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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zjb
TitleStructure of N-acetylmannosamine-6-phosphate-2-epimerase from Vibrio cholerae
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
MALONATE ION / DI(HYDROXYETHYL)ETHER / : / Putative N-acetylmannosamine-6-phosphate 2-epimerase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.699 Å
AuthorsManjunath, L. / Guntupalli, S.
Funding support India, 3items
OrganizationGrant numberCountry
Department of Biotechnology ( DBT-Vinnowa-India-Sweden Collaborative Grant)BT/IN/SWEDEN/41/SR/2013 India
Department of Biotechnology ( DBT-Vinnowa-India-Sweden Collaborative Grant)BT/PR12422/MED/31/287/214 India
Department of Biotechnology ( DBT-Vinnowa-India-Sweden Collaborative Grant)BT/PR5081/INF/156/2012 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 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Source and taxonomy
Category: entity_src_gen / struct_ref ...entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id ..._entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.2Nov 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: Putative N-acetylmannosamine-6-phosphate 2-epimerase
B: Putative N-acetylmannosamine-6-phosphate 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,04010
Polymers54,2042
Non-polymers8378
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-10 kcal/mol
Surface area18350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.325, 70.417, 150.399
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
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, C1Y48_01775 / 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-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.41 Å3/Da / Density % sol: 53.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.2M Malonate,20% Peg 3350,pH 5.0 +1M Malonate pH 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9876 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: 0.9876 Å / Relative weight: 1
ReflectionResolution: 1.7→49.33 Å / Num. obs: 58571 / % possible obs: 99.8 % / Redundancy: 6.2 % / Biso Wilson estimate: 18 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.038 / Rrim(I) all: 0.097 / Net I/σ(I): 15.2 / Num. measured all: 365016 / Scaling rejects: 83
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
1.7-1.734.60.4171363929620.9130.2170.4733.797
8.99-49.335.20.04824804800.9970.0230.05328.198.7

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155: ???refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3igs

3igs


Resolution: 1.699→37.6 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.213 2974 5.09 %
Rwork0.1787 55497 -
obs0.1805 58471 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.53 Å2 / Biso mean: 22.1505 Å2 / Biso min: 8.55 Å2
Refinement stepCycle: final / Resolution: 1.699→37.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3442 0 53 351 3846
Biso mean--29.3 28.71 -
Num. residues----464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063576
X-RAY DIFFRACTIONf_angle_d0.7414861
X-RAY DIFFRACTIONf_chiral_restr0.055578
X-RAY DIFFRACTIONf_plane_restr0.005641
X-RAY DIFFRACTIONf_dihedral_angle_d8.7462150
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6989-1.72680.25581390.2062477261696
1.7268-1.75650.26791400.21226622802100
1.7565-1.78850.24991360.220825692705100
1.7885-1.82290.25671350.219426432778100
1.8229-1.86010.29031540.231425712725100
1.8601-1.90050.32681260.235726412767100
1.9005-1.94470.28391270.23125982725100
1.9447-1.99340.29091200.222926482768100
1.9934-2.04730.24491190.213726622781100
2.0473-2.10750.20791420.190525942736100
2.1075-2.17550.20461360.178126372773100
2.1755-2.25330.19331510.172826452796100
2.2533-2.34350.21931470.173126332780100
2.3435-2.45010.22471470.176226252772100
2.4501-2.57920.19811580.169926362794100
2.5792-2.74080.19051470.171326462793100
2.7408-2.95230.20641340.175526842818100
2.9523-3.24930.20071520.17826542806100
3.2493-3.71910.1941570.166926962853100
3.7191-4.68430.17321510.142727202871100
4.6843-37.60890.21991560.166528563012100

+
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