, O. / Chalk, R. / Burgess-Brown, N. / Pinkas, D.M. / von Delft, F. / Krojer, T. ...Mathea, S. / Elkins, J.M. / Strain-Damerell, C. / Salah, E. / Borkowska, O. / Chalk, R. / Burgess-Brown, N. / Pinkas, D.M. / von Delft, F. / Krojer, T. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S.
CitationJournal: To Be Published
Title: Human Dihydropyrimidinase-related Protein 4 (DPYSL4, CRMP3, ULIP-4)
Authors: Mathea, S. / Knapp, S.
History
DepositionMar 31, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 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

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Assembly

Deposited unit
A: Dihydropyrimidinase-related protein 4


Theoretical massNumber of molelcules
Total (without water)62,0441
Polymers62,0441
Non-polymers00
Water5,657314
1
A: Dihydropyrimidinase-related protein 4

A: Dihydropyrimidinase-related protein 4

A: Dihydropyrimidinase-related protein 4

A: Dihydropyrimidinase-related protein 4


Theoretical massNumber of molelcules
Total (without water)248,1744
Polymers248,1744
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_554-x,y,-z-11
crystal symmetry operation4_554x,-y,-z-11
Unit cell
Length a, b, c (Å)80.470, 102.650, 116.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-865-

HOH

21A-877-

HOH

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Components

#1: Protein Dihydropyrimidinase-related protein 4 / DRP-4 / Collapsin response mediator protein 3 / CRMP-3 / UNC33-like phosphoprotein 4 / ULIP-4


Mass: 62043.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPYSL4, CRMP3, ULIP4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O14531
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 1.95 Å3/Da / Density % sol: 36.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-tris-propane 0.2 M Sodium fluoride 10% Ethylene glycol 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9797 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.8→27.85 Å / Num. obs: 44328 / % possible obs: 98.3 % / Redundancy: 3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.7
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.651 / Mean I/σ(I) obs: 2 / Num. unique obs: 2548 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementStarting model: 4BKN

4bkn


Resolution: 1.8→77.16 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.332 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20049 2200 5 %RANDOM
Rwork0.15452 ---
obs0.1568 42105 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.729 Å2
Baniso -1Baniso -2Baniso -3
1--1.69 Å20 Å2-0 Å2
2--2.04 Å20 Å2
3----0.34 Å2
Refinement stepCycle: 1 / Resolution: 1.8→77.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3698 0 0 314 4012
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193826
X-RAY DIFFRACTIONr_bond_other_d0.0020.023613
X-RAY DIFFRACTIONr_angle_refined_deg1.8311.9455206
X-RAY DIFFRACTIONr_angle_other_deg1.05538309
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9925499
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11624.321162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16315617
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3011521
X-RAY DIFFRACTIONr_chiral_restr0.1130.2592
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214401
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02856
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_it1.9042.1731981
X-RAY DIFFRACTIONr_mcbond_other1.8972.1711980
X-RAY DIFFRACTIONr_mcangle_it2.6853.2472482
X-RAY DIFFRACTIONr_mcangle_other2.6853.2492483
X-RAY DIFFRACTIONr_scbond_it2.9222.4971844
X-RAY DIFFRACTIONr_scbond_other2.9212.4991845
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.333.6222724
X-RAY DIFFRACTIONr_long_range_B_refined5.87518.4034491
X-RAY DIFFRACTIONr_long_range_B_other5.76218.1114378
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 150 -
Rwork0.281 3003 -
obs--96.3 %

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