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- PDB-7byj: Crystal structure of the FERM domain of FRMPD4 -

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Basic information

Entry
Database: PDB / ID: 7byj
TitleCrystal structure of the FERM domain of FRMPD4
ComponentsFERM and PDZ domain-containing protein 4
KeywordsPROTEIN BINDING / FERM / FRMPD4 / neural scaffold protein
Function / homology
Function and homology information


positive regulation of synapse structural plasticity / phosphatidylinositol-4,5-bisphosphate binding / dendritic spine / cytoskeleton / protein-containing complex
Similarity search - Function
FERM and PDZ domain-containing protein 1/3/4, FERM domain C-lobe / : / FAK1/PYK2, FERM domain C-lobe / FERM central domain / FERM/acyl-CoA-binding protein superfamily / WW/rsp5/WWP domain profile. / WW domain / FERM central domain / FERM superfamily, second domain / FERM domain ...FERM and PDZ domain-containing protein 1/3/4, FERM domain C-lobe / : / FAK1/PYK2, FERM domain C-lobe / FERM central domain / FERM/acyl-CoA-binding protein superfamily / WW/rsp5/WWP domain profile. / WW 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
Similarity search - Domain/homology
FERM and PDZ domain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsLin, L. / Wang, M. / Wang, C. / Zhu, J.
CitationJournal: Biochem.J. / Year: 2020
Title: Structure of the FERM domain of a neural scaffold protein FRMPD4 implicated in X-linked intellectual disability.
Authors: Wang, M. / Lin, L. / Shi, Y. / He, L. / Wang, C. / Zhu, J.
History
DepositionApr 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Nov 29, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FERM and PDZ domain-containing protein 4


Theoretical massNumber of molelcules
Total (without water)38,5631
Polymers38,5631
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.149, 49.149, 350.225
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein FERM and PDZ domain-containing protein 4 / PDZ domain-containing protein 10 / PSD-95-interacting regulator of spine morphogenesis / Preso


Mass: 38562.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FRMPD4, KIAA0316, PDZD10, PDZK10 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q14CM0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.76 Å3/Da / Density % sol: 55.49 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: Lithium citrate tribasic tetrahydrate, Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.49→45.3 Å / Num. obs: 16231 / % possible obs: 100 % / Redundancy: 23.56 % / Biso Wilson estimate: 74.598 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.089 / Χ2: 0.778 / Net I/σ(I): 23.79 / Num. measured all: 382398
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.49-2.6425.8121.0142.764891251625140.8781.03499.9
2.64-2.8226.2850.6064.8962820239023900.9590.617100
2.82-3.0525.3970.31610.2657397226022600.990.322100
3.05-3.3422.8630.17518.2147304206920690.9960.179100
3.34-3.7323.4490.10631.544296188918890.9980.109100
3.73-4.321.3340.07742.3836353170417040.9990.079100
4.3-5.2619.8250.06648.8629084146714670.9990.068100
5.26-7.3921.5350.06350.5925648119111910.9990.064100
7.39-45.319.5520.04857.67146057507470.9990.04999.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6E2Q

6e2q


Resolution: 2.49→45.3 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 28.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2664 1623 10 %RANDOM
Rwork0.2241 14604 --
obs0.2284 16227 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 164.47 Å2 / Biso mean: 73.5663 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.49→45.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2600 0 0 10 2610
Biso mean---57.67 -
Num. residues----331
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.49-2.560.4341300.358811671297
2.56-2.650.37781290.332611631292
2.65-2.740.37891340.289712031337
2.74-2.850.39071290.278411601289
2.85-2.980.29581320.259311881320
2.98-3.140.33181330.264112001333
3.14-3.330.331350.253712061341
3.33-3.590.28641320.250711961328
3.59-3.950.26671350.229712231358
3.95-4.520.25341400.190512451385
4.52-5.690.22931390.19712591398
5.7-45.30.21741550.201413941549

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