[English] 日本語
Yorodumi
- PDB-6rzo: Crystal structure of the N-terminal carbohydrate binding module f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rzo
TitleCrystal structure of the N-terminal carbohydrate binding module family 48 and ferulic acid esterase from the multi-enzyme CE1-GH62-GH10
Components(Ferulic acid esterase) x 2
KeywordsHYDROLASE / ferulic acid esterease / carbohydrate esterase family 1 / CE1 / CBM48 / carbohydrate binding module family 48
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.632 Å
AuthorsFredslund, F. / Welner, D.H. / Wilkens, C.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: A carbohydrate-binding family 48 module enables feruloyl esterase action on polymeric arabinoxylan.
Authors: Holck, J. / Fredslund, F. / Moller, M.S. / Brask, J. / Krogh, K.B.R.M. / Lange, L. / Welner, D.H. / Svensson, B. / Meyer, A.S. / Wilkens, C.
History
DepositionJun 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ferulic acid esterase
B: Ferulic acid esterase


Theoretical massNumber of molelcules
Total (without water)77,8582
Polymers77,8582
Non-polymers00
Water15,781876
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-20 kcal/mol
Surface area27520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.595, 99.816, 114.429
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Ferulic acid esterase


Mass: 38872.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli (E. coli) / References: feruloyl esterase
#2: Protein Ferulic acid esterase


Mass: 38985.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli (E. coli) / References: feruloyl esterase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 876 / 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: 2.44 Å3/Da / Density % sol: 49.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0 w/v Polyethylene glycol 3,350, 100 mM BIS-TRIS propane pH 6.5, 200 mM sodium fluoride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Apr 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.632→49.638 Å / Num. obs: 90065 / % possible obs: 94.38 % / Redundancy: 6.7 % / Net I/σ(I): 7.09
Reflection shellResolution: 1.632→1.69 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
autoPROCdata scaling
PHASER2.8.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JT2

1jt2


Resolution: 1.632→49.638 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 19.31
RfactorNum. reflection% reflection
Rfree0.1948 4438 4.93 %
Rwork0.1701 --
obs0.1713 89975 94.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.632→49.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5448 0 0 876 6324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095634
X-RAY DIFFRACTIONf_angle_d0.8647646
X-RAY DIFFRACTIONf_dihedral_angle_d12.9043324
X-RAY DIFFRACTIONf_chiral_restr0.062788
X-RAY DIFFRACTIONf_plane_restr0.0061021
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6321-1.65070.352920.29831847X-RAY DIFFRACTION62
1.6507-1.67010.31711060.29282081X-RAY DIFFRACTION69
1.6701-1.69050.30411070.27442190X-RAY DIFFRACTION73
1.6905-1.71190.32071180.26822307X-RAY DIFFRACTION77
1.7119-1.73440.27941410.27072403X-RAY DIFFRACTION82
1.7344-1.75820.281390.25032581X-RAY DIFFRACTION86
1.7582-1.78330.26641390.24682683X-RAY DIFFRACTION90
1.7833-1.80990.29131430.23932818X-RAY DIFFRACTION94
1.8099-1.83820.25421500.22432971X-RAY DIFFRACTION99
1.8382-1.86830.28361520.2082985X-RAY DIFFRACTION100
1.8683-1.90050.23521500.20213013X-RAY DIFFRACTION100
1.9005-1.93510.22741390.1942993X-RAY DIFFRACTION100
1.9351-1.97230.21441640.18912991X-RAY DIFFRACTION100
1.9723-2.01260.20631500.18022993X-RAY DIFFRACTION100
2.0126-2.05630.19641650.17132963X-RAY DIFFRACTION99
2.0563-2.10420.2261660.16753011X-RAY DIFFRACTION100
2.1042-2.15680.20081550.16812975X-RAY DIFFRACTION100
2.1568-2.21510.20031590.15713023X-RAY DIFFRACTION100
2.2151-2.28030.19411510.16293003X-RAY DIFFRACTION100
2.2803-2.35390.19891800.15262982X-RAY DIFFRACTION100
2.3539-2.4380.19611540.15843047X-RAY DIFFRACTION100
2.438-2.53560.18461470.15923018X-RAY DIFFRACTION100
2.5356-2.6510.20521700.16123012X-RAY DIFFRACTION100
2.651-2.79080.18211810.16213024X-RAY DIFFRACTION100
2.7908-2.96560.16881450.16693026X-RAY DIFFRACTION100
2.9656-3.19460.18391470.16243060X-RAY DIFFRACTION100
3.1946-3.5160.18381520.15163065X-RAY DIFFRACTION100
3.516-4.02450.14261510.14263091X-RAY DIFFRACTION100
4.0245-5.06970.13941650.12953122X-RAY DIFFRACTION100
5.0697-49.66110.18811600.17663259X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 58.2578 Å / Origin y: 43.5699 Å / Origin z: 38.9441 Å
111213212223313233
T0.1063 Å2-0.0001 Å2-0.0033 Å2-0.0828 Å20.0005 Å2--0.128 Å2
L0.5429 °2-0.0955 °2-0.2344 °2-0.3602 °20.0499 °2--1.1576 °2
S-0.0059 Å °0.0446 Å °-0.0104 Å °0.0034 Å °-0.0368 Å °0.0304 Å °-0.0514 Å °-0.0698 Å °0.0351 Å °
Refinement TLS groupSelection details: all

+
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