[English] 日本語
Yorodumi
- PDB-3qxf: Structure of the bacterial cellulose synthase subunit Z -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qxf
TitleStructure of the bacterial cellulose synthase subunit Z
ComponentsEndoglucanase
KeywordsHYDROLASE / cellulase / GH8 / cellulose synthesis / cellulose degradation
Function / homology
Function and homology information


cellulase / cellulase activity / cellulose catabolic process / extracellular region
Similarity search - Function
Glycoside hydrolase, family 8, conserved site / Glycosyl hydrolases family 8 signature. / 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
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsZimmer, J.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Apo- and cellopentaose-bound structures of the bacterial cellulose synthase subunit BcsZ.
Authors: Mazur, O. / Zimmer, J.
History
DepositionMar 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endoglucanase
B: Endoglucanase
C: Endoglucanase
D: Endoglucanase


Theoretical massNumber of molelcules
Total (without water)164,0864
Polymers164,0864
Non-polymers00
Water27,3291517
1
A: Endoglucanase


Theoretical massNumber of molelcules
Total (without water)41,0221
Polymers41,0221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endoglucanase


Theoretical massNumber of molelcules
Total (without water)41,0221
Polymers41,0221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Endoglucanase


Theoretical massNumber of molelcules
Total (without water)41,0221
Polymers41,0221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Endoglucanase


Theoretical massNumber of molelcules
Total (without water)41,0221
Polymers41,0221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.817, 87.933, 91.754
Angle α, β, γ (deg.)69.96, 74.36, 78.22
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Endoglucanase / Carboxymethylcellulase / CMCase / Cellulase / Endo-1 / 4-beta-glucanase


Mass: 41021.621 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: bcsZ, bcsC, yhjM, b3531, JW3499 / Production host: Escherichia coli (E. coli) / References: UniProt: P37651, cellulase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1517 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 30-40% PEG300, 0.1M sodium citrate/phosphate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97874 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 4, 2010
Details: Si 111, Rosenbaum-Rock double-crystal monochromator, sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97874 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 131388 / Num. obs: 121857 / % possible obs: 99 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 2

-
Processing

Software
NameVersionClassification
HKL-2000data collection
X-PLORmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
X-PLORphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→24.1 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.702 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R Free: 0.108 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17793 6479 5 %RANDOM
Rwork0.13571 ---
obs0.13787 121857 97.69 %-
all-131388 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å2-0.17 Å20.53 Å2
2---0.66 Å20.16 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.85→24.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10888 0 0 1517 12405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02211232
X-RAY DIFFRACTIONr_angle_refined_deg0.9211.93815252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20651348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.24223.574554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.834151842
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0761588
X-RAY DIFFRACTIONr_chiral_restr0.0810.21538
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0218800
X-RAY DIFFRACTIONr_mcbond_it1.7891.56726
X-RAY DIFFRACTIONr_mcangle_it2.458210780
X-RAY DIFFRACTIONr_scbond_it3.81834506
X-RAY DIFFRACTIONr_scangle_it5.1484.54470
X-RAY DIFFRACTIONr_rigid_bond_restr2.985311232
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 470 -
Rwork0.156 8810 -
obs--95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0990.05060.01060.4036-0.17210.4036-0.0325-0.0218-0.0003-0.02290.0164-0.02180.0193-0.03670.01610.02440.00050.00480.0240.00140.004312.593324.6696-27.3819
20.07890.02030.08140.8039-0.03030.15640.0037-0.00930.0202-0.062-0.0083-0.05330.0293-0.01010.00460.0373-0.00190.01360.0055-0.00310.02062.044245.592513.0389
30.40870.0815-0.10480.2783-0.04910.11900.0184-0.0080.0017-0.00380.003-0.01050.00130.00370.0049-0.0037-0.00570.02820.00840.015-8.52913.178212.2029
40.4808-0.0141-0.00720.4147-0.02130.14830.0206-0.02650.04910.0027-0.02440.01490.0037-0.00040.00380.00420.0044-0.00390.0215-0.01090.020512.58187.823645.7742
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 360
2X-RAY DIFFRACTION2B24 - 360
3X-RAY DIFFRACTION3C24 - 360
4X-RAY DIFFRACTION4D24 - 360

+
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