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- PDB-8bp5: Crystal structure of Trichoplax Dlg PDZ1 domain -

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Basic information

Entry
Database: PDB / ID: 8bp5
TitleCrystal structure of Trichoplax Dlg PDZ1 domain
ComponentsDisks large-like protein 1
KeywordsPROTEIN BINDING / PDZ domain / cell polarity / Dlg / Trichoplax
Function / homology
Function and homology information


L27-1 / L27_1 / L27 domain superfamily / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. ...L27-1 / L27_1 / L27 domain superfamily / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Disks large-like protein 1
Similarity search - Component
Biological speciesTrichoplax sp. H2 (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsMaddumage, J.C. / Kvansakul, M.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1103871 Australia
Australian Research Council (ARC)FT130101349 Australia
CitationJournal: To be published
Title: Crystal structure of Trichoplax Dlg PDZ1 domain
Authors: Maddumage, J.C. / Humbert, P.O. / Kvansakul, M.
History
DepositionNov 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Disks large-like protein 1
B: Disks large-like protein 1


Theoretical massNumber of molelcules
Total (without water)19,5482
Polymers19,5482
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.962, 52.632, 43.005
Angle α, β, γ (deg.)90.000, 92.930, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Disks large-like protein 1


Mass: 9774.006 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoplax sp. H2 (invertebrata) / Gene: TrispH2_000924 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Codon+ / References: UniProt: A0A369SI82
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.05 Å3/Da / Density % sol: 39.95 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 2.5 M D-L Malic acid, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.13→42.95 Å / Num. obs: 8858 / % possible obs: 99.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 31.83 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.036 / Net I/σ(I): 20.7
Reflection shellResolution: 2.13→2.19 Å / Rmerge(I) obs: 0.147 / Num. unique obs: 718 / CC1/2: 0.989

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RL7

3rl7


Resolution: 2.13→42.95 Å / SU ML: 0.1767 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 26.6848
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2418 422 4.77 %
Rwork0.1923 8424 -
obs0.1946 8846 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.21 Å2
Refinement stepCycle: LAST / Resolution: 2.13→42.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1336 0 0 110 1446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00291352
X-RAY DIFFRACTIONf_angle_d0.551827
X-RAY DIFFRACTIONf_chiral_restr0.0492213
X-RAY DIFFRACTIONf_plane_restr0.0032240
X-RAY DIFFRACTIONf_dihedral_angle_d5.0266193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.430.2891380.21012779X-RAY DIFFRACTION99.05
2.43-3.070.27781490.21662780X-RAY DIFFRACTION99.83
3.07-42.950.21311350.17792865X-RAY DIFFRACTION99.63
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)
10.384109997374-0.914836406831-1.022101440596.87397623774-0.2973800257057.381819809510.1129821372640.241632996198-0.102779443123-0.06543498710780.1857089672230.0307142718650.267850445688-0.0252432134744-0.2105034929690.1989058804080.0698621003591-0.01435849851390.4573001532360.003624984790460.3522595088284.832462504563.58943785254-0.351808427941
25.000163726611.364673746744.733309020720.857289312381.406665420344.41232860457-0.3314045805170.5081911639880.180571018821-0.3174806871820.114888806399-0.0255942992708-0.1573967548810.2762241528320.1966225689540.1878419514530.00246575509979-0.00846277424620.2322579200880.05460752858880.289171343599-7.771273540858.97531899863-10.5495776776
33.386162817271.0205877037-1.669366600442.35694245562-0.3472275532571.70926094245-0.2245804669930.332918511533-0.183227610173-0.3275639239020.09294714736350.02444192637280.1376757012420.1809167440650.1733520886870.2321791843830.04154040568730.04277225668210.437972899971-0.003705005116160.3223024391683.592731513382.05418313943-6.83734660569
46.37534199218-1.355618033980.2057945038365.20979942052-0.9016251883732.74294223044-0.231023336782-0.3439266063920.03345832433230.2156261250560.329472783370.067900733698-0.0662278692996-0.0572993121922-0.1253408281270.1673190694290.01148910423410.03020353162580.2946874813960.002196202423730.240551949259-3.274635722468.452005691941.25526358316
57.63731049876-2.4040030688-1.494406494418.804517995260.6978070803026.88158280644-0.04932969106970.353227809743-0.594627258396-0.4362485298350.1432447099590.4354170666570.69343135063-0.314364348748-0.1256055420280.385185675763-0.0249199396643-0.02832245544610.3174286131520.01086387622730.312486318535-17.8325806938-2.15954686276-34.8695396717
63.35813999963-0.529249105134-0.05223269993752.49673079046-0.03245228095412.25518743255-0.08491193556150.0485934933468-0.429458105310.2901683979740.0921397915742-0.02945776351480.5237741141190.06961851396620.03177874620730.6721964006710.0282994216322-0.02943550477020.264589409295-0.02148216437140.233009936714-10.3250972123-1.76421322656-20.5891046451
72.33793592739-0.655901611363-1.337786852070.429365863490.03746473115391.8161930752-0.306382294773-0.0662026706378-0.2271502435970.1814387269240.1638030603560.1279338400480.939828752907-0.04802062006930.119661570690.581078323867-0.1010415583940.01140069754130.329452443671-0.04841361355870.251102650815-19.897524867-1.51255639804-24.3134868026
87.11834408315-1.85345313951.512466320734.668761068090.4284300507162.14154192235-0.3540866192170.1115627264420.6642499282430.5881712250590.26785517009-0.6252282309410.332117111330.6125924250580.1391404154050.3983810427460.0350730409622-0.080384383120.266800204902-0.03662621748130.318784117257-6.337185051325.53234377405-26.4060469624
95.66044956952-4.01178668783-1.112283098733.982025896293.289647573985.857014863630.3330030329160.4898325985940.150178894452-0.474737761484-0.164904959945-0.453697100384-0.588658319138-0.134347809089-0.1310049707190.322060058865-0.05373176299420.009884524684730.3038142371840.007045143695060.243032256651-16.31909069334.35261636642-30.4799847689
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 15 )AA1 - 151 - 15
22chain 'A' and (resid 16 through 38 )AA16 - 3816 - 38
33chain 'A' and (resid 39 through 59 )AA39 - 5939 - 59
44chain 'A' and (resid 60 through 89 )AA60 - 8960 - 89
55chain 'B' and (resid -2 through 8 )BB-2 - 81 - 11
66chain 'B' and (resid 9 through 38 )BB9 - 3812 - 41
77chain 'B' and (resid 39 through 59 )BB39 - 5942 - 62
88chain 'B' and (resid 60 through 77 )BB60 - 7763 - 80
99chain 'B' and (resid 78 through 89 )BB78 - 8981 - 92

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