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- PDB-6lxx: Frog EPDR1 with an Ir atom -

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Basic information

Entry
Database: PDB / ID: 6lxx
TitleFrog EPDR1 with an Ir atom
ComponentsEpendymin-related 1
KeywordsUNKNOWN FUNCTION / Ependymin / Ependymin related protein
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
: / Mammalian ependymin-related protein 1
Similarity search - Component
Biological speciesXenopus tropicalis (tropical clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPark, S. / Park, J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2019R1F1A1059170 Korea, Republic Of
CitationJournal: Bull.Korean Chem.Soc. / Year: 2020
Title: A Single Soaked Iridium (IV) Ion Observed in the Frog Ependymin-Related Protein.
Authors: Park, J.K. / Park, S.Y.
History
DepositionFeb 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Category: citation / citation_author / database_2
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 / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ependymin-related 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1405
Polymers22,8371
Non-polymers3034
Water41423
1
A: Ependymin-related 1
hetero molecules

A: Ependymin-related 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,28010
Polymers45,6732
Non-polymers6068
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area1140 Å2
ΔGint-74 kcal/mol
Surface area23860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.008, 62.008, 233.409
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-302-

IR

21A-421-

HOH

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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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#3: Chemical ChemComp-IR / IRIDIUM ION


Mass: 192.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ir / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
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: 2.99 Å3/Da / Density % sol: 58.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2M Calcium acetate hydrate, 0.1M Sodium cacodylate trihydrate pH 6.5, 10-25% w/v Polyethylene glycol 8000

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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: 1.1054 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1054 Å / Relative weight: 1
ReflectionResolution: 2.4→53.7 Å / Num. obs: 11076 / % possible obs: 98.3 % / Redundancy: 18.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.078 / Net I/σ(I): 79.3
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 17.7 / Num. unique obs: 535 / CC1/2: 0.991

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JL9

6jl9


Resolution: 2.4→35.26 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.904 / SU B: 7.712 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.348 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29333 526 4.8 %RANDOM
Rwork0.23344 ---
obs0.23629 10455 98.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.342 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20.54 Å20 Å2
2--1.08 Å2-0 Å2
3----3.51 Å2
Refinement stepCycle: 1 / Resolution: 2.4→35.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1524 0 4 23 1551
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131582
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171395
X-RAY DIFFRACTIONr_angle_refined_deg1.6591.6652161
X-RAY DIFFRACTIONr_angle_other_deg1.2161.5713261
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5055186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26922.90786
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.70415258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.128158
X-RAY DIFFRACTIONr_chiral_restr0.0680.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021751
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02333
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.5965.098744
X-RAY DIFFRACTIONr_mcbond_other4.5855.097743
X-RAY DIFFRACTIONr_mcangle_it6.7657.63930
X-RAY DIFFRACTIONr_mcangle_other6.7697.633931
X-RAY DIFFRACTIONr_scbond_it5.275.611836
X-RAY DIFFRACTIONr_scbond_other5.2695.618837
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.1698.191232
X-RAY DIFFRACTIONr_long_range_B_refined11.32656.7871650
X-RAY DIFFRACTIONr_long_range_B_other11.3356.7471646
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 45 -
Rwork0.292 739 -
obs--99.62 %

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