[English] 日本語
Yorodumi
- PDB-2gn9: Crystal structure of UDP-GlcNAc inverting 4,6-dehydratase in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2gn9
TitleCrystal structure of UDP-GlcNAc inverting 4,6-dehydratase in complex with NADP and UDP-Glc
ComponentsUDP-GlcNAc C6 dehydratase
KeywordsLYASE / Rossmann fold / TYK triad / SDR / enzyme / dehydratase / UDP-GlcNAc / NADP
Function / homology
Function and homology information


UDP-N-acetylglucosamine 4,6-dehydratase (configuration-inverting) / lyase activity / nucleotide binding
Similarity search - Function
UDP-N-acetylglucosamine 4,6-dehydratase (inverting) / Polysaccharide biosynthesis protein, CapD-like domain / Polysaccharide biosynthesis protein, CapD-like domain / Polysaccharide biosynthesis protein / UDP-galactose 4-epimerase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / URIDINE-5'-DIPHOSPHATE-GLUCOSE / UDP-N-acetylglucosamine 4,6-dehydratase (inverting)
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsIshiyama, N. / Creuzenet, C. / Lam, J.S. / Berghuis, A.M.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structural Studies of FlaA1 from Helicobacter pylori Reveal the Mechanism for Inverting 4,6-Dehydratase Activity.
Authors: Ishiyama, N. / Creuzenet, C. / Miller, W.L. / Demendi, M. / Anderson, E.M. / Harauz, G. / Lam, J.S. / Berghuis, A.M.
History
DepositionApr 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-GlcNAc C6 dehydratase
B: UDP-GlcNAc C6 dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,2647
Polymers77,4492
Non-polymers2,8155
Water1,36976
1
A: UDP-GlcNAc C6 dehydratase
B: UDP-GlcNAc C6 dehydratase
hetero molecules

A: UDP-GlcNAc C6 dehydratase
B: UDP-GlcNAc C6 dehydratase
hetero molecules

A: UDP-GlcNAc C6 dehydratase
B: UDP-GlcNAc C6 dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,79221
Polymers232,3486
Non-polymers8,44415
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
MethodPQS
2
B: UDP-GlcNAc C6 dehydratase
hetero molecules

A: UDP-GlcNAc C6 dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,2647
Polymers77,4492
Non-polymers2,8155
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area8000 Å2
ΔGint-40 kcal/mol
Surface area25800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.376, 112.376, 107.349
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
DetailsThe biological assembly is a hexamer generated from the two protomers in the asymmetric unit by the operations:(-Y,X-Y,Z) and (-X+Y,-X,Z)

-
Components

#1: Protein UDP-GlcNAc C6 dehydratase / flaA1 protein


Mass: 38724.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: HP0840 / Plasmid: pET23 derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: O25511, Lyases; Carbon-oxygen lyases; Hydro-lyases
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER / Uridine diphosphate glucose


Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.53 Å3/Da / Density % sol: 51.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10% (v/v) PEG-200, 100 mM MES, 5% (v/w) PEG-3000, 4% (v/v) acetone, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 11, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 18312 / % possible obs: 99.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.083 / Χ2: 0.989 / Net I/σ(I): 8.7
Reflection shellResolution: 2.8→2.9 Å / % possible obs: 99.1 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.259 / Num. unique obs: 1849 / Χ2: 0.937

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.701data extraction
ADSCdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1SB8

1sb8


Resolution: 2.8→50 Å / FOM work R set: 0.76 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.307 1802 9.5 %random
Rwork0.22 ---
obs-18312 96.1 %-
Solvent computationBsol: 54.111 Å2
Displacement parametersBiso mean: 50.6 Å2
Baniso -1Baniso -2Baniso -3
1--11.551 Å2-17.56 Å20 Å2
2---11.551 Å20 Å2
3---23.102 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5163 0 180 76 5419
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it3.4711.5
X-RAY DIFFRACTIONc_scbond_it5.4222
X-RAY DIFFRACTIONc_mcangle_it5.3252
X-RAY DIFFRACTIONc_scangle_it7.1042.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 36

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.8-2.830.378390.306322361
2.83-2.850.317500.264406456
2.85-2.880.385470.272452499
2.88-2.910.386530.275418471
2.91-2.940.334400.293461501
2.94-2.980.418470.271470517
2.98-3.010.319490.263450499
3.01-3.040.444460.275482528
3.04-3.080.331530.279437490
3.08-3.120.433430.246458501
3.12-3.160.304620.255461523
3.16-3.210.394500.29450500
3.21-3.250.394520.244473525
3.25-3.30.272450.173490535
3.3-3.350.304560.201448504
3.35-3.410.348540.234470524
3.41-3.460.331420.231488530
3.46-3.530.272430.215486529
3.53-3.60.285480.221456504
3.6-3.670.254530.193476529
3.67-3.750.341550.209457512
3.75-3.840.237510.18470521
3.84-3.930.216530.149461514
3.93-4.040.317420.168490532
4.04-4.160.264690.18456525
4.16-4.290.175490.137469518
4.29-4.440.328460.182487533
4.44-4.620.227450.169473518
4.62-4.830.23510.17478529
4.83-5.090.21540.163474528
5.09-5.410.245560.183474530
5.41-5.820.224540.188471525
5.82-6.410.359640.219458522
6.41-7.340.312520.201492544
7.34-9.250.228400.206502542
9.25-500.010.913490.651344393
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2nap_ni.par
X-RAY DIFFRACTION3upg_ni.par
X-RAY DIFFRACTION4mes_ni.par
X-RAY DIFFRACTION5CNS_TOPPAR:water_rep.param

+
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