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- PDB-6jl9: Crystal structure of a frog ependymin related protein -

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Basic information

Entry
Database: PDB / ID: 6jl9
TitleCrystal structure of a frog ependymin related protein
ComponentsEpendymin-related 1
KeywordsUNKNOWN FUNCTION / Ependymin
Function / homologyEpendymin / Ependymin / Ependymins / cell-matrix adhesion / lysosome / calcium ion binding / extracellular region / Mammalian ependymin-related protein 1
Function and homology information
Biological speciesXenopus tropicalis (tropical clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsPark, S.Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)2016R1D1A1A09918187 Korea, Republic Of
CitationJournal: Iucrj / Year: 2019
Title: Structures of three ependymin-related proteins suggest their function as a hydrophobic molecule binder.
Authors: Park, J.K. / Kim, K.Y. / Sim, Y.W. / Kim, Y.I. / Kim, J.K. / Lee, C. / Han, J. / Kim, C.U. / Lee, J.E. / Park, S.
History
DepositionMar 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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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)22,8772
Polymers22,8371
Non-polymers401
Water99155
1
A: Ependymin-related 1
hetero molecules

A: Ependymin-related 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7534
Polymers45,6732
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_775-y+2,-x+2,-z+1/61
Buried area4600 Å2
ΔGint-27 kcal/mol
Surface area19940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.208, 61.208, 236.196
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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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: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.8 Å3/Da / Density % sol: 56.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2M Calcium acetate hydrate, 0.1M Sodium cacodylate trihydrate pH 6.5, 18%(w/v) Polyethylene glycol 8,000

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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→53.01 Å / Num. obs: 18642 / % possible obs: 99.7 % / Redundancy: 19.8 % / Net I/σ(I): 70.5
Reflection shellResolution: 2→2.03 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
ARP/wARP8model building
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→53.01 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.903 / SU B: 9.651 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.287 / ESU R Free: 0.171 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27753 952 5.1 %RANDOM
Rwork0.1942 ---
obs0.19819 17685 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 55.467 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20.48 Å20 Å2
2--0.95 Å20 Å2
3----3.08 Å2
Refinement stepCycle: 1 / Resolution: 2→53.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1554 0 1 55 1610
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191623
X-RAY DIFFRACTIONr_bond_other_d0.0010.021465
X-RAY DIFFRACTIONr_angle_refined_deg1.741.9342217
X-RAY DIFFRACTIONr_angle_other_deg1.47333395
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5675191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91824.02482
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.54115261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.925158
X-RAY DIFFRACTIONr_chiral_restr0.1030.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211826
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02388
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_it10.0025.114759
X-RAY DIFFRACTIONr_mcbond_other9.995.118758
X-RAY DIFFRACTIONr_mcangle_it11.3447.694947
X-RAY DIFFRACTIONr_mcangle_other11.3387.696948
X-RAY DIFFRACTIONr_scbond_it11.3615.78863
X-RAY DIFFRACTIONr_scbond_other11.3555.779864
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.9528.3891269
X-RAY DIFFRACTIONr_long_range_B_refined13.96742.7161808
X-RAY DIFFRACTIONr_long_range_B_other13.94142.6951800
X-RAY DIFFRACTIONr_rigid_bond_restr5.13233084
X-RAY DIFFRACTIONr_sphericity_free37.313516
X-RAY DIFFRACTIONr_sphericity_bonded28.53753072
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 77 -
Rwork0.237 1259 -
obs--99.26 %

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