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- PDB-6jla: Crystal structure of a mouse ependymin related protein -

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Basic information

Entry
Database: PDB / ID: 6jla
TitleCrystal structure of a mouse ependymin related protein
ComponentsMammalian ependymin-related protein 1
KeywordsUNKNOWN FUNCTION / Ependymin
Function / homology
Function and homology information


myofibroblast contraction / ganglioside GM1 binding / cell-matrix adhesion / lysosomal lumen / phospholipid binding / lysosome / calcium ion binding / extracellular region / identical protein binding
Similarity search - Function
Ependymin / Ependymin / Ependymins
Similarity search - Domain/homology
Mammalian ependymin-related protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPark, S.
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 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_mod_residue.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 16, 2020Group: Database references / Derived calculations / Structure summary
Category: audit_author / chem_comp ...audit_author / chem_comp / citation / citation_author / struct_conn
Item: _audit_author.name / _chem_comp.pdbx_synonyms ..._audit_author.name / _chem_comp.pdbx_synonyms / _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.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mammalian ependymin-related protein 1
B: Mammalian ependymin-related protein 1
D: Mammalian ependymin-related protein 1
C: Mammalian ependymin-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,2469
Polymers91,7914
Non-polymers1,4555
Water1,964109
1
A: Mammalian ependymin-related protein 1
D: Mammalian ependymin-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5595
Polymers45,8962
Non-polymers6643
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-0 kcal/mol
Surface area19640 Å2
MethodPISA
2
B: Mammalian ependymin-related protein 1
C: Mammalian ependymin-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6874
Polymers45,8962
Non-polymers7922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-0 kcal/mol
Surface area18840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.966, 59.671, 137.336
Angle α, β, γ (deg.)90.00, 101.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Mammalian ependymin-related protein 1 / MERP-1


Mass: 22947.750 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Epdr2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q99M71
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.49 Å3/Da / Density % sol: 50.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 0.5 M Ammonium sulfate, 1.0 M Lithium sulfate monohydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.00065 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00065 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 35643 / % possible obs: 99.9 % / Redundancy: 7.2 % / Net I/σ(I): 44.4
Reflection shellResolution: 2.4→2.44 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.171 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.374 / ESU R Free: 0.251 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24007 1787 5 %RANDOM
Rwork0.18481 ---
obs0.18766 33843 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 53.975 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å2-0 Å21.77 Å2
2---0.23 Å2-0 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5995 0 94 109 6198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.026260
X-RAY DIFFRACTIONr_bond_other_d0.0020.025751
X-RAY DIFFRACTIONr_angle_refined_deg1.8381.9668519
X-RAY DIFFRACTIONr_angle_other_deg0.874313230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7685736
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23524.528318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.046151040
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1991544
X-RAY DIFFRACTIONr_chiral_restr0.1070.2916
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217091
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021467
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_it4.5114.9642950
X-RAY DIFFRACTIONr_mcbond_other4.5114.9622949
X-RAY DIFFRACTIONr_mcangle_it6.8577.433681
X-RAY DIFFRACTIONr_mcangle_other6.8577.4323682
X-RAY DIFFRACTIONr_scbond_it5.4115.6733310
X-RAY DIFFRACTIONr_scbond_other5.4115.6733310
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.458.244838
X-RAY DIFFRACTIONr_long_range_B_refined11.68640.4716900
X-RAY DIFFRACTIONr_long_range_B_other11.6940.4826889
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 116 -
Rwork0.228 2389 -
obs--96.09 %

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