[English] 日本語
Yorodumi
- PDB-7p25: Crystal structure of Paradendryphiella salina PL7A alginate lyase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7p25
TitleCrystal structure of Paradendryphiella salina PL7A alginate lyase in complex with hexa-mannuronic acid products
ComponentsAlginate lyase (PL7)
KeywordsLYASE / complex / beta jelly roll / mutant / alginate lyase
Function / homologyAlginate lyase 2 / Alginate lyase / Concanavalin A-like lectin/glucanase domain superfamily / lyase activity / Alginate lyase (PL7)
Function and homology information
Biological speciesParadendryphiella salina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsFredslund, F. / Welner, D.H. / Wilkens, C.
Funding support Denmark, 1items
OrganizationGrant numberCountry
European Union (EU)9082-00021B Denmark
CitationJournal: To Be Published
Title: Crystal structure of Paradendryphiella salina PL7A alginate lyase in complex with hexa-mannuronic acid products
Authors: Fredslund, F. / Welner, D.H. / Wilkens, C.
History
DepositionJul 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alginate lyase (PL7)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5433
Polymers25,4691
Non-polymers1,0752
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint15 kcal/mol
Surface area9260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.600, 74.300, 79.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Alginate lyase (PL7)


Mass: 25468.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paradendryphiella salina (fungus) / Gene: PsAlg7A / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A485PVH1
#2: Polysaccharide 4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D- ...4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid


Type: oligosaccharide / Mass: 528.372 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a1122A-1b_1-5][a11eEA-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-4-deoxy-ManpA]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid


Type: oligosaccharide / Mass: 546.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpAb1-4DManpAb1-4DManpAb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a1122A-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 38.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 20% PEG 1500 and 0.1 M TBG buffer pH 4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976261 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976261 Å / Relative weight: 1
ReflectionResolution: 1.47→37.15 Å / Num. obs: 68024 / % possible obs: 99.7 % / Redundancy: 6.86 % / Biso Wilson estimate: 18.09 Å2 / CC1/2: 1 / Net I/σ(I): 10.88
Reflection shellResolution: 1.47→1.55 Å / Num. unique obs: 10843 / CC1/2: 0.49

-
Processing

Software
NameVersionClassification
MxCuBE3data collection
XDSdata reduction
XDSdata scaling
Cootmodel building
PHASER1.19.2_4158phasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NCZ

7ncz


Resolution: 1.47→37.15 Å / SU ML: 0.2271 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.4625
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1941 2079 3.06 %
Rwork0.1701 65904 -
obs0.1708 67983 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.88 Å2
Refinement stepCycle: LAST / Resolution: 1.47→37.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1752 0 73 126 1951
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00791941
X-RAY DIFFRACTIONf_angle_d1.06762665
X-RAY DIFFRACTIONf_chiral_restr0.0858327
X-RAY DIFFRACTIONf_plane_restr0.007344
X-RAY DIFFRACTIONf_dihedral_angle_d14.1201662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.50.40771290.45134216X-RAY DIFFRACTION95.54
1.5-1.540.37451400.37154426X-RAY DIFFRACTION99.87
1.54-1.580.31271420.31924401X-RAY DIFFRACTION99.96
1.58-1.630.2711320.28974384X-RAY DIFFRACTION99.96
1.63-1.680.27691440.24964452X-RAY DIFFRACTION99.91
1.68-1.740.27581400.22054396X-RAY DIFFRACTION99.91
1.74-1.810.23231370.18794376X-RAY DIFFRACTION99.98
1.81-1.890.19731350.17334396X-RAY DIFFRACTION99.93
1.89-1.990.20311430.14554428X-RAY DIFFRACTION99.87
1.99-2.110.21231380.14444413X-RAY DIFFRACTION99.96
2.11-2.280.17451380.13624423X-RAY DIFFRACTION99.89
2.28-2.510.18531400.14814381X-RAY DIFFRACTION99.87
2.51-2.870.18751420.15714426X-RAY DIFFRACTION99.89
2.87-3.610.14351360.16054375X-RAY DIFFRACTION99.91
3.61-37.150.15871430.13564411X-RAY DIFFRACTION99.87
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)
13.517269125910.7231984939150.7033550343773.01421099798-0.009192638718982.259862418330.00440138227754-0.06710998373250.1027578306420.121725492187-0.03915550848710.0227417398422-0.288440615298-0.09225394988280.03361990832750.199938635990.02658202421430.0126619570610.116042961992-0.01169568998240.124152627916-14.62111.6659.485
20.6049737449470.104077061818-0.2638581208271.118665398130.1300255581132.47945938446-0.0236571431090.0531462073939-0.076523011852-0.0919520137913-0.000211378308496-0.00824372460.05030371506150.06626227673250.02104010001780.1905376082320.00900656078142-0.007793017725370.146459423872-0.007573661243510.18515939477-9.336-1.774-4.213
32.890495131831.93350049467-1.325510075832.1977804759-1.006891732184.37228374769-0.0134539249282-0.0115509097178-0.02487659897-0.06784345644440.0295175187213-0.0273580313542-0.0893560063915-0.0371776434472-0.0505610490.1688423501190.0458868343678-0.01331804445660.0937632121209-0.01164208353140.171691389716-12.0812.3815.179
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 0:77 )A0 - 77
2X-RAY DIFFRACTION2( CHAIN A AND RESID 78:223 )A78 - 223
3X-RAY DIFFRACTION3( CHAIN A AND RESID 224:247 )A224 - 247

+
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