[English] 日本語
Yorodumi
- PDB-6dq2: Cronobacter sakazakii (Enterobacter sakazakii) Metallo-beta-lacta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dq2
TitleCronobacter sakazakii (Enterobacter sakazakii) Metallo-beta-lactamse HARLDQ motif mutant S60
ComponentsBeta-lactamase
KeywordsHYDROLASE / Metallo-beta-lactamse / METAL BINDING PROTEIN / Beta-lactamase
Function / homology
Function and homology information


Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesCronobacter sakazakii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.158 Å
AuthorsMonteiro Pedroso, M. / Waite, D. / Natasa, M. / McGeary, R. / Guddat, L. / Hugenholtz, P. / Schenk, G.
Funding support Australia, 3items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP108477 Australia
Australian Research Council (ARC)DP150104358 Australia
Australian Research Council (ARC)T120100694 Australia
CitationJournal: Protein Cell / Year: 2020
Title: Broad spectrum antibiotic-degrading metallo-beta-lactamases are phylogenetically diverse
Authors: Monteiro Pedroso, M. / Waite, D. / Melse, O. / Wilson, L. / Mitic, N. / McGeary, R. / Antes, I. / Guddat, L. / Hugenholtz, P. / Schenk, G.
History
DepositionJun 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jun 24, 2020Group: 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.title / _citation.year
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2653
Polymers32,0751
Non-polymers1902
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.406, 74.406, 107.471
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-517-

HOH

21A-527-

HOH

-
Components

#1: Protein Beta-lactamase /


Mass: 32074.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cronobacter sakazakii (bacteria) / Gene: CSK29544_03680 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0F6VWC7
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.68 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.49 M NaH2PO4 0.91 M K2HPO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.7107 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 20, 2016
RadiationMonochromator: MX2 Beamline Australian Synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7107 Å / Relative weight: 1
ReflectionResolution: 2.158→35.16 Å / Num. obs: 18134 / % possible obs: 99.7 % / Redundancy: 3.2 % / R split: 0.2148 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.083 / Net I/σ(I): 10.9
Reflection shellResolution: 2.16→2.22 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.701 / Num. unique obs: 17897 / R split: 0.7131 / Rpim(I) all: 0.638 / % possible all: 93

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
Blu-Icedata collection
HKL-2000data reduction
PHENIXphasing
XDSdata scaling
RefinementResolution: 2.158→35.156 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2282 1796 10.04 %
Rwork0.1861 --
obs0.1904 17884 93.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.158→35.156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1988 0 10 63 2061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032052
X-RAY DIFFRACTIONf_angle_d0.5692788
X-RAY DIFFRACTIONf_dihedral_angle_d16.5411219
X-RAY DIFFRACTIONf_chiral_restr0.042298
X-RAY DIFFRACTIONf_plane_restr0.003368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1575-2.21590.30121330.29461188X-RAY DIFFRACTION92
2.2159-2.28110.30721380.26941238X-RAY DIFFRACTION96
2.2811-2.35470.26111410.23371249X-RAY DIFFRACTION96
2.3547-2.43880.25831390.22721247X-RAY DIFFRACTION96
2.4388-2.53640.27371420.21751252X-RAY DIFFRACTION96
2.5364-2.65180.26181380.2281243X-RAY DIFFRACTION95
2.6518-2.79160.26191330.20811240X-RAY DIFFRACTION95
2.7916-2.96640.26361400.20221240X-RAY DIFFRACTION95
2.9664-3.19530.24561370.18951238X-RAY DIFFRACTION94
3.1953-3.51660.21551390.17281251X-RAY DIFFRACTION94
3.5166-4.02480.20411290.15671228X-RAY DIFFRACTION93
4.0248-5.06840.16711390.14951241X-RAY DIFFRACTION92
5.0684-35.16080.23971480.18351233X-RAY DIFFRACTION87
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)
16.265-0.5925-2.41626.0262-0.90136.73170.08380.08960.38440.10160.054-0.3809-0.0982-0.0847-0.13020.2093-0.00560.01930.3496-0.02980.2867-8.412534.780419.3916
24.7308-3.3381-0.6953.8139-0.04395.7612-0.2518-0.14070.04570.1329-0.078-0.0676-0.0342-0.08380.2930.2371-0.07520.00560.33780.00560.3069-11.41731.041227.4339
34.1142-1.7384-1.99391.76620.47953.937-0.4221-0.328-0.42430.26570.09580.02730.49210.27010.33710.4535-0.02330.06730.42910.11080.4285-0.019819.687227.416
46.0254-1.0305-0.7733.31790.5712.8401-0.19810.4344-0.7097-0.0847-0.15810.50980.552-0.60640.34270.3641-0.14540.05920.4888-0.08630.4126-9.455719.858514.0258
58.2879-1.6936-2.44667.47980.11937.3364-0.2711-0.7161-0.40260.22280.0204-0.50580.50740.51730.19930.34260.01150.07020.42670.07120.438613.590916.728914.9204
68.2481-5.8533-1.1389.21291.00312.62310.19880.7851-0.1056-0.2968-0.37760.3686-0.1082-0.55850.11910.2732-0.02040.04670.48890.03290.2501-3.765728.9347.525
76.6083-3.49812.32825.7731-0.1845.85530.22770.06610.1785-0.2664-0.0689-0.29220.36310.0564-0.17070.2792-0.01820.08680.3259-0.0320.255412.547322.46954.4012
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 46 through 80 )
2X-RAY DIFFRACTION2chain 'A' and (resid 81 through 113 )
3X-RAY DIFFRACTION3chain 'A' and (resid 114 through 175 )
4X-RAY DIFFRACTION4chain 'A' and (resid 176 through 212 )
5X-RAY DIFFRACTION5chain 'A' and (resid 213 through 230 )
6X-RAY DIFFRACTION6chain 'A' and (resid 231 through 279 )
7X-RAY DIFFRACTION7chain 'A' and (resid 280 through 303 )

+
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