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- PDB-7de7: Crystal structure of PDZD7 HHD domain -

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Basic information

Entry
Database: PDB / ID: 7de7
TitleCrystal structure of PDZD7 HHD domain
ComponentsPDZ domain-containing protein 7
KeywordsLIPID BINDING PROTEIN / PDZD7 / HHD domain / membrane-targeting
Function / homology
Function and homology information


stereocilia ankle link / USH2 complex / stereocilia ankle link complex / inner ear receptor cell differentiation / auditory receptor cell development / detection of mechanical stimulus involved in sensory perception of sound / stereocilium / auditory receptor cell stereocilium organization / establishment of protein localization / establishment of localization in cell ...stereocilia ankle link / USH2 complex / stereocilia ankle link complex / inner ear receptor cell differentiation / auditory receptor cell development / detection of mechanical stimulus involved in sensory perception of sound / stereocilium / auditory receptor cell stereocilium organization / establishment of protein localization / establishment of localization in cell / ciliary basal body / nucleoplasm / identical protein binding
Similarity search - Function
PDZD7, Harmonin N-like domain / : / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
Chem-2Q5 / PDZ domain-containing protein 7
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsWang, H. / Lin, L. / Lu, Q.
CitationJournal: Front Cell Dev Biol / Year: 2021
Title: Structure and Membrane Targeting of the PDZD7 Harmonin Homology Domain (HHD) Associated With Hearing Loss.
Authors: Lin, L. / Wang, H. / Ren, D. / Xia, Y. / He, G. / Lu, Q.
History
DepositionNov 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PDZ domain-containing protein 7
B: PDZ domain-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7733
Polymers23,5232
Non-polymers2501
Water2,720151
1
A: PDZ domain-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0122
Polymers11,7621
Non-polymers2501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PDZ domain-containing protein 7


Theoretical massNumber of molelcules
Total (without water)11,7621
Polymers11,7621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.782, 75.005, 42.939
Angle α, β, γ (deg.)90.000, 103.100, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PDZ domain-containing protein 7


Mass: 11761.536 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pdzd7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: E9Q9W7
#2: Chemical ChemComp-2Q5 / (2R)-2-{[(2R)-2-{[(2S)-2-{[(2R)-2-hydroxypropyl]oxy}propyl]oxy}propyl]oxy}propan-1-ol


Mass: 250.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.19 Å3/Da / Density % sol: 43.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris pH 6.5, 45% Polypropylene glycol P400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97891 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 1.49→37.5 Å / Num. obs: 32592 / % possible obs: 99.4 % / Redundancy: 6.74 % / Biso Wilson estimate: 25.745 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.091 / Χ2: 0.819 / Net I/σ(I): 13.49
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
1.49-1.586.4421.1971.5633241525751600.7251.30198.2
1.58-1.696.9210.7312.7434015494949150.8860.7999.3
1.69-1.836.7450.4354.3331136464046160.9530.47199.5
1.83-26.7020.237.7828364423942320.9820.2599.8
2-2.246.9050.12514.5826599385838520.9930.13599.8
2.24-2.586.6990.07822.1322896342234180.9970.08499.9
2.58-3.166.9370.05929.8319992288428820.9980.06499.9
3.16-4.466.6580.04340.515000225622530.9980.04799.9
4.46-37.56.6780.03844.528454127112660.9990.04199.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FDD

6fdd


Resolution: 1.49→37.5 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1936 1998 6.14 %
Rwork0.1774 60231 -
obs0.1784 32580 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.51 Å2 / Biso mean: 22.9697 Å2 / Biso min: 11.7 Å2
Refinement stepCycle: final / Resolution: 1.49→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 17 151 1684
Biso mean--36.05 33.8 -
Num. residues----190
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.49-1.510.40181300.35351993212393
1.51-1.530.36221440.34382182232699
1.53-1.550.3231380.30472122226099
1.55-1.570.31941390.29292106224599
1.57-1.60.29251390.28032165230499
1.6-1.620.3091380.255221332271100
1.62-1.640.29581460.25522188233499
1.64-1.670.22951340.23962120225499
1.67-1.70.25941400.22752180232099
1.7-1.730.25511400.2221462286100
1.73-1.760.24571420.212421542296100
1.76-1.80.25111390.202521572296100
1.8-1.840.23171440.20242179232399
1.84-1.880.28161390.183821192258100
1.88-1.930.19221470.18722062353100
1.93-1.980.18241390.162321042243100
1.98-2.040.17641420.165822012343100
2.04-2.110.2171380.15421252263100
2.11-2.180.14941460.158221992345100
2.18-2.270.20651420.147321432285100
2.27-2.370.16961410.165321602301100
2.37-2.50.18061400.147821832323100
2.5-2.650.18461420.15721442286100
2.65-2.860.16371400.158621702310100
2.86-3.140.17921390.167521622301100
3.15-3.60.14341460.164421722318100
3.6-4.530.14711420.144221652307100
4.54-37.50.20361460.18921532299100

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