[English] 日本語
Yorodumi
- PDB-6in8: Crystal structure of MucB -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6in8
TitleCrystal structure of MucB
ComponentsSigma factor AlgU regulatory protein MucB
KeywordsMEMBRANE PROTEIN / Outer membrane protein
Function / homology
Function and homology information


regulation of polysaccharide biosynthetic process / antisigma factor binding / alginic acid biosynthetic process / outer membrane-bounded periplasmic space
Similarity search - Function
MucB/RseB / MucB/RseB, N-terminal / MucB/RseB, C-terminal / MucB/RseB, C-terminal domain superfamily / MucB/RseB N-terminal domain / MucB/RseB C-terminal domain
Similarity search - Domain/homology
Sigma factor AlgU regulatory protein MucB
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLi, S. / Zhang, Q. / Bartlam, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570128 China
CitationJournal: Febs J. / Year: 2019
Title: Structural basis for the recognition of MucA by MucB and AlgU in Pseudomonas aeruginosa.
Authors: Li, S. / Lou, X. / Xu, Y. / Teng, X. / Liu, R. / Zhang, Q. / Wu, W. / Wang, Y. / Bartlam, M.
History
DepositionOct 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sigma factor AlgU regulatory protein MucB


Theoretical massNumber of molelcules
Total (without water)32,7391
Polymers32,7391
Non-polymers00
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.076, 69.076, 223.103
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-426-

HOH

-
Components

#1: Protein Sigma factor AlgU regulatory protein MucB


Mass: 32738.725 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: mucB, algN, PA0764 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P38108
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.35 Å3/Da / Density % sol: 47.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2 M Ammonium dibasic phosphate, 0.1 M Tris pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 16960 / % possible obs: 100 % / Redundancy: 37 % / Rpim(I) all: 0.025 / Net I/σ(I): 38.5
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 15 % / Mean I/σ(I) obs: 4.5 / Num. unique obs: 813 / Rpim(I) all: 0.138 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P4B

2p4b


Resolution: 2.2→40.795 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.48
RfactorNum. reflection% reflection
Rfree0.2407 842 4.99 %
Rwork0.1864 --
obs0.1892 16885 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→40.795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2137 0 0 120 2257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082180
X-RAY DIFFRACTIONf_angle_d1.0832957
X-RAY DIFFRACTIONf_dihedral_angle_d14.518800
X-RAY DIFFRACTIONf_chiral_restr0.042326
X-RAY DIFFRACTIONf_plane_restr0.005394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.33790.27531500.20672561X-RAY DIFFRACTION100
2.3379-2.51840.28471190.21462620X-RAY DIFFRACTION100
2.5184-2.77170.28171170.21862648X-RAY DIFFRACTION100
2.7717-3.17270.26851440.21452648X-RAY DIFFRACTION100
3.1727-3.99670.2351530.16882678X-RAY DIFFRACTION100
3.9967-40.80180.20851590.16762888X-RAY DIFFRACTION100
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)
11.3629-0.65150.0027.0306-5.13224.7775-0.09110.4059-0.1212-0.7925-0.0378-0.04161.9706-0.13060.270.683-0.04910.10140.315-0.07860.295940.51438.484812.4041
21.9201-0.0541-1.03882.2695-1.23743.6768-0.14550.1359-0.0136-0.28160.0444-0.14260.4805-0.0370.14750.256-0.06750.09920.25190.02920.288338.069837.719333.0285
33.20561.96572.41754.38831.62143.7224-0.1010.111-0.2543-0.3918-0.06290.12310.8049-0.74640.10190.5294-0.13460.17370.2897-0.00130.316733.608629.631634.5165
44.4118-3.0208-2.67895.82890.60993.75180.04050.0969-0.17510.1986-0.34280.4280.3035-0.13480.30240.3877-0.14890.04260.6386-0.0590.359524.828733.446235.1734
51.9424-0.69110.56041.1894-0.33522.633-0.09250.10540.0402-0.1248-0.0840.02460.41-0.33890.23130.2843-0.03720.12890.27410.00730.320337.681444.425118.2743
61.372-0.19930.20180.9984-1.04973.3963-0.11620.01070.051-0.1344-0.01030.00170.0972-0.08480.15470.2054-0.05510.06160.1980.02460.266537.449547.504923.5174
71.1801-0.055111.4735-1.18772.92890.1814-0.9153-0.3796-0.2774-0.1898-0.00810.6835-0.054-0.06760.6223-0.11040.1730.3420.01350.509834.392825.007336.3573
81.93330.247-0.70182.066-0.41121.8126-0.64540.1853-0.94260.06840.14380.23980.5574-0.99370.23650.3942-0.08660.09860.57950.05050.450315.621739.511824.6243
93.52271.8252-2.25972.5092-2.1692.8346-0.1173-0.3742-0.25770.0834-0.00290.16870.4602-0.50120.32110.2651-0.15120.07640.4868-0.01140.335219.459840.825126.6619
102.66431.4417-0.67280.7561-0.36880.16970.1617-1.598-0.34680.349-0.21280.3134-0.4008-1.00120.01460.35590.00390.06681.0838-0.02480.529912.279947.267338.0149
115.18021.2535-1.02341.4074-0.62310.9012-0.1607-0.11710.0780.06840.0310.15780.0604-0.95740.0270.2236-0.03420.05840.6748-0.02770.315312.745546.87727.1193
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 37 )
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 61 )
3X-RAY DIFFRACTION3chain 'A' and (resid 62 through 84 )
4X-RAY DIFFRACTION4chain 'A' and (resid 85 through 102 )
5X-RAY DIFFRACTION5chain 'A' and (resid 103 through 141 )
6X-RAY DIFFRACTION6chain 'A' and (resid 142 through 182 )
7X-RAY DIFFRACTION7chain 'A' and (resid 183 through 213 )
8X-RAY DIFFRACTION8chain 'A' and (resid 214 through 239 )
9X-RAY DIFFRACTION9chain 'A' and (resid 240 through 258 )
10X-RAY DIFFRACTION10chain 'A' and (resid 259 through 283 )
11X-RAY DIFFRACTION11chain 'A' and (resid 284 through 311 )

+
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