[English] 日本語
Yorodumi
- PDB-5uam: Structure of a new family of Polysaccharide lyase PL25-Ulvanlyase. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uam
TitleStructure of a new family of Polysaccharide lyase PL25-Ulvanlyase.
ComponentsUlvan Lyase-PL25
KeywordsLYASE / Beta propellar fold / degrades Ulvan polysaccharide
Function / homology
Function and homology information


Lyases; Carbon-oxygen lyases; Acting on polysaccharides / lyase activity / metal ion binding / plasma membrane
Similarity search - Function
BNR repeat-containing family member / Sialidase superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
: / PHOSPHATE ION / Ulvan Lyase-PL25
Similarity search - Component
Biological speciesPseudoalteromonas sp. PLSV (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsUlaganathan, T.S. / Boniecki, M.T. / Cygler, M.
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: New Ulvan-Degrading Polysaccharide Lyase Family: Structure and Catalytic Mechanism Suggests Convergent Evolution of Active Site Architecture.
Authors: Ulaganathan, T. / Boniecki, M.T. / Foran, E. / Buravenkov, V. / Mizrachi, N. / Banin, E. / Helbert, W. / Cygler, M.
History
DepositionDec 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ulvan Lyase-PL25
B: Ulvan Lyase-PL25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,31220
Polymers106,1912
Non-polymers1,12118
Water20,3211128
1
A: Ulvan Lyase-PL25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,79512
Polymers53,0961
Non-polymers69911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ulvan Lyase-PL25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5178
Polymers53,0961
Non-polymers4217
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)174.260, 72.110, 109.510
Angle α, β, γ (deg.)90.00, 122.50, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Ulvan Lyase-PL25


Mass: 53095.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas sp. PLSV (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1W2VMZ5*PLUS

-
Non-polymers , 7 types, 1146 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1128 / Source method: isolated from a natural source / Formula: H2O

-
Details

Source detailsThe sequence is present in NCBI database under the ID WP_033186995.1

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.98 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 20% PEG3500, 0.2M Ammonium acetate, 0.1M Bis-Tris pH 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9791 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Sep 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.41→45.2 Å / Num. obs: 206055 / % possible obs: 93.7 % / Redundancy: 3.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Net I/σ(I): 19.15

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→45.2 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 13.93
RfactorNum. reflection% reflection
Rfree0.1429 1892 0.97 %
Rwork0.1339 --
obs0.134 194554 96.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→45.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6909 0 58 1128 8095
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077269
X-RAY DIFFRACTIONf_angle_d1.0039855
X-RAY DIFFRACTIONf_dihedral_angle_d17.1042621
X-RAY DIFFRACTIONf_chiral_restr0.087996
X-RAY DIFFRACTIONf_plane_restr0.0071308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.48630.34441100.272311216X-RAY DIFFRACTION79
1.4863-1.52650.23671340.211513615X-RAY DIFFRACTION95
1.5265-1.57140.18471360.175313844X-RAY DIFFRACTION97
1.5714-1.62210.17011350.164913798X-RAY DIFFRACTION97
1.6221-1.68010.15071370.145113938X-RAY DIFFRACTION97
1.6801-1.74730.15641370.131913944X-RAY DIFFRACTION98
1.7473-1.82690.12111360.130713900X-RAY DIFFRACTION98
1.8269-1.92320.13581380.128614006X-RAY DIFFRACTION98
1.9232-2.04370.14531380.123614052X-RAY DIFFRACTION98
2.0437-2.20150.12241380.120614091X-RAY DIFFRACTION99
2.2015-2.4230.11921390.12214168X-RAY DIFFRACTION99
2.423-2.77360.15771400.127114169X-RAY DIFFRACTION99
2.7736-3.49420.13741380.129214091X-RAY DIFFRACTION98
3.4942-45.25690.1331360.131413830X-RAY DIFFRACTION95
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)
11.23570.4929-0.11681.7773-0.14211.4831-0.0017-0.0070.06780.0634-0.00930.1733-0.0277-0.12730.00230.09150.00760.00750.125-0.00650.1221-0.481380.046338.8679
20.9480.2924-0.25271.152-0.02971.06730.0249-0.07270.03220.06550.0265-0.0239-0.07590.1023-0.05320.1057-0.0039-0.00540.1015-0.01450.097815.365785.529842.0374
31.81070.25140.09021.67080.71542.15-0.00590.12160.1044-0.22940.0977-0.1428-0.31170.2221-0.04230.1427-0.04060.0410.1474-0.02740.107923.365484.673923.4832
41.18350.153-0.23221.39640.28811.2013-0.01590.10980.0314-0.15770.1123-0.2035-0.13020.2353-0.08880.153-0.01660.03040.1865-0.03510.135223.568876.976820.3706
52.37050.0997-0.33051.11860.0331.4774-0.04040.3207-0.1363-0.1770.02330.08870.0597-0.08150.01180.1454-0.0035-0.01640.1644-0.03530.11648.939370.436717.2487
65.1563-2.6107-1.14073.48061.37261.28980.05360.3489-0.4263-0.1082-0.14620.25890.1465-0.12360.07760.1206-0.0189-0.02320.1674-0.0220.12030.617767.299319.8103
72.87640.00380.12021.7157-0.3992.2089-0.0099-0.0236-0.05660.0598-0.03970.16960.0732-0.19110.04230.0964-0.0240.00250.1238-0.0210.122-4.043972.724534.983
81.5426-0.27010.21031.76030.29811.65670.01040.05490.0397-0.16390.0742-0.2722-0.05980.1868-0.07330.1062-0.01630.02570.1388-0.01960.144958.442544.30076.6088
91.1807-0.3688-0.11411.57170.371.17480.01930.06910.0483-0.19230.0361-0.0147-0.106-0.0575-0.06160.1361-0.0019-0.00830.10280.01420.104542.711449.89474.3469
101.5552-0.59970.21881.8365-0.54141.5851-0.0733-0.3070.05430.27690.12540.1326-0.1747-0.2348-0.03490.1440.03280.02570.22920.01380.11737.483145.314226.2216
113.35290.8985-0.16942.0473-0.38521.69420.039-0.4798-0.38880.21550.0063-0.19120.15850.0586-0.04970.12530.0187-0.03860.19130.03750.175856.035132.221326.3611
122.8439-0.13310.381.7620.27572.13470.00450.1618-0.2388-0.15320.0857-0.35440.06870.2694-0.04970.10780.01220.01270.1523-0.03280.183462.275136.87039.789
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 47 through 126 )
2X-RAY DIFFRACTION2chain 'A' and (resid 127 through 227 )
3X-RAY DIFFRACTION3chain 'A' and (resid 228 through 301 )
4X-RAY DIFFRACTION4chain 'A' and (resid 302 through 348 )
5X-RAY DIFFRACTION5chain 'A' and (resid 349 through 416 )
6X-RAY DIFFRACTION6chain 'A' and (resid 417 through 439 )
7X-RAY DIFFRACTION7chain 'A' and (resid 440 through 486 )
8X-RAY DIFFRACTION8chain 'B' and (resid 48 through 126 )
9X-RAY DIFFRACTION9chain 'B' and (resid 127 through 227 )
10X-RAY DIFFRACTION10chain 'B' and (resid 228 through 376 )
11X-RAY DIFFRACTION11chain 'B' and (resid 377 through 439 )
12X-RAY DIFFRACTION12chain 'B' and (resid 440 through 487 )

+
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