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- PDB-5zds: Crystal structure of the second PDZ domain of Frmpd2 -

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Basic information

Entry
Database: PDB / ID: 5zds
TitleCrystal structure of the second PDZ domain of Frmpd2
ComponentsFERM and PDZ domain-containing 2
KeywordsSIGNALING PROTEIN / Frmpd2 / PDZ
Function / homology
Function and homology information


1-phosphatidylinositol binding / bicellular tight junction assembly / bicellular tight junction / basolateral plasma membrane / cytoskeleton
Similarity search - Function
FERM and PDZ domain-containing protein 2 / KIND domain / KIND domain profile. / kinase non-catalytic C-lobe domain / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / FERM central domain ...FERM and PDZ domain-containing protein 2 / KIND domain / KIND domain profile. / kinase non-catalytic C-lobe domain / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / FERM central domain / FERM/acyl-CoA-binding protein superfamily / PDZ domain / Pdz3 Domain / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
FERM and PDZ domain-containing 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLu, X. / Wang, X.F.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: The second PDZ domain of scaffold protein Frmpd2 binds to GluN2A of NMDA receptors.
Authors: Lu, X. / Zhang, Q. / Wang, T.
History
DepositionFeb 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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
Revision 1.2Apr 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FERM and PDZ domain-containing 2


Theoretical massNumber of molelcules
Total (without water)9,9981
Polymers9,9981
Non-polymers00
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4940 Å2
Unit cell
Length a, b, c (Å)48.176, 56.842, 32.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1242-

HOH

21A-1248-

HOH

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Components

#1: Protein FERM and PDZ domain-containing 2


Mass: 9998.396 Da / Num. of mol.: 1 / Fragment: UNP residues 934-1027
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Frmpd2, Gm626 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A140LI67
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.2 Å3/Da / Density % sol: 44.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG3350 20%, sodium thiocyanate 0.2M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97858 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2017
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97858 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 12699 / % possible obs: 99.7 % / Redundancy: 6.3 % / Rrim(I) all: 0.065 / Net I/σ(I): 22.52
Reflection shellResolution: 1.58→1.64 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 7.7 / Num. unique obs: 1248 / Rrim(I) all: 0.268 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VJ6

1vj6


Resolution: 1.8→50 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 22.57
RfactorNum. reflection% reflection
Rfree0.2347 860 9.99 %
Rwork0.198 --
obs0.2017 8610 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms639 0 0 152 791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005670
X-RAY DIFFRACTIONf_angle_d0.831911
X-RAY DIFFRACTIONf_dihedral_angle_d18.38399
X-RAY DIFFRACTIONf_chiral_restr0.059108
X-RAY DIFFRACTIONf_plane_restr0.006119
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.91280.27091400.22541265X-RAY DIFFRACTION100
1.9128-2.06050.26461410.20651258X-RAY DIFFRACTION100
2.0605-2.26780.24491410.20161271X-RAY DIFFRACTION100
2.2678-2.59590.26391420.20851284X-RAY DIFFRACTION100
2.5959-3.270.22651450.20021305X-RAY DIFFRACTION100
3.27-32.20510.20381510.18031367X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -1.8541 Å / Origin y: 11.818 Å / Origin z: -9.8617 Å
111213212223313233
T0.0271 Å2-0.0007 Å20.0117 Å2-0.0311 Å20.0078 Å2--0.0312 Å2
L0.1176 °2-0.0635 °2-0.1042 °2-0.3326 °20.1896 °2--0.2527 °2
S-0.0293 Å °-0.0338 Å °-0.033 Å °0.0003 Å °0.0161 Å °0.0547 Å °-0.0111 Å °0.0489 Å °-0.0557 Å °
Refinement TLS groupSelection details: all

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