[English] 日本語
Yorodumi
- PDB-5egh: Structure of ENPP6, a choline-specific glycerophosphodiester-phos... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5egh
TitleStructure of ENPP6, a choline-specific glycerophosphodiester-phosphodiesterase in complex with phosphocholine
ComponentsEctonucleotide pyrophosphatase/phosphodiesterase family member 6
KeywordsHYDROLASE / Choline metabolism / Phosphodiesterase
Function / homology
Function and homology information


glycerophosphocholine cholinephosphodiesterase / glycerophosphocholine cholinephosphodiesterase activity / Glycerophospholipid catabolism / glycerophosphodiester phosphodiesterase activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / phosphoric diester hydrolase activity / choline metabolic process / lipid catabolic process / lipid metabolic process / extracellular region ...glycerophosphocholine cholinephosphodiesterase / glycerophosphocholine cholinephosphodiesterase activity / Glycerophospholipid catabolism / glycerophosphodiester phosphodiesterase activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / phosphoric diester hydrolase activity / choline metabolic process / lipid catabolic process / lipid metabolic process / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Gyrase A; domain 2 - #180 / Type I phosphodiesterase/nucleotide pyrophosphatase/phosphate transferase / Type I phosphodiesterase / nucleotide pyrophosphatase / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / Gyrase A; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOCHOLINE / Glycerophosphocholine cholinephosphodiesterase ENPP6
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.803 Å
AuthorsMorita, J. / Kano, K. / Kato, K. / Takita, H. / Ishitani, R. / Nishimasu, H. / Nureki, O. / Aoki, J.
CitationJournal: Sci Rep / Year: 2016
Title: Structure and biological function of ENPP6, a choline-specific glycerophosphodiester-phosphodiesterase
Authors: Morita, J. / Kano, K. / Kato, K. / Takita, H. / Sakagami, H. / Yamamoto, Y. / Mihara, E. / Ueda, H. / Sato, T. / Tokuyama, H. / Arai, H. / Asou, H. / Takagi, J. / Ishitani, R. / Nishimasu, H. ...Authors: Morita, J. / Kano, K. / Kato, K. / Takita, H. / Sakagami, H. / Yamamoto, Y. / Mihara, E. / Ueda, H. / Sato, T. / Tokuyama, H. / Arai, H. / Asou, H. / Takagi, J. / Ishitani, R. / Nishimasu, H. / Nureki, O. / Aoki, J.
History
DepositionOct 27, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2016Provider: 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_conn_angle / pdbx_struct_oper_list / struct_asym / struct_conn / struct_conn_type / 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 / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ectonucleotide pyrophosphatase/phosphodiesterase family member 6
B: Ectonucleotide pyrophosphatase/phosphodiesterase family member 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,77319
Polymers99,1972
Non-polymers3,57617
Water9,512528
1
A: Ectonucleotide pyrophosphatase/phosphodiesterase family member 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,51910
Polymers49,5991
Non-polymers1,9219
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-31 kcal/mol
Surface area16130 Å2
MethodPISA
2
B: Ectonucleotide pyrophosphatase/phosphodiesterase family member 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2549
Polymers49,5991
Non-polymers1,6558
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-33 kcal/mol
Surface area15950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.620, 68.849, 69.761
Angle α, β, γ (deg.)60.590, 86.990, 68.100
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Ectonucleotide pyrophosphatase/phosphodiesterase family member 6 / NPP-6 / Choline-specific glycerophosphodiester phosphodiesterase / Glycerophosphocholine ...NPP-6 / Choline-specific glycerophosphodiester phosphodiesterase / Glycerophosphocholine cholinephosphodiesterase / GPC-Cpde


Mass: 49598.664 Da / Num. of mol.: 2 / Fragment: UNP residues 1-421 / Mutation: C393A, C412S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Enpp6 / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
References: UniProt: Q8BGN3, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases, glycerophosphocholine cholinephosphodiesterase

-
Sugars , 3 types, 6 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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

-
Non-polymers , 4 types, 539 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PC / PHOSPHOCHOLINE / Phosphocholine


Mass: 184.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H15NO4P
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 528 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: sodium acetate, ammonium chloride, PEG 6000, zinc sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.278 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.278 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 81806 / % possible obs: 94 % / Redundancy: 3.5 % / Net I/σ(I): 12.8
Reflection shellRejects: 0

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XSCALEdata scaling
MOLREPphasing
Cootmodel building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.803→45.634 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 22.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2111 4090 5 %
Rwork0.1748 77701 -
obs0.1766 81791 93.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.81 Å2 / Biso mean: 32.8955 Å2 / Biso min: 12.67 Å2
Refinement stepCycle: final / Resolution: 1.803→45.634 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6391 0 220 528 7139
Biso mean--50.45 38.35 -
Num. residues----785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076859
X-RAY DIFFRACTIONf_angle_d0.8959349
X-RAY DIFFRACTIONf_chiral_restr0.0561014
X-RAY DIFFRACTIONf_plane_restr0.0051172
X-RAY DIFFRACTIONf_dihedral_angle_d12.5454044
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8032-1.82440.3731170.34532213233077
1.8244-1.84660.32751380.32082617275593
1.8466-1.870.33581400.28492666280692
1.87-1.89460.32331370.27662595273292
1.8946-1.92060.30321370.23912637277492
1.9206-1.9480.26491420.22842684282693
1.948-1.97710.24291380.21382623276193
1.9771-2.0080.23951410.20372684282593
2.008-2.04090.24661390.19172636277594
2.0409-2.07610.23311390.19172645278493
2.0761-2.11380.23661430.1892723286694
2.1138-2.15450.23671410.19432673281495
2.1545-2.19850.22221420.19242702284494
2.1985-2.24630.22751440.18542723286795
2.2463-2.29850.24091410.18292691283295
2.2985-2.3560.21331420.18582696283895
2.356-2.41970.19461440.17992729287395
2.4197-2.49090.25611430.18752715285895
2.4909-2.57130.2191430.18352716285995
2.5713-2.66320.24331430.17652727287096
2.6632-2.76980.22341450.17952760290596
2.7698-2.89580.2141440.18282737288196
2.8958-3.04850.23331440.18192721286596
3.0485-3.23940.19751410.17312686282795
3.2394-3.48950.1961430.16242717286095
3.4895-3.84050.19251440.15452742288696
3.8405-4.39580.16291450.1392750289596
4.3958-5.53670.16651430.13412713285696
5.5367-45.64850.18351470.16262780292797

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more