[English] 日本語
Yorodumi
- PDB-6e4r: Crystal Structure of the Drosophila Melanogaster Polypeptide N-Ac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6e4r
TitleCrystal Structure of the Drosophila Melanogaster Polypeptide N-Acetylgalactosaminyl Transferase PGANT9B
Componentspolypeptide N-acetylgalactosaminyltransferase 9
KeywordsTRANSFERASE / O-Glycosyltransferase / GT-A fold catalytic domain / Ricin B-type lectin domain / metal-dependent enzyme
Function / homology
Function and homology information


polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / Golgi cisterna / sexual reproduction / protein O-linked glycosylation / carbohydrate binding / Golgi membrane / Golgi apparatus / membrane / metal ion binding / cytosol
Similarity search - Function
N-acetylgalactosaminyltransferase / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Putative polypeptide N-acetylgalactosaminyltransferase 9
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.061 Å
AuthorsSamara, N.L. / Tabak, L.A. / Ten Hagen, K.G.
CitationJournal: Nat Commun / Year: 2018
Title: A molecular switch orchestrates enzyme specificity and secretory granule morphology.
Authors: Ji, S. / Samara, N.L. / Revoredo, L. / Zhang, L. / Tran, D.T. / Muirhead, K. / Tabak, L.A. / Ten Hagen, K.G.
History
DepositionJul 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: polypeptide N-acetylgalactosaminyltransferase 9
B: polypeptide N-acetylgalactosaminyltransferase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,63620
Polymers115,8722
Non-polymers1,76418
Water12,791710
1
A: polypeptide N-acetylgalactosaminyltransferase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,89210
Polymers57,9361
Non-polymers9569
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: polypeptide N-acetylgalactosaminyltransferase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,74410
Polymers57,9361
Non-polymers8089
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.913, 48.440, 232.037
Angle α, β, γ (deg.)90.000, 91.400, 90.000
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 143 and (name N or name...
21(chain B and ((resid 143 and (name O or name...

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY

Dom-IDComponent-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLY(chain A and ((resid 143 and (name N or name...AA1433
12LEULEU(chain A and ((resid 143 and (name N or name...AA143 - 6473 - 507
13LEULEU(chain A and ((resid 143 and (name N or name...AA143 - 6473 - 507
21GLYGLY(chain B and ((resid 143 and (name O or name...BB1433
22LEULEU(chain B and ((resid 143 and (name O or name...BB143 - 6473 - 507
23LEULEU(chain B and ((resid 143 and (name O or name...BB143 - 6473 - 507

-
Components

-
Protein / Sugars , 2 types, 4 molecules AB

#1: Protein polypeptide N-acetylgalactosaminyltransferase 9 / / pp-GaNTase 9 / Protein-UDP acetylgalactosaminyltransferase 9 / UDP-GalNAc:polypeptide N- ...pp-GaNTase 9 / Protein-UDP acetylgalactosaminyltransferase 9 / UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 9


Mass: 57936.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: pgant9, CG30463 / Production host: Komagataella pastoris (fungus) / Strain (production host): SMD1168
References: UniProt: Q8MRC9, polypeptide N-acetylgalactosaminyltransferase
#2: 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.: 2
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, 726 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 710 / 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: 2.76 Å3/Da / Density % sol: 55.46 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 20% PEG3350 and 0.18 M ammonium citrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.06→20.07 Å / Num. obs: 76401 / % possible obs: 96.9 % / Redundancy: 1 % / Biso Wilson estimate: 27.84 Å2 / Net I/σ(I): 6.7 / Num. measured all: 76401
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsDiffraction-ID% possible all
2.06-2.113479173.7
10.31-20.071549179.7

-
Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XHB

1xhb


Resolution: 2.061→20.07 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.88
RfactorNum. reflection% reflection
Rfree0.2068 3758 4.92 %
Rwork0.1644 --
obs0.1665 76401 97.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 144.89 Å2 / Biso mean: 37.1941 Å2 / Biso min: 11.77 Å2
Refinement stepCycle: final / Resolution: 2.061→20.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8034 0 114 711 8859
Biso mean--57.46 40.8 -
Num. residues----999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078424
X-RAY DIFFRACTIONf_angle_d0.97311391
X-RAY DIFFRACTIONf_chiral_restr0.0671176
X-RAY DIFFRACTIONf_plane_restr0.0061470
X-RAY DIFFRACTIONf_dihedral_angle_d18.7595017
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4363X-RAY DIFFRACTION12.385TORSIONAL
12B4363X-RAY DIFFRACTION12.385TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0615-2.08490.31091340.25272588272254
2.0849-2.10940.34382580.25974838509698
2.1094-2.13510.28442450.249248025047100
2.1351-2.16210.2952660.240247885054100
2.1621-2.19050.27342790.235748715150100
2.1905-2.22050.25632450.23374758500399
2.2205-2.25220.32172670.24564786505399
2.2522-2.28570.26092570.230848805137100
2.2857-2.32140.25662710.2084751502299
2.3214-2.35940.24372450.195647494994100
2.3594-2.40.24012200.196448915111100
2.4-2.44360.29482520.20884831508399
2.4436-2.49050.27242180.19074855507399
2.4905-2.54120.21952390.18254850508999
2.5412-2.59640.22932270.17894756498399
2.5964-2.65660.2392730.1844825509899
2.6566-2.72290.23341990.17674844504399
2.7229-2.79640.21781830.16964846502999
2.7964-2.87840.21312340.16134856509099
2.8784-2.9710.21423160.16044612492899
2.971-3.07690.19082920.16174779507199
3.0769-3.19960.18292770.1584743502098
3.1996-3.34460.19322770.14794721499898
3.3446-3.520.20562240.14314731495598
3.52-3.73920.16822370.14044818505598
3.7392-4.02580.16152280.12874728495697
4.0258-4.4270.15152280.11694686491497
4.427-5.05860.14632440.12164613485796
5.0586-6.33980.20442160.14974674489096
6.3398-20.07160.16042390.14954557479694
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.52310.10970.45440.82-0.29261.5704-0.0205-0.0419-0.1168-0.01860.07710.05710.1043-0.093-0.04110.153-0.0080.01730.12580.02760.164311.58970.471773.6425
25.48221.1335-1.15031.70830.08871.4418-0.0122-0.17010.230.073-0.06390.4003-0.16040.17340.08350.2638-0.0218-0.06830.15580.00520.2424-13.6493-1.059460.5924
32.54780.97840.34434.2916-0.25791.8443-0.1348-0.27630.15330.0595-0.04951.09180.0083-0.20950.13830.3003-0.0205-0.0450.1209-0.02960.5446-27.8788-9.284461.8156
41.20670.28810.58850.84940.39873.45710.0222-0.03510.0661-0.04040.0177-0.0135-0.24340.1182-0.03710.1882-0.0040.03950.21920.03260.152228.25588.4609114.7045
51.766-0.4539-1.33191.35660.85153.2174-0.2201-0.2669-0.2420.15610.07210.14070.44040.23590.11710.2683-0.01030.0460.28570.06850.216425.28222.9578137.0661
65.3798-0.0458-1.06184.2183-0.85423.39910.03890.48950.3665-0.538-0.02780.1486-0.417-0.0963-0.00710.3177-0.0282-0.030.21110.02130.19537.667223.5471147.5048
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 143 through 496 )A143 - 496
2X-RAY DIFFRACTION2chain 'A' and (resid 497 through 572 )A497 - 572
3X-RAY DIFFRACTION3chain 'A' and (resid 573 through 647 )A573 - 647
4X-RAY DIFFRACTION4chain 'B' and (resid 143 through 398 )B143 - 398
5X-RAY DIFFRACTION5chain 'B' and (resid 399 through 523 )B399 - 523
6X-RAY DIFFRACTION6chain 'B' and (resid 524 through 647 )B524 - 647

+
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