[English] 日本語
Yorodumi
- PDB-5mrj: Crystal structure of Endo-1,4-beta-xylanase-like protein from Acr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mrj
TitleCrystal structure of Endo-1,4-beta-xylanase-like protein from Acremonium chrysogenum
ComponentsBeta-xylanaseXylanase
KeywordsHYDROLASE / xylanase-like protein / Endo-1 / 4-beta-xylanase-like protein
Function / homology
Function and homology information


cellulose binding / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / extracellular region
Similarity search - Function
Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycosidases ...Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesAcremonium chrysogenum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGabdulkhakov, A. / Tishchenko, S. / Lisov, A. / Leontievsky, A.
CitationJournal: To Be Published
Title: Crystal structure of Endo-1,4-beta-xylanase-like protein from Acremonium chrysogenum
Authors: Gabdulkhakov, A. / Tishchenko, S. / Lisov, A. / Leontievsky, A.
History
DepositionDec 23, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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: Beta-xylanase
B: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,6295
Polymers86,3402
Non-polymers2883
Water73941
1
A: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3623
Polymers43,1701
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2662
Polymers43,1701
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.210, 124.828, 165.575
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein Beta-xylanase / Xylanase / Endo-1 / 4-beta-xylanase-like protein


Mass: 43170.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acremonium chrysogenum (strain ATCC 11550 / CBS 779.69 / DSM 880 / JCM 23072 / IMI 49137) (fungus)
Strain: ATCC 11550 / CBS 779.69 / DSM 880 / JCM 23072 / IMI 49137
Gene: ACRE_072080 / Plasmid: pPic9m / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: A0A086SY89, endo-1,4-beta-xylanase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 3.37 Å3/Da / Density % sol: 63.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 15% PEG 4K, 50 mM Sodium Citrate, 20 mM Sodium chloride, 20 mM Ammonium Sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.64→50 Å / Num. obs: 25746 / % possible obs: 94.3 % / Redundancy: 3.95 % / Net I/σ(I): 21
Reflection shellResolution: 2.64→2.8 Å / Redundancy: 3.71 % / % possible all: 96.6

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1b30

1b30


Resolution: 2.7→46.809 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 0.09 / Phase error: 32.56
RfactorNum. reflection% reflection
Rfree0.2848 2327 5.13 %
Rwork0.2207 --
obs0.224 23759 93.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→46.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4761 0 15 41 4817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094887
X-RAY DIFFRACTIONf_angle_d1.0846651
X-RAY DIFFRACTIONf_dihedral_angle_d8.8342841
X-RAY DIFFRACTIONf_chiral_restr0.058720
X-RAY DIFFRACTIONf_plane_restr0.006872
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.75510.43461300.3232657X-RAY DIFFRACTION96
2.7551-2.8150.44931340.30062626X-RAY DIFFRACTION97
2.815-2.88050.34511270.29682498X-RAY DIFFRACTION92
2.8805-2.95250.4121130.30792438X-RAY DIFFRACTION88
2.9525-3.03230.34451160.27192194X-RAY DIFFRACTION82
3.0323-3.12160.39451410.30222370X-RAY DIFFRACTION87
3.1216-3.22230.41111160.28642541X-RAY DIFFRACTION93
3.2223-3.33740.33871060.29082573X-RAY DIFFRACTION95
3.3374-3.4710.27841600.27072554X-RAY DIFFRACTION94
3.471-3.62890.3471350.24272621X-RAY DIFFRACTION96
3.6289-3.82020.2881690.20712529X-RAY DIFFRACTION95
3.8202-4.05940.25931540.19272564X-RAY DIFFRACTION95
4.0594-4.37260.27371550.19022541X-RAY DIFFRACTION95
4.3726-4.81220.20841400.16262560X-RAY DIFFRACTION94
4.8122-5.50760.23921530.16282558X-RAY DIFFRACTION95
5.5076-6.93540.19881490.17692623X-RAY DIFFRACTION96
6.9354-46.81580.1931290.15842584X-RAY DIFFRACTION95

+
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