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- PDB-6l9x: Xenons in frog EPDR1 -

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Basic information

Entry
Database: PDB / ID: 6l9x
TitleXenons in frog EPDR1
ComponentsEpendymin-related 1
KeywordsUNKNOWN FUNCTION / EPDR1 / Xenon
Function / homology
Function and homology information


lysosomal lumen / cell-matrix adhesion / lysosome / calcium ion binding / extracellular region
Similarity search - Function
Ependymin / Ependymin / Ependymins
Similarity search - Domain/homology
XENON / Mammalian ependymin-related protein 1
Similarity search - Component
Biological speciesXenopus tropicalis (tropical clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsPark, S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)2019R1F1A1059170 Korea, Republic Of
CitationJournal: Crystals / Year: 2020
Title: De novo Phasing Xenons Observed in the Frog Ependymin-Related Protein
Authors: Park, S.
History
DepositionNov 11, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ependymin-related 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3625
Polymers22,8371
Non-polymers5254
Water00
1
A: Ependymin-related 1
hetero molecules

A: Ependymin-related 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,72410
Polymers45,6732
Non-polymers1,0508
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_775-y+2,-x+2,-z+1/61
Buried area5770 Å2
ΔGint-9 kcal/mol
Surface area18380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.455, 61.455, 233.838
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-303-

XE

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Components

#1: Protein Ependymin-related 1


Mass: 22836.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus tropicalis (tropical clawed frog)
Gene: epdr1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: F6VRB7
#2: Chemical
ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Xe / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: 2.96 Å3/Da / Density % sol: 58.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: PEG 8000, 0.2M calcium acetate, 0.1M sodium cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.54 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 6390 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.976 / Rmerge(I) obs: 0.097 / Net I/σ(I): 71
Reflection shellResolution: 2.9→2.95 Å / Rmerge(I) obs: 0.582 / Num. unique obs: 2312 / CC1/2: 0.976

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.868 / SU B: 16.812 / SU ML: 0.325 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.454
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3076 295 4.6 %RANDOM
Rwork0.219 ---
obs0.2228 6093 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 185.66 Å2 / Biso mean: 63.6 Å2 / Biso min: 39.49 Å2
Baniso -1Baniso -2Baniso -3
1-1.53 Å20.76 Å20 Å2
2--1.53 Å20 Å2
3----4.96 Å2
Refinement stepCycle: final / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1514 0 4 0 1518
Biso mean--131.49 --
Num. residues----185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021561
X-RAY DIFFRACTIONr_bond_other_d0.0020.021417
X-RAY DIFFRACTIONr_angle_refined_deg1.51.9522130
X-RAY DIFFRACTIONr_angle_other_deg0.78733284
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2265184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.95524.34276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.49115255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.278158
X-RAY DIFFRACTIONr_chiral_restr0.0740.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211749
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02357
LS refinement shellResolution: 2.903→2.978 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 18 -
Rwork0.271 426 -
all-444 -
obs--99.78 %

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