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- PDB-4bkn: Human Dihydropyrimidinase-related protein 3 (DPYSL3) -

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Basic information

Entry
Database: PDB / ID: 4bkn
TitleHuman Dihydropyrimidinase-related protein 3 (DPYSL3)
ComponentsDIHYDROPYRIMIDINASE-RELATED PROTEIN 3
KeywordsHYDROLASE / AXON OUTGROWTH / HOMOTETRAMER
Function / homology
Function and homology information


chondroitin sulfate binding / filamin binding / actin crosslink formation / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / exocytic vesicle / CRMPs in Sema3A signaling / positive regulation of filopodium assembly / neuron development / cellular response to cytokine stimulus / filamentous actin ...chondroitin sulfate binding / filamin binding / actin crosslink formation / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / exocytic vesicle / CRMPs in Sema3A signaling / positive regulation of filopodium assembly / neuron development / cellular response to cytokine stimulus / filamentous actin / response to axon injury / actin filament bundle assembly / negative regulation of cell migration / positive regulation of neuron projection development / negative regulation of neuron projection development / SH3 domain binding / phosphoprotein binding / lamellipodium / growth cone / cell body / synapse / extracellular region / identical protein binding / 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 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMathea, S. / Elkins, J.M. / Alegre-Abarrategui, J. / Shrestha, L. / Burgess-Brown, N. / Puranik, S. / Coutandin, D. / Bradley, A. / Vollmar, M. / von Delft, F. ...Mathea, S. / Elkins, J.M. / Alegre-Abarrategui, J. / Shrestha, L. / Burgess-Brown, N. / Puranik, S. / Coutandin, D. / Bradley, A. / Vollmar, M. / von Delft, F. / Bountra, C. / Arrowsmith, C. / Edwards, A. / Knapp, S.
CitationJournal: To be Published
Title: Structure of Dpysl3
Authors: Mathea, S.
History
DepositionApr 26, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIHYDROPYRIMIDINASE-RELATED PROTEIN 3
B: DIHYDROPYRIMIDINASE-RELATED PROTEIN 3


Theoretical massNumber of molelcules
Total (without water)124,2722
Polymers124,2722
Non-polymers00
Water7,098394
1
A: DIHYDROPYRIMIDINASE-RELATED PROTEIN 3
B: DIHYDROPYRIMIDINASE-RELATED PROTEIN 3

A: DIHYDROPYRIMIDINASE-RELATED PROTEIN 3
B: DIHYDROPYRIMIDINASE-RELATED PROTEIN 3


Theoretical massNumber of molelcules
Total (without water)248,5454
Polymers248,5454
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area10540 Å2
ΔGint-29.4 kcal/mol
Surface area62820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.230, 96.650, 119.270
Angle α, β, γ (deg.)90.00, 137.26, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2082-

HOH

21A-2110-

HOH

31B-2078-

HOH

41B-2101-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 570
2111B1 - 570

NCS oper:
IDCodeMatrixVector
1given(-0.15315, 0.00166, -0.9882), (0.00322, -0.99999, -0.00217), (-0.9882, -0.00351, 0.15314)0.01316, -76.46546, -0.04018
2given(1), (1), (1)
3given(-0.153151, 0.003229, -0.988197), (0.001619, -0.999992, -0.003519), (-0.988201, -0.002139, 0.153145)0.21019, -76.46858, -0.14569

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Components

#1: Protein DIHYDROPYRIMIDINASE-RELATED PROTEIN 3 / DRP-3 / COLLAPSIN RESPONSE MEDIATOR PROTEIN 4 / CRMP-4 / UNC-33-LIKE PHOSPHOPROTEIN 1 / ULIP-1 / ...DRP-3 / COLLAPSIN RESPONSE MEDIATOR PROTEIN 4 / CRMP-4 / UNC-33-LIKE PHOSPHOPROTEIN 1 / ULIP-1 / DIHYDROPYRIMIDINASE-RELATED PROTEIN 3


Mass: 62136.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q14195
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.27 Å3/Da / Density % sol: 45.9 % / Description: NONE
Crystal growpH: 8.5
Details: 0.2M KSCN; 0.1M BISTRISPROPANE PH 8.5; 20% PEG 3350 10% ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→42.85 Å / Num. obs: 60144 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 5.6
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.9 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
Aimlessdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VM8

2vm8


Resolution: 2.1→42.89 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.896 / SU B: 9.574 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23813 3020 5.1 %RANDOM
Rwork0.19739 ---
obs0.19946 56748 92.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.207 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å20 Å20.46 Å2
2---0.71 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.1→42.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7366 0 0 394 7760
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197519
X-RAY DIFFRACTIONr_bond_other_d0.0010.027068
X-RAY DIFFRACTIONr_angle_refined_deg1.3021.94910202
X-RAY DIFFRACTIONr_angle_other_deg0.816316298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7855958
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.73624.985325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.163151254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4461531
X-RAY DIFFRACTIONr_chiral_restr0.0740.21143
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218587
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021654
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_it0.7261.5093844
X-RAY DIFFRACTIONr_mcbond_other0.7261.5093843
X-RAY DIFFRACTIONr_mcangle_it1.1982.2574798
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.9031.613675
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
Refine LS restraints NCSNumber: 7151 / Type: tight thermal / Rms dev position: 1.91 Å / Weight position: 0.5
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 225 -
Rwork0.223 4208 -
obs--93.01 %
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)
11.3907-0.0483-0.17620.5851-0.08880.55880.0046-0.04320.14820.00380.02130.0884-0.0933-0.1165-0.02580.030.0350.00470.0444-0.00920.1496-23.298-23.0968.134
21.1409-0.1861-0.1430.78520.22290.6488-0.0971-0.3946-0.160.19580.08250.03250.11570.03640.01450.06570.040.03430.1390.0640.0658-4.464-53.47824.434
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 570
2X-RAY DIFFRACTION2B1 - 570

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