[English] 日本語
Yorodumi
- PDB-4z4l: Crystal Structure of cellobiose 2-epimerase from Caldicellulosiru... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4z4l
TitleCrystal Structure of cellobiose 2-epimerase from Caldicellulosiruptor saccharolyticus DSM 8903
ComponentsCellobiose 2-epimeraseCellobiose epimerase
KeywordsISOMERASE / Cellobiose 2-epimerase / latulose / lactose
Function / homology
Function and homology information


cellobiose epimerase / cellobiose epimerase activity / carbohydrate metabolic process
Similarity search - Function
Cellobiose 2-epimerase / N-acylglucosamine 2-epimerase/Cellobiose 2-epimerase / N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Cellobiose 2-epimerase
Similarity search - Component
Biological speciesCaldicellulosiruptor saccharolyticus DSM 8903 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.671 Å
AuthorsShen, Q.Y. / Zhang, Y.Z.
CitationJournal: to be published
Title: Crystal Structure of cellobiose 2-epimerase from Caldicellulosiruptor saccharolyticus DSM 8903
Authors: Shen, Q.Y. / Zhang, Y.Z.
History
DepositionApr 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cellobiose 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7522
Polymers47,6901
Non-polymers621
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.787, 75.543, 91.382
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Cellobiose 2-epimerase / Cellobiose epimerase / CE


Mass: 47690.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldicellulosiruptor saccharolyticus DSM 8903 (bacteria)
Strain: DSM8903 / Gene: Csac_0294 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4XGA6, cellobiose epimerase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.02 Å3/Da / Density % sol: 39.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M HEPES sodium pH 7.5, 0.2 M Magnesium chloride hexahydrate, 30% v/v PEG 400

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.968 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 25, 2014
RadiationMonochromator: ID / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 1.67→29.59 Å / Num. obs: 37768 / % possible obs: 84.2 % / Redundancy: 4.4 % / Biso Wilson estimate: 23.23 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.026 / Net I/σ(I): 16.1 / Num. measured all: 164764
Reflection shell

Diffraction-ID: 1 / Redundancy: 4 % / Rejects: 0

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.67-1.70.81.8777619270.5950.41284.8
9-29.590.0545.78962240.9940.02767.2

-
Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z4J

4z4j


Resolution: 1.671→29.59 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1979 1980 5.25 %
Rwork0.1631 35761 -
obs0.1649 37741 83.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.76 Å2 / Biso mean: 28.2086 Å2 / Biso min: 13.64 Å2
Refinement stepCycle: final / Resolution: 1.671→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3285 0 4 74 3363
Biso mean--47.76 29.7 -
Num. residues----392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073451
X-RAY DIFFRACTIONf_angle_d1.0514664
X-RAY DIFFRACTIONf_chiral_restr0.044483
X-RAY DIFFRACTIONf_plane_restr0.005590
X-RAY DIFFRACTIONf_dihedral_angle_d15.0311299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6712-1.7130.2821990.23382635X-RAY DIFFRACTION86
1.713-1.75930.25691980.22252550X-RAY DIFFRACTION86
1.7593-1.81110.326990.20672670X-RAY DIFFRACTION87
1.8111-1.86950.24481980.19442594X-RAY DIFFRACTION86
1.8695-1.93630.2169990.18522640X-RAY DIFFRACTION86
1.9363-2.01380.20951980.17582567X-RAY DIFFRACTION86
2.0138-2.10550.208990.16392636X-RAY DIFFRACTION85
2.1055-2.21640.2111980.16152509X-RAY DIFFRACTION84
2.2164-2.35520.2023990.16292598X-RAY DIFFRACTION83
2.3552-2.5370.18781690.16612526X-RAY DIFFRACTION83
2.537-2.79210.18921280.16782515X-RAY DIFFRACTION82
2.7921-3.19570.2161990.17342519X-RAY DIFFRACTION80
3.1957-4.02470.15981980.1512375X-RAY DIFFRACTION78
4.0247-29.590.2092990.13722427X-RAY DIFFRACTION73
Refinement TLS params.Method: refined / Origin x: 26.3724 Å / Origin y: 0.1618 Å / Origin z: -8.2913 Å
111213212223313233
T0.1497 Å2-0.0091 Å20.0036 Å2-0.1807 Å2-0.0001 Å2--0.142 Å2
L1.192 °20.13 °2-0.0524 °2-1.5241 °2-0.0808 °2--1.1448 °2
S0.012 Å °0.0358 Å °-0.0918 Å °0.0017 Å °-0.0266 Å °-0.0283 Å °0.0852 Å °-0.0574 Å °0.013 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-1 - 390
2X-RAY DIFFRACTION1allC1 - 68
3X-RAY DIFFRACTION1allC69 - 74
4X-RAY DIFFRACTION1allC75
5X-RAY DIFFRACTION1allC76 - 78
6X-RAY DIFFRACTION1allB1

+
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