[English] 日本語
Yorodumi
- PDB-6jku: Crystal structure of N-acetylglucosamine-6-phosphate deacetylase ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jku
TitleCrystal structure of N-acetylglucosamine-6-phosphate deacetylase from Pasteurella Multocida
ComponentsN-acetylglucosamine-6-phosphate deacetylase
KeywordsMETAL BINDING PROTEIN / deacetylase / sialic acid catabolism pathway
Function / homology
Function and homology information


N-acetylglucosamine-6-phosphate deacetylase / N-acetylglucosamine-6-phosphate deacetylase activity / N-acetylglucosamine metabolic process / carbohydrate metabolic process / metal ion binding
Similarity search - Function
N-acetylglucosamine-6-phosphate deacetylase / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel ...N-acetylglucosamine-6-phosphate deacetylase / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / N-acetylglucosamine-6-phosphate deacetylase / N-acetylglucosamine-6-phosphate deacetylase
Similarity search - Component
Biological speciesPasteurella multocida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsManjunath, L. / Bose, S. / Subramanian, R.
Funding support India, 4items
OrganizationGrant numberCountry
Department of Biotechnology (India)BT/INF/22/SP22660/2017 India
Department of Biotechnology (India)BT/PR12422/MED /31/287/214 India
Department of Biotechnology (India)BT/PR5081/INF/156/2012 India
Department of Biotechnology (India)BT/IN/SWEDEN/06/SR/2017-2018 India
CitationJournal: Proteins / Year: 2020
Title: Quaternary variations in the structural assembly of N-acetylglucosamine-6-phosphate deacetylase from Pasteurella multocida.
Authors: Manjunath, L. / Coombes, D. / Davies, J. / Dhurandhar, M. / Tiwari, V.R. / Dobson, R.C.J. / Sowdhamini, R. / Ramaswamy, S. / Bose, S.
History
DepositionMar 1, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Mar 17, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N-acetylglucosamine-6-phosphate deacetylase
B: N-acetylglucosamine-6-phosphate deacetylase
C: N-acetylglucosamine-6-phosphate deacetylase
D: N-acetylglucosamine-6-phosphate deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,91551
Polymers171,5874
Non-polymers3,32847
Water20,7711153
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Cryo electron microscopy was also performed
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15060 Å2
ΔGint-258 kcal/mol
Surface area51550 Å2
Unit cell
Length a, b, c (Å)89.162, 139.549, 166.556
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
N-acetylglucosamine-6-phosphate deacetylase


Mass: 42896.750 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pasteurella multocida (bacteria) / Strain: Pm70 / Gene: BGK37_09560 / Plasmid: pET300 NT/DEST / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1E3XI56, UniProt: Q9CMF5*PLUS

-
Non-polymers , 6 types, 1200 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: PO4
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1153 / 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: 3.02 Å3/Da / Density % sol: 59.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES sodium salt pH 7.5, 0.8 M Sodium phosphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.975 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.95→47.13 Å / Num. obs: 134675 / % possible obs: 89.8 % / Redundancy: 4.9 % / Biso Wilson estimate: 13.96 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.052 / Rrim(I) all: 0.124 / Net I/σ(I): 10
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 6848 / CC1/2: 0.636 / Rpim(I) all: 0.526 / % possible all: 92.7

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P50

2p50


Resolution: 1.95→47.129 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1998 6601 4.9 %
Rwork0.1632 128029 -
obs0.165 134630 88.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.85 Å2 / Biso mean: 27.3031 Å2 / Biso min: 12.44 Å2
Refinement stepCycle: final / Resolution: 1.95→47.129 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11432 0 183 1154 12769
Biso mean--41.08 34.24 -
Num. residues----1528
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 (%)
1.95-1.97220.27792260.24674368459492
1.9722-1.99540.26822240.22824388461292
1.9954-2.01970.29322190.23324468468794
2.0197-2.04530.25962080.2274430463893
2.0453-2.07220.26782310.2124444467593
2.0722-2.10060.27312120.20884408462093
2.1006-2.13060.24672390.20144392463192
2.1306-2.16240.26511990.19844398459792
2.1624-2.19620.25582090.19954377458691
2.1962-2.23220.25752250.19574364458991
2.2322-2.27070.21552280.19454273450190
2.2707-2.31190.24752380.19174240447890
2.3119-2.35640.2332680.18524234450289
2.3564-2.40450.2392080.18084293450190
2.4045-2.45680.22852080.18294161436987
2.4568-2.51390.24532090.18214146435587
2.5139-2.57680.24292180.17684079429786
2.5768-2.64650.23632080.17654046425484
2.6465-2.72430.20781960.17774060425685
2.7243-2.81230.23332300.17824032426285
2.8123-2.91280.23651910.18093966415782
2.9128-3.02940.21431890.16923904409381
3.0294-3.16720.20411960.16373988418483
3.1672-3.33410.20042110.15774114432585
3.3341-3.5430.16212380.14764294453289
3.543-3.81640.15062240.13224470469492
3.8164-4.20030.15492500.12214443469391
4.2003-4.80750.13872310.11014401463290
4.8075-6.0550.15672370.1324426466390
6.055-47.14270.16372310.15254422465386

+
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