[English] 日本語
Yorodumi
- PDB-6vhs: Crystal structure of CTX-M-14 in complex with beta-lactamase inhi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vhs
TitleCrystal structure of CTX-M-14 in complex with beta-lactamase inhibitor ETX1317
ComponentsBeta-lactamase
KeywordsHYDROLASE / CTX-M-14 / beta-lactamase / b-lactamase / etx3517 / etx-3517 / avibactam / dbo
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
PHOSPHATE ION / Chem-X57 / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsSacco, M.D. / Chen, Y.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Discovery of an Orally Available Diazabicyclooctane Inhibitor (ETX0282) of Class A, C, and D Serine beta-Lactamases.
Authors: Durand-Reville, T.F. / Comita-Prevoir, J. / Zhang, J. / Wu, X. / May-Dracka, T.L. / Romero, J.A.C. / Wu, F. / Chen, A. / Shapiro, A.B. / Carter, N.M. / McLeod, S.M. / Giacobbe, R.A. / ...Authors: Durand-Reville, T.F. / Comita-Prevoir, J. / Zhang, J. / Wu, X. / May-Dracka, T.L. / Romero, J.A.C. / Wu, F. / Chen, A. / Shapiro, A.B. / Carter, N.M. / McLeod, S.M. / Giacobbe, R.A. / Verheijen, J.C. / Lahiri, S.D. / Sacco, M.D. / Chen, Y. / O'Donnell, J.P. / Miller, A.A. / Mueller, J.P. / Tommasi, R.A.
History
DepositionJan 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 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: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9929
Polymers55,9672
Non-polymers1,0257
Water16,592921
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4494
Polymers27,9841
Non-polymers4653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5445
Polymers27,9841
Non-polymers5604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.250, 106.920, 47.870
Angle α, β, γ (deg.)90.000, 101.810, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Beta-lactamase


Mass: 27983.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaCTX-M-14 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A2S1PK93, UniProt: Q9L5C7*PLUS, beta-lactamase
#2: Chemical ChemComp-X57 / (2R)-({[(3R,6S)-6-carbamoyl-1-formyl-4-methyl-1,2,3,6-tetrahydropyridin-3-yl]amino}oxy)(fluoro)acetic acid


Mass: 275.234 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14FN3O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 921 / 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: 2.03 Å3/Da / Density % sol: 39.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9 / Details: 1.2 M potassium phosphate pH 7.9

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.275→106.92 Å / Num. all: 111890 / Num. obs: 111890 / % possible obs: 96.9 % / Redundancy: 3.6 % / Rpim(I) all: 0.036 / Rrim(I) all: 0.069 / Rsym value: 0.059 / Net I/av σ(I): 7.5 / Net I/σ(I): 13.5 / Num. measured all: 402946
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.28-1.343.70.0976.660425163700.0580.1140.0979.197.3
1.34-1.433.50.097.154539155040.0550.1060.099.797.6
1.43-1.523.30.0817.847586142260.0510.0960.08110.794.8
1.52-1.653.80.0778.252003137110.0450.090.07712.798.2
1.65-1.83.60.0699.245748125940.0410.080.06913.798.2
1.8-2.023.30.05910.136711110020.0370.070.05915.294.6
2.02-2.333.80.0551138257100660.0320.0640.05518.298.3
2.33-2.853.90.0639.63323985480.0360.0730.06319.398.5
2.85-4.033.40.04913.12158863730.0310.0590.04919.294.7
4.03-53.463.70.04613.61285034960.0280.0540.0462094.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6mz1

6mz1


Resolution: 1.28→53.52 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.538 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1485 5618 5 %RANDOM
Rwork0.1285 ---
obs0.1295 106217 96.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.53 Å2 / Biso mean: 9.355 Å2 / Biso min: 2.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.16 Å2
2---0.09 Å2-0 Å2
3---0.05 Å2
Refinement stepCycle: final / Resolution: 1.28→53.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3920 0 63 960 4943
Biso mean--22.18 23.87 -
Num. residues----525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0134239
X-RAY DIFFRACTIONr_bond_other_d0.0030.0173962
X-RAY DIFFRACTIONr_angle_refined_deg2.0511.6655798
X-RAY DIFFRACTIONr_angle_other_deg1.7161.5829194
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6445561
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03422.184206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.02115698
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9251532
X-RAY DIFFRACTIONr_chiral_restr0.1150.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024871
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02836
LS refinement shellResolution: 1.28→1.308 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.166 407 -
Rwork0.143 7862 -
obs--96.96 %

+
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://pdbjlvh1.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