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- PDB-4pqq: The crystal structure of discoidin domain from muskelin -

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Basic information

Entry
Database: PDB / ID: 4pqq
TitleThe crystal structure of discoidin domain from muskelin
ComponentsMuskelin
KeywordsPROTEIN BINDING / jelly-roll / cell spreading mediator / prostaglandin EP3 receptor / alpha isoform / RANBP9 / Phosphorylation
Function / homology
Function and homology information


: / regulation of receptor internalization / ubiquitin ligase complex / ruffle / cell-matrix adhesion / cell cortex / regulation of cell shape / postsynapse / protein homodimerization activity / nucleoplasm ...: / regulation of receptor internalization / ubiquitin ligase complex / ruffle / cell-matrix adhesion / cell cortex / regulation of cell shape / postsynapse / protein homodimerization activity / nucleoplasm / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Muskelin, N-terminal / Muskelin N-terminus / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / Lissencephaly type-1-like homology motif / Galactose oxidase/kelch, beta-propeller / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Kelch repeat type 1 / Kelch motif ...Muskelin, N-terminal / Muskelin N-terminus / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / Lissencephaly type-1-like homology motif / Galactose oxidase/kelch, beta-propeller / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Kelch repeat type 1 / Kelch motif / Kelch-type beta propeller / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Muskelin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsKim, K.-H. / Hong, S.K. / Kim, E.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure of mouse muskelin discoidin domain and biochemical characterization of its self-association.
Authors: Kim, K.H. / Hong, S.K. / Hwang, K.Y. / Kim, E.E.
History
DepositionMar 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Muskelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7644
Polymers18,2811
Non-polymers4833
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.303, 98.303, 57.317
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Muskelin /


Mass: 18280.912 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, UNP residues 12-167
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mkln1 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: O89050
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% PEG 1500, 0.1M SPG(succinate-Phosphate-glycine), pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 5C (4A)10.97951
SYNCHROTRONPAL/PLS 5C (4A)20.97918
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 315r1CCDMar 28, 2013mirrors
ADSC QUANTUM 315r2CCDJun 20, 2013mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystalSINGLE WAVELENGTHMx-ray1
2double crystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979511
20.979181
ReflectionResolution: 1.55→50 Å / Num. all: 29472 / % possible obs: 98.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Biso Wilson estimate: 15.31 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 24.395
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 5.69 / % possible all: 90.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.55→27.161 Å / SU ML: 0.13 / σ(F): 2.27 / Phase error: 17.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1762 2024 6.87 %RANDOM
Rwork0.153 ---
all0.163 29472 --
obs0.1546 29469 98.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→27.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1288 0 29 203 1520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071353
X-RAY DIFFRACTIONf_angle_d1.1421827
X-RAY DIFFRACTIONf_dihedral_angle_d14.894512
X-RAY DIFFRACTIONf_chiral_restr0.091190
X-RAY DIFFRACTIONf_plane_restr0.006228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5498-1.58860.22681310.19381807X-RAY DIFFRACTION89
1.5886-1.63150.19121420.19161918X-RAY DIFFRACTION97
1.6315-1.67950.2121500.17641938X-RAY DIFFRACTION98
1.6795-1.73370.20761400.17331953X-RAY DIFFRACTION98
1.7337-1.79570.20481570.15741977X-RAY DIFFRACTION98
1.7957-1.86760.16321390.151983X-RAY DIFFRACTION99
1.8676-1.95250.19311480.15141954X-RAY DIFFRACTION100
1.9525-2.05540.19261290.15081998X-RAY DIFFRACTION99
2.0554-2.18420.171460.14321998X-RAY DIFFRACTION100
2.1842-2.35270.19881620.15411962X-RAY DIFFRACTION100
2.3527-2.58930.15141510.16182000X-RAY DIFFRACTION100
2.5893-2.96360.2121370.16552000X-RAY DIFFRACTION100
2.9636-3.73230.17591540.14771980X-RAY DIFFRACTION100
3.7323-27.1650.13641380.13551977X-RAY DIFFRACTION99

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