[English] 日本語
Yorodumi
- PDB-5zjn: Structure of N-acetylmannosamine-6-phosphate-2-epimerase from Vib... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zjn
TitleStructure of N-acetylmannosamine-6-phosphate-2-epimerase from Vibrio cholerae with N-acetylmannosamine-6-phosphate
ComponentsPutative N-acetylmannosamine-6-phosphate 2-epimerase
KeywordsISOMERASE / Sialic acid catabolic pathway Epimerase
Function / homology
Function and homology information


N-acetylmannosamine catabolic process / N-acylglucosamine-6-phosphate 2-epimerase / N-acylmannosamine-6-phosphate 2-epimerase activity / N-acylglucosamine-6-phosphate 2-epimerase activity / N-acetylneuraminate catabolic process / carbohydrate metabolic process / cytosol
Similarity search - Function
Putative N-acetylmannosamine-6-phosphate epimerase / Putative N-acetylmannosamine-6-phosphate epimerase / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
N-acetylmannosamine-6-phosphate / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / : / Putative N-acetylmannosamine-6-phosphate 2-epimerase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsManjunath, L. / Guntupalli, S.
Funding support India, 4items
OrganizationGrant numberCountry
DBT/IN/SWEDEN/41/SR/2013 India
BT/PR5081/INF/156/2012
BT/PR12422/MED/31/287/214,
BT/INF/22/SP22660/2017 India
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Crystal structures and kinetic analyses of N-acetylmannosamine-6-phosphate 2-epimerases from Fusobacterium nucleatum and Vibrio cholerae
Authors: Manjunath, L. / Guntupalli, S.R. / Currie, M.J. / North, R.A. / Dobson, R.C.J. / Nayak, V. / Subramanian, R.
History
DepositionMar 21, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Structure summary / Category: entity / Item: _entity.pdbx_fragment
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative N-acetylmannosamine-6-phosphate 2-epimerase
B: Putative N-acetylmannosamine-6-phosphate 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2308
Polymers54,2042
Non-polymers1,0276
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-21 kcal/mol
Surface area17440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.959, 70.653, 149.362
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain D
21chain C
12(chain A and (resseq 8:160 or resseq 165:221 or (resid...
22(chain B and (resseq 8:160 or resseq 165:221 or (resid...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain DD301
211chain CC301
112(chain A and (resseq 8:160 or resseq 165:221 or (resid...A8 - 160
122(chain A and (resseq 8:160 or resseq 165:221 or (resid...A165 - 221
132(chain A and (resseq 8:160 or resseq 165:221 or (resid...A8 - 231
142(chain A and (resseq 8:160 or resseq 165:221 or (resid...A8 - 231
152(chain A and (resseq 8:160 or resseq 165:221 or (resid...A8 - 231
162(chain A and (resseq 8:160 or resseq 165:221 or (resid...A8 - 231
172(chain A and (resseq 8:160 or resseq 165:221 or (resid...A8 - 231
182(chain A and (resseq 8:160 or resseq 165:221 or (resid...A8 - 231
192(chain A and (resseq 8:160 or resseq 165:221 or (resid...A8 - 231
1102(chain A and (resseq 8:160 or resseq 165:221 or (resid...A8 - 231
1112(chain A and (resseq 8:160 or resseq 165:221 or (resid...A8 - 231
212(chain B and (resseq 8:160 or resseq 165:221 or (resid...B8 - 160
222(chain B and (resseq 8:160 or resseq 165:221 or (resid...B165 - 221
232(chain B and (resseq 8:160 or resseq 165:221 or (resid...B6 - 232
242(chain B and (resseq 8:160 or resseq 165:221 or (resid...B6 - 232
252(chain B and (resseq 8:160 or resseq 165:221 or (resid...B6 - 232
262(chain B and (resseq 8:160 or resseq 165:221 or (resid...B6 - 232
272(chain B and (resseq 8:160 or resseq 165:221 or (resid...B6 - 232
282(chain B and (resseq 8:160 or resseq 165:221 or (resid...B6 - 232
292(chain B and (resseq 8:160 or resseq 165:221 or (resid...B6 - 232
2102(chain B and (resseq 8:160 or resseq 165:221 or (resid...B6 - 232
2112(chain B and (resseq 8:160 or resseq 165:221 or (resid...B6 - 232
2122(chain B and (resseq 8:160 or resseq 165:221 or (resid...B6 - 232

NCS ensembles :
ID
1
2

-
Components

#1: Protein Putative N-acetylmannosamine-6-phosphate 2-epimerase / ManNAc-6-P epimerase


Mass: 27101.770 Da / Num. of mol.: 2 / Fragment: UNP residues 6-240
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: nanE / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A2K2UT85, UniProt: Q9KR62*PLUS, N-acylglucosamine-6-phosphate 2-epimerase
#2: Chemical ChemComp-LRY / N-acetylmannosamine-6-phosphate


Mass: 301.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16NO9P
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.2M Malonate, pH 5.0, 20% PEG3350, 1M malonate pH 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.66→49.79 Å / Num. obs: 15416 / % possible obs: 99.1 % / Redundancy: 5.8 % / Biso Wilson estimate: 43.02 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.062 / Rrim(I) all: 0.152 / Net I/σ(I): 8.7 / Num. measured all: 89562 / Scaling rejects: 15
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.66-2.795.30.4931002219000.8920.230.5452.494.3
8.82-49.795.20.05726134990.9950.0270.06418.899.2

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→40.945 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2807 737 4.8 %
Rwork0.2301 14624 -
obs0.2327 15361 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.99 Å2 / Biso mean: 41.3865 Å2 / Biso min: 22.25 Å2
Refinement stepCycle: final / Resolution: 2.66→40.945 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3275 0 66 0 3341
Biso mean--50.23 --
Num. residues----443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083385
X-RAY DIFFRACTIONf_angle_d0.9354596
X-RAY DIFFRACTIONf_chiral_restr0.061556
X-RAY DIFFRACTIONf_plane_restr0.007593
X-RAY DIFFRACTIONf_dihedral_angle_d11.2812028
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A0X-RAY DIFFRACTION7.489TORSIONAL
12B0X-RAY DIFFRACTION7.489TORSIONAL
21A1932X-RAY DIFFRACTION7.489TORSIONAL
22B1932X-RAY DIFFRACTION7.489TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.66-2.86540.35521510.28122787293896
2.8654-3.15360.32471290.25172876300599
3.1536-3.60970.27151630.231629053068100
3.6097-4.54690.24351410.208729633104100
4.5469-40.94960.27971530.225730933246100

+
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://pdbjlvh1.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