[English] 日本語
Yorodumi
- PDB-4nk8: Crystal Structure of the periplasmic alginate epimerase AlgG D317... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nk8
TitleCrystal Structure of the periplasmic alginate epimerase AlgG D317A mutant
ComponentsPoly(beta-D-mannuronate) C5 epimerase
KeywordsISOMERASE / AlgG / Pseudomonas / parallel beta-helix / alginate / mannuronate / polysaccharide epimerase / lysine methylation
Function / homology
Function and homology information


mannuronan 5-epimerase / alginic acid biosynthetic process / isomerase activity / ubiquitin-dependent protein catabolic process / regulation of apoptotic process / periplasmic space
Similarity search - Function
Right handed beta helix domain / Right handed beta helix region / Parallel beta-helix repeat-2 / Carbohydrate-binding/sugar hydrolysis domain / Domain present in carbohydrate binding proteins and sugar hydrolses / Parallel beta-helix repeat / Parallel beta-helix repeats / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold ...Right handed beta helix domain / Right handed beta helix region / Parallel beta-helix repeat-2 / Carbohydrate-binding/sugar hydrolysis domain / Domain present in carbohydrate binding proteins and sugar hydrolses / Parallel beta-helix repeat / Parallel beta-helix repeats / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
Mannuronan C5-epimerase
Similarity search - Component
Biological speciesPseudomonas syringae pv. tomato (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2924 Å
AuthorsHowell, P.L. / Wolfram, F. / Robinson, H.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Catalytic Mechanism and Mode of Action of the Periplasmic Alginate Epimerase AlgG.
Authors: Wolfram, F. / Kitova, E.N. / Robinson, H. / Walvoort, M.T. / Codee, J.D. / Klassen, J.S. / Howell, P.L.
History
DepositionNov 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Mar 19, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Poly(beta-D-mannuronate) C5 epimerase


Theoretical massNumber of molelcules
Total (without water)55,0921
Polymers55,0921
Non-polymers00
Water52229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Poly(beta-D-mannuronate) C5 epimerase

A: Poly(beta-D-mannuronate) C5 epimerase


Theoretical massNumber of molelcules
Total (without water)110,1842
Polymers110,1842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1610 Å2
ΔGint-12 kcal/mol
Surface area31190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.599, 125.599, 98.487
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-604-

HOH

-
Components

#1: Protein Poly(beta-D-mannuronate) C5 epimerase


Mass: 55091.824 Da / Num. of mol.: 1 / Mutation: D317A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Strain: DC3000 / Gene: algG, PSPTO_1238 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RP
References: UniProt: Q887Q3, Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 4.07 Å3/Da / Density % sol: 69.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.26 M (NH4)2SO4, 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 5, 2012
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.292→50 Å / Num. obs: 40515 / % possible obs: 100 % / Redundancy: 23.7 % / Biso Wilson estimate: 50.27 Å2 / Rmerge(I) obs: 0.11 / Χ2: 1.208 / Net I/σ(I): 11.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.292-2.38190.72439880.866199.7
2.38-2.4821.60.55539960.9151100
2.48-2.5922.30.43340140.9551100
2.59-2.7322.30.30940111.0851100
2.73-2.922.30.21740101.2351100
2.9-3.1222.30.16340501.3941100
3.12-3.4422.10.12940391.6211100
3.44-3.9321.90.10540671.7461100
3.93-4.9530.80.11140961.393199.9
4.95-5031.30.07442440.8871100

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.45 Å47.61 Å
Translation7.45 Å47.61 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2924→47.609 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7645 / SU ML: 0.31 / σ(F): 1.34 / Phase error: 29.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2363 3844 4.95 %
Rwork0.2085 --
obs0.2099 40446 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.61 Å2 / Biso mean: 39.1219 Å2 / Biso min: 21.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2924→47.609 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3328 0 0 29 3357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083394
X-RAY DIFFRACTIONf_angle_d1.1514594
X-RAY DIFFRACTIONf_chiral_restr0.08507
X-RAY DIFFRACTIONf_plane_restr0.004587
X-RAY DIFFRACTIONf_dihedral_angle_d12.9731258
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2924-2.32140.36471400.31652575271594
2.3214-2.35190.42451320.30812723285599
2.3519-2.38410.31311460.289427712917100
2.3841-2.41820.35571440.276627242868100
2.4182-2.45430.31081440.254627522896100
2.4543-2.49260.33371330.274727422875100
2.4926-2.53350.27571390.266127282867100
2.5335-2.57720.33861360.269527392875100
2.5772-2.6240.37271460.268327752921100
2.624-2.67450.3121460.278526932839100
2.6745-2.72910.31681440.266327612905100
2.7291-2.78840.28651360.257127272863100
2.7884-2.85330.34581440.251527622906100
2.8533-2.92460.26521400.249227202860100
2.9246-3.00370.30841480.262127462894100
3.0037-3.09210.35221440.260427412885100
3.0921-3.19180.29531520.258227632915100
3.1918-3.30590.20641490.245927552904100
3.3059-3.43820.2731480.233426872835100
3.4382-3.59470.26171380.22527692907100
3.5947-3.78410.23291460.206227792925100
3.7841-4.02110.20381460.18827172863100
4.0211-4.33130.19991360.169627812917100
4.3313-4.76690.18161420.143226972839100
4.7669-5.45580.19751460.163227602906100
5.4558-6.87040.17771330.186527352868100
6.8704-47.61950.1641460.165827522898100

+
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