[English] 日本語
Yorodumi
- PDB-6ywf: Crystal structure of Paradendryphiella salina PL7A alginate lyase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ywf
TitleCrystal structure of Paradendryphiella salina PL7A alginate lyase
ComponentsAlginate lyase (PL7)
KeywordsLYASE / Alginate lyase / fungal / polysaccharide lyase family 7 / PL7
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: 1.9 Å
AuthorsWilkens, C. / Fredslund, F. / Welner, D.H.
CitationJournal: To Be Published
Title: Crystal structure of Paradendryphiella salina PL7A alginate lyase
Authors: Wilkens, C. / Fredslund, F. / Welner, D.H.
History
DepositionApr 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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: Alginate lyase (PL7)


Theoretical massNumber of molelcules
Total (without water)25,4691
Polymers25,4691
Non-polymers00
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.768, 80.442, 81.375
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) / Variant (production host): X-33 / References: UniProt: A0A485PVH1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.23 Å3/Da / Density % sol: 44.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 20% PEG 1500, 0.1 M TBG buffer

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.9→40.22 Å / Num. obs: 18624 / % possible obs: 98.32 % / Redundancy: 8.5 % / Biso Wilson estimate: 17.72 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.07987 / Rpim(I) all: 0.02868 / Rrim(I) all: 0.08505 / Net I/σ(I): 17.26
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 4.94 / Num. unique obs: 11623 / CC1/2: 0.947 / CC star: 0.986 / Rpim(I) all: 0.1418 / Rrim(I) all: 0.3682 / % possible all: 93.09

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASER2.7.16phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CWS

2cws


Resolution: 1.9→40.22 Å / SU ML: 0.1473 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.3243
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1878 1830 9.96 %
Rwork0.1507 16542 -
obs0.1545 18372 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.56 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 0 237 1968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311769
X-RAY DIFFRACTIONf_angle_d0.70542416
X-RAY DIFFRACTIONf_chiral_restr0.0496287
X-RAY DIFFRACTIONf_plane_restr0.0033313
X-RAY DIFFRACTIONf_dihedral_angle_d15.3529619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.22221310.17781186X-RAY DIFFRACTION92.94
1.95-2.010.24941350.17681210X-RAY DIFFRACTION95.73
2.01-2.070.19961300.15931231X-RAY DIFFRACTION97.01
2.07-2.150.19351350.15371256X-RAY DIFFRACTION98.1
2.15-2.230.21011340.151251X-RAY DIFFRACTION98.37
2.23-2.340.19751440.14691272X-RAY DIFFRACTION98.81
2.34-2.460.18681370.14381260X-RAY DIFFRACTION99.01
2.46-2.610.18041440.14591277X-RAY DIFFRACTION99.58
2.61-2.810.17821410.15411279X-RAY DIFFRACTION99.58
2.81-3.10.20311510.15861288X-RAY DIFFRACTION99.65
3.1-3.540.20041450.15671308X-RAY DIFFRACTION99.86
3.55-4.460.16641470.12921328X-RAY DIFFRACTION100
4.47-40.220.16021560.15211396X-RAY DIFFRACTION99.49
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)
13.88954953242-0.105876678388-0.03901687435673.50266791323-0.8746335383452.76670915799-0.08585584900530.007962223295490.0946000113294-0.1634060694290.0415181594454-0.1133270670130.1487687923730.1836571904940.02716982668460.1028925660860.02060786549480.0164886844980.103000672346-0.01599096790680.07948504331564.1210820303713.20675956125.04708140962
20.7868164129780.1235737727920.1691379627461.46937095896-0.3458916303111.32060105142-0.016464975884-0.03795364997430.03003899815090.0575228330989-0.00222816781653-0.06731943892120.01845478523180.0612462268430.02872430797980.100706344803-0.0002612906885420.004091530795540.132997453363-0.002176133356270.1378089410933.2305312173819.326953854117.4171637448
31.812341350761.53285598835-0.02336533724311.457598237570.2232809283.708141395860.13025658393-0.4494563605860.02382282010640.771044496282-0.127833874737-0.03254016003570.131845201926-0.07371711574770.006010289834440.2740213783920.0122213962631-0.006519807096460.190232011349-0.01461369185960.1301681397312.219658323822.34405517433.5314312006
46.949664468715.72733034692-0.7905201008549.10729999413-1.804588716924.091713785820.20363039549-0.3888587756780.3148300158580.710764004955-0.185129429424-0.01764302378-0.3138592533780.109404898012-0.004075544461010.1472385523660.0586583190177-0.02352310902640.137009767236-0.02390290675340.1324504371914.2202685950529.324455044628.964483443
51.547261255721.49842228432-0.1559400682262.01903205071-0.6101830166761.14219735449-0.0517550050064-0.07750769141290.0391384272278-0.1224416613470.206989431820.474105025310.186307327264-0.187642546392-0.1720580249940.174451104749-0.01797930786420.01746633821210.182033503870.0002081419564640.17343071997-7.3548230712618.569878335321.7077434317
63.234261292232.27444260047-0.9527225156665.05773404521-0.755921693083.36394164960.185737161098-0.2421806122510.3345520435160.331162496833-0.2418998183220.566179846273-0.313338157543-0.257724800432-0.008321600221330.1578153478760.02299308816620.02245072280140.169837332449-0.02790492584920.226958838534-8.1289951554729.626923145224.5405296493
70.156899923483-0.209493524558-0.05562184231441.113046981340.4280326233041.474945815020.0025253918015-0.0913289845160.09586739216540.124133249483-0.0015564518242-0.26900629983-0.1542230581150.03922849389370.02318440072430.118429812708-0.00769278862093-0.004118622916490.121514225312-0.003149766440020.1717671047244.8704420840728.483342098217.3181302656
82.032517426410.815046595265-0.3162733305472.21837114677-0.1765249527842.63278508456-0.0773112285775-0.133012245884-0.00994510183348-0.0740964947260.1479484014390.0992156591244-0.0692676656724-0.194588194321-0.003638453782660.134775636369-0.009077107993660.006025977762120.0779789925876-0.03076782751130.1069418553981.4285915855615.604559992316.8426013461
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 23 through 63 )23 - 631 - 41
22chain 'A' and (resid 64 through 147 )64 - 14742 - 127
33chain 'A' and (resid 148 through 161 )148 - 161128 - 141
44chain 'A' and (resid 162 through 176 )162 - 176142 - 156
55chain 'A' and (resid 177 through 189 )177 - 189157 - 169
66chain 'A' and (resid 190 through 208 )190 - 208170 - 188
77chain 'A' and (resid 209 through 225 )209 - 225189 - 205
88chain 'A' and (resid 226 through 247 )226 - 247206 - 227

+
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