[English] 日本語
Yorodumi
- PDB-8xfq: Structure of the alginate epimerase/lyase complexed with penta-ma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8xfq
TitleStructure of the alginate epimerase/lyase complexed with penta-mannuronic acid
Componentsmannuronan 5-epimerase
KeywordsISOMERASE / Substrate / Complex / Epimerase
Function / homology
Function and homology information


mannuronan 5-epimerase / alginic acid biosynthetic process / isomerase activity / lyase activity / calcium ion binding / extracellular region
Similarity search - Function
Carbohydrate-binding/sugar hydrolysis domain / Pectate lyase superfamily protein / Pectate lyase superfamily protein / Domain present in carbohydrate binding proteins and sugar hydrolses / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat / RTX calcium-binding nonapeptide repeat (4 copies) / Parallel beta-helix repeat / Parallel beta-helix repeats ...Carbohydrate-binding/sugar hydrolysis domain / Pectate lyase superfamily protein / Pectate lyase superfamily protein / Domain present in carbohydrate binding proteins and sugar hydrolses / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat / RTX calcium-binding nonapeptide repeat (4 copies) / Parallel beta-helix repeat / Parallel beta-helix repeats / Serralysin-like metalloprotease, C-terminal / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / mannuronan 5-epimerase
Similarity search - Component
Biological speciesAzotobacter chroococcum NCIMB 8003 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsFujiwara, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21K06077 Japan
CitationJournal: Febs Lett. / Year: 2024
Title: Structural basis for the minimal bifunctional alginate epimerase AlgE3 from Azotobacter chroococcum.
Authors: Fujiwara, T. / Mano, E. / Nango, E.
History
DepositionDec 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: mannuronan 5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,11511
Polymers51,6131
Non-polymers1,50210
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area17950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.050, 122.050, 118.650
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

-
Components

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein mannuronan 5-epimerase


Mass: 51613.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter chroococcum NCIMB 8003 (bacteria)
Gene: algE7, Achr_39570 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0C4WKK2, mannuronan 5-epimerase
#2: Polysaccharide beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid- ...beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid


Type: oligosaccharide / Mass: 898.634 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpAb1-4DManpAb1-4DManpAb1-4DManpAb1-4DManpAb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a1122A-1b_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{}}}}}LINUCSPDB-CARE

-
Non-polymers , 4 types, 136 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium acetate, pH4.5, 30% w/v PEG 4000, 15% v/v glycerol

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→48.3 Å / Num. obs: 31252 / % possible obs: 100 % / Redundancy: 18.2 % / Biso Wilson estimate: 50.09 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.18 / Net I/σ(I): 13.01
Reflection shellResolution: 2.25→2.39 Å / Redundancy: 17.6 % / Rmerge(I) obs: 1.668 / Mean I/σ(I) obs: 1.48 / Num. unique obs: 5153 / CC1/2: 0.846 / % possible all: 100

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19.2_4158phasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→48.28 Å / SU ML: 0.2714 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 21.1509
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2023 1486 4.76 %
Rwork0.1668 29753 -
obs0.1684 31239 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.75 Å2
Refinement stepCycle: LAST / Resolution: 2.25→48.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3594 0 91 127 3812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00293734
X-RAY DIFFRACTIONf_angle_d0.6645046
X-RAY DIFFRACTIONf_chiral_restr0.0475556
X-RAY DIFFRACTIONf_plane_restr0.0034692
X-RAY DIFFRACTIONf_dihedral_angle_d6.43536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.320.26041370.25622691X-RAY DIFFRACTION100
2.32-2.410.2771410.22382696X-RAY DIFFRACTION100
2.41-2.50.271500.21512682X-RAY DIFFRACTION99.96
2.5-2.620.24881480.20622702X-RAY DIFFRACTION99.96
2.62-2.750.24321180.21812695X-RAY DIFFRACTION99.96
2.75-2.930.2361320.19452733X-RAY DIFFRACTION100
2.93-3.150.21951300.1882706X-RAY DIFFRACTION100
3.15-3.470.23891320.19142714X-RAY DIFFRACTION100
3.47-3.970.20141440.14782718X-RAY DIFFRACTION100
3.97-50.14551270.13072701X-RAY DIFFRACTION99.72
5-48.280.17571270.14412715X-RAY DIFFRACTION99.93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0707482929034-0.103580571471-0.01056212145820.3396155051470.04118456637590.190517546124-0.424799556236-0.391839744038-0.40829281161.15658082567-0.1737412317110.9626298810840.5748784196650.240590761776-1.34331843740.9947372437780.2179999028570.7508829022181.031779511350.4308074847940.824394051623-26.434484274-24.715119060464.0749399367
21.08550143998-0.133959387448-0.2528164369860.8234102810250.529378723381.16659508787-0.233432806868-0.200902951227-0.1108404563990.7234447898850.4660539533650.572724575044-0.261084369058-0.3123907528480.1835596464560.7417085924810.1738254693410.3002971021430.5868884480250.2298419581230.709394271231-18.0892797409-19.57096287653.3059451539
31.23571258474-0.894680918754-0.6271815783251.2974542588-0.4379554734592.39322464033-0.1339083156860.0759176236057-0.2025445447640.1131615525310.2283713410360.377287856180.169214160234-0.119385813361-1.23859902652E-50.386867460672-0.0389590646923-0.01505858133470.3389463637380.04586765492980.49232094592-7.30011756946-21.981836116134.8993031459
40.972072944651-0.493279766568-0.6349606924070.869846915573-0.6853643773091.22473124804-0.05185116861060.3712931160810.00551310727852-0.07641610202350.1313991034760.06939925642360.07601258217350.055885456941-2.03596642361E-50.393049854012-0.0341899372852-0.05257349693670.444631063862-0.01078988619680.4276266650282.72108542288-16.907042740623.0153632912
50.625725841574-0.191941981094-1.145042536140.1676132942270.2755840004711.116814945520.141653131090.1529183020050.0788540779788-0.190358751198-0.135226992679-0.1294429545550.2421743537410.1814915403089.66425989764E-60.4939975381860.062739019295-0.04895021627640.630845402333-0.05681784746310.45212407680314.779580714-21.72098939689.8784969785
60.3052888582990.060152914439-0.142329253958-0.02959735964980.0334909690704-0.0276715443836-0.031905155525-0.384063557445-0.1473998903340.1444973346350.0608337262677-0.4264161739760.3270046861080.427703683618-3.24040611077E-50.5907694310590.1527112173830.1097313835990.643556257325-0.1088449051760.52620640435524.8841847445-24.2286942465.5996673446
70.2348198513550.144612958386-0.1067496877630.03530881135180.06020861169690.1139214243290.004242102317380.675813964671-0.0956278501863-0.3853301816030.09097884161080.3946556100610.179209997717-0.529515381561-0.0002298845815150.610359513040.09822110537890.0102838687520.815337849021-0.008845360557370.4982933247659.71362299497-19.25608447661.43180464021
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 31 )1 - 311 - 31
22chain 'A' and (resid 32 through 155 )32 - 15532 - 155
33chain 'A' and (resid 156 through 291 )156 - 291156 - 291
44chain 'A' and (resid 292 through 343 )292 - 343292 - 343
55chain 'A' and (resid 344 through 420 )344 - 420344 - 420
66chain 'A' and (resid 421 through 448 )421 - 448421 - 448
77chain 'A' and (resid 449 through 480 )449 - 480449 - 480

+
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