[English] 日本語
Yorodumi
- PDB-6ppw: Crystal structure of NeuB, an N-acetylneuraminate synthase from N... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ppw
TitleCrystal structure of NeuB, an N-acetylneuraminate synthase from Neisseria meningitidis, in complex with magnesium and malate
ComponentsN-acetylneuraminate synthase
KeywordsBIOSYNTHETIC PROTEIN / TRANSFERASE / NeuB / sialic acid synthase / N-acetylneuraminate synthase
Function / homology
Function and homology information


N-acetylneuraminate synthase / N-acetylneuraminate synthase activity / carbohydrate biosynthetic process / metal ion binding
Similarity search - Function
: / N-acetylneuraminic acid synthase, N-terminal / NeuB family / SAF domain / SAF / SAF domain / Type Iii Antifreeze Protein Isoform Hplc 12 / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal / Antifreeze protein-like domain profile. ...: / N-acetylneuraminic acid synthase, N-terminal / NeuB family / SAF domain / SAF / SAF domain / Type Iii Antifreeze Protein Isoform Hplc 12 / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal / Antifreeze protein-like domain profile. / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain superfamily / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
D-MALATE / N-acetylneuraminate synthase
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsRosanally, A.Z. / Junop, M.S. / Berti, P.J.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-64422 Canada
Canadian Institutes of Health Research (CIHR)MOP-89903 Canada
CitationJournal: Biochemistry / Year: 2019
Title: NeuNAc Oxime: A Slow-Binding and Effectively Irreversible Inhibitor of the Sialic Acid Synthase NeuB.
Authors: Popovic, V. / Morrison, E. / Rosanally, A.Z. / Balachandran, N. / Senson, A.W. / Szabla, R. / Junop, M.S. / Berti, P.J.
History
DepositionJul 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
SupersessionOct 9, 2019ID: 2ZDR
Revision 1.1Oct 9, 2019Group: Advisory / Data collection / Category: pdbx_database_PDB_obs_spr
Revision 1.2Oct 23, 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.title / _citation_author.identifier_ORCID
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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-acetylneuraminate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5543
Polymers38,3961
Non-polymers1582
Water5,621312
1
A: N-acetylneuraminate synthase
hetero molecules

A: N-acetylneuraminate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1086
Polymers76,7912
Non-polymers3174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area8310 Å2
ΔGint-55 kcal/mol
Surface area25550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.793, 76.030, 77.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

-
Components

#1: Protein N-acetylneuraminate synthase / SynC protein


Mass: 38395.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria)
Gene: synC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H2VFG5, N-acetylneuraminate synthase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 10mM MgCl2 3% (v/v) MPD 1.7M Malic acid

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.85→77.38 Å / Num. obs: 30334 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 20.93 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.054 / Rrim(I) all: 0.117 / Net I/σ(I): 2.2
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.778 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2959 / CC1/2: 0.641 / Rpim(I) all: 0.409 / Rrim(I) all: 0.882 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XUZ

1xuz


Resolution: 1.85→29.74 Å / SU ML: 0.1927 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.5966
RfactorNum. reflection% reflection
Rfree0.2227 1533 5.07 %
Rwork0.1781 --
obs0.1803 30218 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.23 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2667 0 10 312 2989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00642722
X-RAY DIFFRACTIONf_angle_d0.79613674
X-RAY DIFFRACTIONf_chiral_restr0.0545408
X-RAY DIFFRACTIONf_plane_restr0.005484
X-RAY DIFFRACTIONf_dihedral_angle_d27.63351022
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.910.26061150.24922560X-RAY DIFFRACTION99.59
1.91-1.980.25971460.19692578X-RAY DIFFRACTION99.93
1.98-2.060.23411570.18952562X-RAY DIFFRACTION99.96
2.06-2.150.23461400.1712565X-RAY DIFFRACTION99.96
2.15-2.260.20711320.17672603X-RAY DIFFRACTION99.96
2.26-2.410.23651360.19432581X-RAY DIFFRACTION99.82
2.41-2.590.27011320.20612591X-RAY DIFFRACTION99.6
2.59-2.850.26641200.2022638X-RAY DIFFRACTION99.96
2.85-3.260.2291610.18112617X-RAY DIFFRACTION100
3.26-4.110.19891500.14942638X-RAY DIFFRACTION100
4.11-29.750.19181440.16172752X-RAY DIFFRACTION98.4

+
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