[English] 日本語
Yorodumi
- PDB-5cd2: The crystal structure of endo-1,4-D-glucanase from Vibrio fischer... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5cd2
TitleThe crystal structure of endo-1,4-D-glucanase from Vibrio fischeri ES114
ComponentsEndo-1,4-D-glucanase
KeywordsHYDROLASE / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


cellulase / cellulase activity / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 8 / Glycosyl hydrolases family 8 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / Cellulase
Similarity search - Component
Biological speciesVibrio fischeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsTan, K. / Li, H. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102318 United States
CitationJournal: To Be Published
Title: The crystal structure of endo-1,4-D-glucanase from Vibrio fischeri ES114
Authors: Tan, K. / Li, H. / Endres, M. / Joachimiak, A.
History
DepositionJul 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endo-1,4-D-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3996
Polymers42,0281
Non-polymers3705
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-16 kcal/mol
Surface area14300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.563, 67.489, 101.192
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Endo-1,4-D-glucanase


Mass: 42028.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio fischeri (strain ATCC 700601 / ES114) (bacteria)
Strain: ATCC 700601 / ES114 / Gene: bcsZ, VF_A0882 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q5DZ44, cellulase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.2M MgCl2, 0.1M Tris:HCl, 20%(w/v) PEG8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.55→40.5 Å / Num. all: 56160 / Num. obs: 56160 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 11.28 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 20.362
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.602 / Mean I/σ(I) obs: 1.67 / % possible all: 96.8

-
Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.55→40.5 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.176 2628 4.84 %random selection
Rwork0.1354 ---
obs0.1374 54330 97.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→40.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2743 0 20 360 3123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062943
X-RAY DIFFRACTIONf_angle_d1.0254016
X-RAY DIFFRACTIONf_dihedral_angle_d13.8011079
X-RAY DIFFRACTIONf_chiral_restr0.079425
X-RAY DIFFRACTIONf_plane_restr0.005520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.57820.2472970.17061823X-RAY DIFFRACTION66
1.5782-1.60850.25971290.1582342X-RAY DIFFRACTION85
1.6085-1.64140.21091240.15312635X-RAY DIFFRACTION95
1.6414-1.67710.20611540.14062714X-RAY DIFFRACTION99
1.6771-1.71610.23421400.14072757X-RAY DIFFRACTION100
1.7161-1.7590.21571050.14062794X-RAY DIFFRACTION100
1.759-1.80660.20561470.13092779X-RAY DIFFRACTION100
1.8066-1.85970.19191570.12352756X-RAY DIFFRACTION100
1.8597-1.91970.16631270.11132780X-RAY DIFFRACTION100
1.9197-1.98840.19181380.11662802X-RAY DIFFRACTION100
1.9884-2.0680.17931360.12192765X-RAY DIFFRACTION100
2.068-2.16210.17081340.11782811X-RAY DIFFRACTION100
2.1621-2.27610.14091430.11972778X-RAY DIFFRACTION100
2.2761-2.41860.18141360.1252825X-RAY DIFFRACTION100
2.4186-2.60540.15171420.12862812X-RAY DIFFRACTION100
2.6054-2.86750.16361590.14372807X-RAY DIFFRACTION100
2.8675-3.28230.17081590.15172838X-RAY DIFFRACTION100
3.2823-4.13470.16161480.13132868X-RAY DIFFRACTION100
4.1347-40.49660.17521530.15373016X-RAY DIFFRACTION100

+
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