[English] 日本語
Yorodumi
- PDB-9enx: Enmetazobactam-Derived GES-1 Acyl-Enzyme -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9enx
TitleEnmetazobactam-Derived GES-1 Acyl-Enzyme
Componentsbeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / beta-lactamase / antibiotic resistance / enzyme / inhibitor / complex / ligand
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / response to antibiotic
Similarity search - Function
Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Enmetazobactam derived trans-enamine adduct. / Beta-lactamase GES-1
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsBeer, M. / Hinchliffe, P. / Spencer, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T008741/10 United Kingdom
CitationJournal: To Be Published
Title: Enmetazobactam-Derived GES-1 Acyl-Enzyme
Authors: Beer, M. / Hinchliffe, P. / Spencer, J.
History
DepositionMar 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: beta-lactamase
B: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4379
Polymers62,9392
Non-polymers1,4987
Water11,007611
1
A: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3966
Polymers31,4701
Non-polymers9265
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0413
Polymers31,4701
Non-polymers5722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.804, 81.034, 71.551
Angle α, β, γ (deg.)90.000, 101.810, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein beta-lactamase


Mass: 31469.564 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ges-1, blaGES-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KJY7, beta-lactamase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-M9W / Enmetazobactam derived trans-enamine adduct / (2S,3S)-3-methyl-4-(3-methyl-1,2,3-triazol-3-ium-1-yl)-2-[[(E)-3-oxidanylideneprop-1-enyl]amino]-3-sulfino-butanoic acid


Mass: 333.341 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17N4O6S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 611 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.26 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: 20 mM HEPES pH 7.6, 10% PEG8000, 10% PEG10000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.73379 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.73379 Å / Relative weight: 1
ReflectionResolution: 1.23→81.03 Å / Num. obs: 138378 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 14.69 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.045 / Net I/σ(I): 8.1
Reflection shellResolution: 1.23→1.25 Å / Mean I/σ(I) obs: 0.3 / Num. unique obs: 6614 / CC1/2: 0.314 / Rpim(I) all: 1.151

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.23→70.04 Å / SU ML: 0.2163 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.28
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1935 6783 5 %
Rwork0.1519 128782 -
obs0.1539 135565 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.06 Å2
Refinement stepCycle: LAST / Resolution: 1.23→70.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4039 0 96 611 4746
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00794279
X-RAY DIFFRACTIONf_angle_d0.95935805
X-RAY DIFFRACTIONf_chiral_restr0.0738657
X-RAY DIFFRACTIONf_plane_restr0.0095747
X-RAY DIFFRACTIONf_dihedral_angle_d13.94091622
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.23-1.240.41811740.4113188X-RAY DIFFRACTION73.31
1.24-1.260.42412100.41423795X-RAY DIFFRACTION85.82
1.26-1.270.40571860.40553850X-RAY DIFFRACTION88.28
1.27-1.290.42832220.3984082X-RAY DIFFRACTION93.5
1.29-1.310.41582090.38764282X-RAY DIFFRACTION97.82
1.31-1.320.37292460.37324272X-RAY DIFFRACTION97.96
1.32-1.340.36272070.3654330X-RAY DIFFRACTION99
1.34-1.360.3792370.34114367X-RAY DIFFRACTION99.72
1.36-1.380.35092300.3244421X-RAY DIFFRACTION99.83
1.38-1.410.34452460.2994322X-RAY DIFFRACTION99.83
1.41-1.430.30772590.27784359X-RAY DIFFRACTION99.74
1.43-1.460.2962280.25184330X-RAY DIFFRACTION99.74
1.46-1.490.27162200.23824394X-RAY DIFFRACTION99.89
1.49-1.520.27862520.20894353X-RAY DIFFRACTION99.89
1.52-1.550.24042220.19344372X-RAY DIFFRACTION99.96
1.55-1.580.24172210.17964429X-RAY DIFFRACTION100
1.58-1.620.19842250.16614355X-RAY DIFFRACTION99.91
1.62-1.670.21312450.15434374X-RAY DIFFRACTION99.87
1.67-1.720.21792430.14574387X-RAY DIFFRACTION99.87
1.72-1.770.19872270.13754357X-RAY DIFFRACTION99.93
1.77-1.840.19232040.12894419X-RAY DIFFRACTION99.96
1.84-1.910.18572110.1294401X-RAY DIFFRACTION100
1.91-20.18372200.12314409X-RAY DIFFRACTION99.98
2-2.10.14472540.10964382X-RAY DIFFRACTION99.98
2.1-2.230.16322160.10754432X-RAY DIFFRACTION99.98
2.23-2.410.15372380.1114377X-RAY DIFFRACTION100
2.41-2.650.15112350.10944396X-RAY DIFFRACTION100
2.65-3.030.1542370.11224413X-RAY DIFFRACTION100
3.03-3.820.1442360.10784440X-RAY DIFFRACTION100
3.82-70.040.15442230.12474494X-RAY DIFFRACTION99.94

+
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