[English] 日本語
Yorodumi
- PDB-8pec: OXA-48_Q5-CAZ. Epistasis Arises from Shifting the Rate-Limiting S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8pec
TitleOXA-48_Q5-CAZ. Epistasis Arises from Shifting the Rate-Limiting Step during Enzyme Evolution
ComponentsBeta-lactamase
KeywordsHYDROLASE / Protein evolution. Antibiotic resistance. OXA-48. HYDROLASE. Serine-Beta-lactamase.
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase / beta-lactamase activity / response to antibiotic / plasma membrane
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Chem-CTJ / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsLeiros, H.-K.S. / Frohlich, C.
Funding support1items
OrganizationGrant numberCountry
Not funded0000
CitationJournal: Nat Catal / Year: 2024
Title: Epistasis arises from shifting the rate-limiting step during enzyme evolution of a beta-lactamase.
Authors: Frohlich, C. / Bunzel, H.A. / Buda, K. / Mulholland, A.J. / van der Kamp, M.W. / Johnsen, P.J. / Leiros, H.S. / Tokuriki, N.
History
DepositionJun 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,7319
Polymers112,0114
Non-polymers1,7205
Water1,51384
1
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5904
Polymers56,0052
Non-polymers5852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-7 kcal/mol
Surface area21030 Å2
MethodPISA
2
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1405
Polymers56,0052
Non-polymers1,1353
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-9 kcal/mol
Surface area20860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)202.147, 202.147, 55.699
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

-
Components

#1: Protein
Beta-lactamase


Mass: 28002.713 Da / Num. of mol.: 4 / Mutation: A33V, K51E, F72L, S212A, T213A
Source method: isolated from a genetically manipulated source
Details: This is a A33V K51E F72L S212A T213A mutant / Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla OXA-48, blaOXA-48, KPE71T_00045 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6XEC0, beta-lactamase
#2: Chemical ChemComp-CTJ / 1-({(2R)-2-[(1R)-1-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-{[(2-carboxypropan-2-yl)oxy]imino}acetyl]amino}-2-oxoethyl]-4-carboxy-3,6-dihydro-2H-1,3-thiazin-5-yl}methyl)pyridinium


Mass: 549.600 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H25N6O7S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1 M Tris, pH 9.0 28-30% polyethylene glycol (PEG) mono ethylene ether 500

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.66→24.39 Å / Num. obs: 37514 / % possible obs: 99.2 % / Redundancy: 6.1 % / Biso Wilson estimate: 73.12 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.052 / Rrim(I) all: 0.129 / Net I/σ(I): 9.1
Reflection shellResolution: 2.66→2.78 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.555 / Num. unique obs: 4578 / CC1/2: 0.367 / Rpim(I) all: 0.761 / Rrim(I) all: 1.846 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→24.39 Å / SU ML: 0.4187 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.1778
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2707 1809 4.87 %
Rwork0.2023 35301 -
obs0.2055 37110 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 95.81 Å2
Refinement stepCycle: LAST / Resolution: 2.66→24.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7472 0 113 84 7669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00857765
X-RAY DIFFRACTIONf_angle_d1.05310511
X-RAY DIFFRACTIONf_chiral_restr0.05511107
X-RAY DIFFRACTIONf_plane_restr0.00571343
X-RAY DIFFRACTIONf_dihedral_angle_d27.71822836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.730.37471270.3322468X-RAY DIFFRACTION90.54
2.73-2.810.34981570.30962608X-RAY DIFFRACTION96.38
2.81-2.90.38731560.30772681X-RAY DIFFRACTION98.92
2.9-3.010.34711440.29612723X-RAY DIFFRACTION99.48
3.01-3.130.36441400.28442737X-RAY DIFFRACTION99.07
3.13-3.270.31211340.26792748X-RAY DIFFRACTION99.76
3.27-3.440.25451440.22982734X-RAY DIFFRACTION99.65
3.44-3.650.29991350.2172732X-RAY DIFFRACTION99.34
3.66-3.940.25081630.19292732X-RAY DIFFRACTION99.38
3.94-4.330.2661190.18092755X-RAY DIFFRACTION98.66
4.33-4.950.23071040.15822794X-RAY DIFFRACTION99.38
4.95-6.220.2541280.19342778X-RAY DIFFRACTION98.11
6.22-24.390.23791580.16612811X-RAY DIFFRACTION98.18

+
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