[English] 日本語
Yorodumi
- PDB-7xzd: Mutant (F179A) of the N-terminal domain of fucoidan lyase FdlA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xzd
TitleMutant (F179A) of the N-terminal domain of fucoidan lyase FdlA
ComponentsFucoidan lyase
KeywordsLYASE / Fucobacter marina / fucoidan lyase / polysaccharide lyase
Function / homologyIMIDAZOLE
Function and homology information
Biological speciesFlavobacteriaceae bacterium SA-0082 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsWang, J. / Li, M. / Pan, X.
Funding support China, 3items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB27020106 China
National Natural Science Foundation of China (NSFC)21877114 China
National Natural Science Foundation of China (NSFC)31930064 China
CitationJournal: Mar Drugs / Year: 2022
Title: Structural and Biochemical Analysis Reveals Catalytic Mechanism of Fucoidan Lyase from Flavobacterium sp. SA-0082.
Authors: Wang, J. / Liu, Z. / Pan, X. / Wang, N. / Li, L. / Du, Y. / Li, J. / Li, M.
History
DepositionJun 2, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.country

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fucoidan lyase
B: Fucoidan lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,4303
Polymers100,3612
Non-polymers691
Water17,799988
1
A: Fucoidan lyase


Theoretical massNumber of molelcules
Total (without water)50,1801
Polymers50,1801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fucoidan lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2492
Polymers50,1801
Non-polymers691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.009, 58.000, 88.501
Angle α, β, γ (deg.)89.976, 101.389, 92.045
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

#1: Protein Fucoidan lyase


Mass: 50180.336 Da / Num. of mol.: 2 / Fragment: N-terminal domain / Mutation: F179A
Source method: isolated from a genetically manipulated source
Details: Genbank AAO00510.1,Sequence 3 from patent US 6489155
Source: (gene. exp.) Flavobacteriaceae bacterium SA-0082 (bacteria)
Gene: AAO5510.1 / Production host: Escherichia (bacteria)
References: Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 988 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 0.1 M CAPS pH 10.5, 0.2 M lithium sulfate, 2 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 193.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.65→58 Å / Num. obs: 112145 / % possible obs: 71.1 % / Redundancy: 2.3 % / Biso Wilson estimate: 14.04 Å2 / Rrim(I) all: 0.088 / Net I/σ(I): 6
Reflection shellResolution: 1.65→1.74 Å / Num. unique obs: 10128 / Rrim(I) all: 0.37

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XZF

7xzf


Resolution: 1.75→27.79 Å / SU ML: 0.1916 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 19.519
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.195 3632 4.81 %
Rwork0.1687 71831 -
obs0.17 75463 71.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.96 Å2
Refinement stepCycle: LAST / Resolution: 1.75→27.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6722 0 5 988 7715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00886964
X-RAY DIFFRACTIONf_angle_d1.06829495
X-RAY DIFFRACTIONf_chiral_restr0.07461076
X-RAY DIFFRACTIONf_plane_restr0.00711269
X-RAY DIFFRACTIONf_dihedral_angle_d17.42592506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.770.25281740.20913150X-RAY DIFFRACTION81.85
1.77-1.80.22941360.20873327X-RAY DIFFRACTION84.14
1.8-1.820.2491740.19973296X-RAY DIFFRACTION85.47
1.82-1.850.24831780.19263313X-RAY DIFFRACTION85.54
1.85-1.880.27371160.19812171X-RAY DIFFRACTION73.75
1.88-1.910.2514720.21431426X-RAY DIFFRACTION80.24
1.91-1.940.2744770.18631536X-RAY DIFFRACTION39.77
1.94-1.980.20131250.16492135X-RAY DIFFRACTION56.08
1.98-2.020.20031590.16433349X-RAY DIFFRACTION85.44
2.02-2.060.20341840.17323264X-RAY DIFFRACTION84.22
2.06-2.10.22081500.20693070X-RAY DIFFRACTION79.25
2.1-2.150.20451460.16323332X-RAY DIFFRACTION83.99
2.15-2.20.19221500.15723175X-RAY DIFFRACTION82.79
2.2-2.260.20251090.16161797X-RAY DIFFRACTION47.39
2.26-2.330.18181590.15943139X-RAY DIFFRACTION80.85
2.33-2.410.21041440.16383207X-RAY DIFFRACTION82.97
2.41-2.490.19031840.16123141X-RAY DIFFRACTION81.74
2.49-2.590.19751560.16733208X-RAY DIFFRACTION81.65
2.59-2.710.2071160.1363160X-RAY DIFFRACTION52.69
2.71-2.850.21881570.17122876X-RAY DIFFRACTION81.62
2.85-3.030.1971800.17343137X-RAY DIFFRACTION81.6
3.03-3.260.18351590.1663117X-RAY DIFFRACTION80.41
3.26-3.590.17541280.1563047X-RAY DIFFRACTION77.82
3.59-4.110.15091140.1522654X-RAY DIFFRACTION67.78
4.11-5.170.1541550.14342921X-RAY DIFFRACTION75.54
5.17-27.790.1821300.18592883X-RAY DIFFRACTION73.74

+
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