[English] 日本語
Yorodumi
- PDB-6bne: Crystal structure of the intrinsic colistin resistance enzyme ICR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bne
TitleCrystal structure of the intrinsic colistin resistance enzyme ICR(Mc) from Moraxella catarrhalis, catalytic domain, phosphate-bound complex
ComponentsPhosphoethanolamine transferase
KeywordsTRANSFERASE / antibiotic resistance / colistin / polymycin / phosphoethanolamine transferase / sulfatase fold / alpha/beta protein / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


transferase activity, transferring phosphorus-containing groups / sulfuric ester hydrolase activity / plasma membrane
Similarity search - Function
Phosphoethanolamine transferase, N-terminal / Phosphoethanolamine transferase EptA/EptB / Phosphoethanolamine transferase / Sulfatase, N-terminal / Sulfatase / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / PHOSPHATE ION / Phosphoethanolamine transferase
Similarity search - Component
Biological speciesMoraxella sp. HMSC061H09 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsStogios, P.J. / Evdokimova, E. / Wawrzak, Z. / Di Leo, R. / Savchenko, A. / Anderson, W.F. / Satchell, K.J. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Substrate recognition by a colistin resistance enzyme from Moraxella catarrhalis.
Authors: Stogios, P.J. / Cox, G. / Zubyk, H.L. / Evdokimova, E. / Wawrzak, Z. / Wright, G.D. / Savchenko, A.
History
DepositionNov 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphoethanolamine transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5067
Polymers37,9711
Non-polymers5346
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)147.524, 147.524, 147.524
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Phosphoethanolamine transferase


Mass: 37971.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moraxella sp. HMSC061H09 (bacteria) / Gene: HMPREF2573_04170 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / References: UniProt: A0A1E9VP98

-
Non-polymers , 5 types, 122 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 3.52 Å3/Da / Density % sol: 65.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium acetate pH 4.6, 1.2 M ammonium sulfate, cryoprotectant 8% glycerol, 8% ethylene glycol and 8% sucrose

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.27424 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27424 Å / Relative weight: 1
ReflectionResolution: 2.61→104.32 Å / Num. obs: 17315 / % possible obs: 100 % / Redundancy: 77.3 % / CC1/2: 1 / Rpim(I) all: 0.028 / Rsym value: 0.181 / Net I/σ(I): 24.7
Reflection shellResolution: 2.61→2.68 Å / Redundancy: 79.5 % / Rmerge(I) obs: 3.313 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1250 / CC1/2: 0.84 / Rpim(I) all: 0.515 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(dev_2733: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphenix.phaserphasing
PHENIXphenix.autobuildmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KAY

4kay


Resolution: 2.61→60.226 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2705 830 5.02 %RANDOM
Rwork0.234 ---
obs0.2358 16528 95.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.61→60.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2602 0 30 116 2748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062689
X-RAY DIFFRACTIONf_angle_d1.383666
X-RAY DIFFRACTIONf_dihedral_angle_d13.067958
X-RAY DIFFRACTIONf_chiral_restr0.07407
X-RAY DIFFRACTIONf_plane_restr0.006480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6103-2.77390.48721150.48012354X-RAY DIFFRACTION88
2.7739-2.9880.41411470.34092650X-RAY DIFFRACTION99
2.988-3.28870.30691380.27632675X-RAY DIFFRACTION100
3.2887-3.76450.33381220.27582474X-RAY DIFFRACTION91
3.7645-4.74260.23161620.18062625X-RAY DIFFRACTION96
4.7426-60.24240.21251460.19322920X-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)
13.57780.52770.43285.75940.74312.10310.07510.12510.04750.4903-0.1187-0.59260.18170.37660.03460.46390.1025-0.06060.6544-0.02840.5617-1.614533.2738-22.6078
23.23841.67771.4136.4350.026.5286-0.22160.10150.52730.64470.15270.2528-0.587-0.51450.07090.48380.1140.02780.529-0.07860.5283-6.889847.6967-23.808
36.31562.5691-0.74664.1871-0.99811.9026-0.00750.9884-0.0311-0.12060.11470.0592-0.02240.0417-0.08820.39570.0982-0.00220.6833-0.08380.4387-15.557435.5657-33.4867
49.15211.9128-1.4084.5438-2.11363.6202-0.0811-0.2705-0.66240.2739-0.1664-0.58740.18520.50990.25570.44360.0946-0.01630.552-0.06450.5644-2.455128.5242-22.8446
55.27621.7869-4.0188.9091.53014.07440.0249-0.26150.81930.05060.3733-2.4983-0.5291.8927-0.49270.72710.1166-0.1971.0217-0.15641.666511.932230.7377-22.3021
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 243:342)
2X-RAY DIFFRACTION2(chain A and resid 343:383)
3X-RAY DIFFRACTION3(chain A and resid 384:488)
4X-RAY DIFFRACTION4(chain A and resid 489:566)
5X-RAY DIFFRACTION5(chain A and resid 567:578)

+
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