[English] 日本語
Yorodumi
- PDB-9f0u: Structure of KPC-2 complexed with benzoxaborole AK-425 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9f0u
TitleStructure of KPC-2 complexed with benzoxaborole AK-425
ComponentsCarbapenem-hydrolyzing beta-lactamase KPC
KeywordsANTIMICROBIAL PROTEIN / Inhibitor / beta-lactamase / SBL / antibiotic resistance / boronate
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / 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
: / Carbapenem-hydrolyzing beta-lactamase KPC-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.11 Å
AuthorsTooke, C.L. / Hinchliffe, P. / Spencer, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/T016035/1 United Kingdom
CitationJournal: To Be Published
Title: Structure of KPC-2 complexed with benzoxaborole AK-425
Authors: Tooke, C.L. / Hinchliffe, P. / Spencer, J.
History
DepositionApr 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carbapenem-hydrolyzing beta-lactamase KPC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4658
Polymers30,8071
Non-polymers6587
Water7,404411
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-52 kcal/mol
Surface area11160 Å2
Unit cell
Length a, b, c (Å)60.190, 79.110, 55.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-505-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Carbapenem-hydrolyzing beta-lactamase KPC / Carbapenem-hydrolyzing beta-lactamase KPC-1


Mass: 30806.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla, kpc, kpc1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Solu / References: UniProt: Q9F663, beta-lactamase

-
Non-polymers , 5 types, 418 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-XR9 / (9S)-7-oxidanyl-8-oxa-7-boranuidabicyclo[4.3.0]nona-1,3,5-triene-9-carbonitrile


Mass: 158.950 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6BNO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.07 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / Details: 2.0 M ammonium sulphate, 5% ethanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.7746 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7746 Å / Relative weight: 1
ReflectionResolution: 1.11→36.38 Å / Num. obs: 105821 / % possible obs: 99.9 % / Redundancy: 13.5 % / Biso Wilson estimate: 14.16 Å2 / CC1/2: 1 / Rpim(I) all: 0.028 / Net I/σ(I): 10.3
Reflection shellResolution: 1.11→1.13 Å / Redundancy: 13.1 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 5230 / CC1/2: 0.365 / Rpim(I) all: 0.907 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.11→32.29 Å / SU ML: 0.1548 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.9685
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1576 5491 5.2 %
Rwork0.1347 100204 -
obs0.1359 105695 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.28 Å2
Refinement stepCycle: LAST / Resolution: 1.11→32.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2016 0 39 411 2466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072306
X-RAY DIFFRACTIONf_angle_d1.00053170
X-RAY DIFFRACTIONf_chiral_restr0.0754349
X-RAY DIFFRACTIONf_plane_restr0.0128424
X-RAY DIFFRACTIONf_dihedral_angle_d11.606848
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.11-1.120.42571710.42543271X-RAY DIFFRACTION98.31
1.12-1.140.39871790.3833288X-RAY DIFFRACTION98.97
1.14-1.150.34472060.34673252X-RAY DIFFRACTION99.88
1.15-1.160.33731710.32053324X-RAY DIFFRACTION99.21
1.16-1.180.29681740.29383296X-RAY DIFFRACTION99.54
1.18-1.20.29341710.26883302X-RAY DIFFRACTION99.86
1.2-1.210.25962000.26083303X-RAY DIFFRACTION99.55
1.21-1.230.24891890.24633266X-RAY DIFFRACTION99.65
1.23-1.250.23431770.23293313X-RAY DIFFRACTION99.97
1.25-1.270.2521740.21843324X-RAY DIFFRACTION99.69
1.27-1.290.2141850.19933306X-RAY DIFFRACTION99.77
1.29-1.320.2191750.19373307X-RAY DIFFRACTION99.77
1.32-1.340.21781760.17983357X-RAY DIFFRACTION99.89
1.34-1.370.19821590.16923344X-RAY DIFFRACTION99.91
1.37-1.40.18111720.15153335X-RAY DIFFRACTION100
1.4-1.430.17561660.14123319X-RAY DIFFRACTION99.94
1.43-1.470.17811750.13083355X-RAY DIFFRACTION99.97
1.47-1.510.16972160.11653284X-RAY DIFFRACTION100
1.51-1.550.15342060.10663328X-RAY DIFFRACTION99.94
1.55-1.60.13041750.10463343X-RAY DIFFRACTION100
1.6-1.660.13761680.09533345X-RAY DIFFRACTION99.91
1.66-1.720.15221920.09613329X-RAY DIFFRACTION99.97
1.72-1.80.13531640.10323385X-RAY DIFFRACTION100
1.8-1.90.10771700.10553380X-RAY DIFFRACTION99.97
1.9-2.020.13631610.10643390X-RAY DIFFRACTION99.97
2.02-2.170.1382100.10623348X-RAY DIFFRACTION100
2.17-2.390.13162020.10733359X-RAY DIFFRACTION100
2.39-2.740.12772110.10893412X-RAY DIFFRACTION100
2.74-3.450.14111740.11863468X-RAY DIFFRACTION100
3.45-32.290.15122220.13943571X-RAY DIFFRACTION99.92

+
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