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- PDB-8bnb: Crystal structure of Trichoplax Scribble PDZ2 domain -

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Basic information

Entry
Database: PDB / ID: 8bnb
TitleCrystal structure of Trichoplax Scribble PDZ2 domain
ComponentsLeucine-rich repeat-containing protein 1
KeywordsPROTEIN BINDING / PDZ domain / cell polarity / Scribble / Trichoplax
Function / homology
Function and homology information


receptor localization to synapse / establishment or maintenance of epithelial cell apical/basal polarity / receptor clustering / adherens junction / cell-cell adhesion / basolateral plasma membrane / protein kinase binding
Similarity search - Function
: / : / Leucine-rich repeat region / Leucine-rich repeats, bacterial type / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / PDZ domain / Leucine-rich repeat ...: / : / Leucine-rich repeat region / Leucine-rich repeats, bacterial type / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / PDZ domain / Leucine-rich repeat / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Leucine-rich repeat-containing protein 1
Similarity search - Component
Biological speciesTrichoplax sp. H2 (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 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 Scribble PDZ2 domain
Authors: Maddumage, J.C. / Humbert, P.O. / Kvansakul, M.
History
DepositionNov 14, 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

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Assembly

Deposited unit
A: Leucine-rich repeat-containing protein 1
B: Leucine-rich repeat-containing protein 1


Theoretical massNumber of molelcules
Total (without water)20,1732
Polymers20,1732
Non-polymers00
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-9 kcal/mol
Surface area9410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.781, 32.946, 42.710
Angle α, β, γ (deg.)93.630, 95.650, 113.740
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid -4 through 38 or (resid 39...
d_2ens_1(chain "B" and (resid -4 through 6 or (resid 7...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLYGLYGLNGLNAA-4 - 891 - 94
d_21GLYGLYARGARGBB-4 - 761 - 81
d_22GLUGLUGLNGLNBB78 - 9083 - 95

NCS oper: (Code: givenMatrix: (-0.397229353546, 0.917661721918, -0.0102861463736), (0.917673773036, 0.397072938497, -0.0144197016082), (-0.0091480578409, -0.0151672555008, -0.999843121394)Vector: 7. ...NCS oper: (Code: given
Matrix: (-0.397229353546, 0.917661721918, -0.0102861463736), (0.917673773036, 0.397072938497, -0.0144197016082), (-0.0091480578409, -0.0151672555008, -0.999843121394)
Vector: 7.74408597271, -5.2387828865, -13.9560106337)

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Components

#1: Protein Leucine-rich repeat-containing protein 1


Mass: 10086.501 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoplax sp. H2 (invertebrata) / Gene: TrispH2_005790 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Codon+ / References: UniProt: A0A369S7Y8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.07 Å3/Da / Density % sol: 40.57 % / Description: Plate
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 1.6 M sodium citrate, pH 5.5.

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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 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.11→29.97 Å / Num. obs: 8998 / % possible obs: 97.16 % / Redundancy: 3.3 % / Biso Wilson estimate: 30.64 Å2 / CC1/2: 0.992 / Net I/σ(I): 5.54
Reflection shellResolution: 2.11→2.19 Å / Num. unique obs: 874 / CC1/2: 0.622

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JO7

7jo7


Resolution: 2.11→29.97 Å / SU ML: 0.3122 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.6288
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2542 425 4.73 %
Rwork0.2297 8565 -
obs0.2309 8990 97.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.87 Å2
Refinement stepCycle: LAST / Resolution: 2.11→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1352 0 0 63 1415
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00171365
X-RAY DIFFRACTIONf_angle_d0.40371839
X-RAY DIFFRACTIONf_chiral_restr0.0479223
X-RAY DIFFRACTIONf_plane_restr0.0026234
X-RAY DIFFRACTIONf_dihedral_angle_d11.8759487
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.518100455343 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.420.32621470.2692800X-RAY DIFFRACTION95.71
2.42-3.050.27461320.27242881X-RAY DIFFRACTION97.32
3.05-29.970.22761460.20212884X-RAY DIFFRACTION98.47
Refinement TLS params.Method: refined / Origin x: 2.72252818653 Å / Origin y: -3.58850075293 Å / Origin z: -6.89742642158 Å
111213212223313233
T0.23606215486 Å20.0285535452949 Å20.0242887100496 Å2-0.243371480631 Å20.0220314091286 Å2--0.388353160143 Å2
L2.06920327146 °2-0.985552855817 °2-0.744714307622 °2-2.10893738514 °20.849130995003 °2--1.92038515735 °2
S-0.0229766745731 Å °-0.0061080682557 Å °0.108891395732 Å °0.0442752438504 Å °0.0593866879114 Å °0.00187506341942 Å °-0.0594457023248 Å °0.0466401235639 Å °-0.0518668978971 Å °
Refinement TLS groupSelection details: all

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