[English] 日本語
Yorodumi
- PDB-4len: CTX-M-9 in complex with the broad spectrum inhibitor 3-(2- carbox... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4len
TitleCTX-M-9 in complex with the broad spectrum inhibitor 3-(2- carboxyvinyl)benzo(b)thiophene-2-boronic acid
ComponentsBeta-lactamase
Keywordshydrolase/hydrolase inhibitor / Binding Sites / structure base drug design / Drug Discovery / Molecular / Enzyme Inhibitors / beta lactamases / boronic acids / broad spectrum / bacterial resistance / double perturbation cycle analysis / thermodynamics / structure activity relationship / hydrolase-hydrolase inhibitor complex
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 active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-2GK / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsTondi, D.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Targeting Class A and C Serine beta-Lactamases with a Broad-Spectrum Boronic Acid Derivative.
Authors: Tondi, D. / Venturelli, A. / Bonnet, R. / Pozzi, C. / Shoichet, B.K. / Costi, M.P.
History
DepositionJun 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Oct 19, 2016Group: Structure summary
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
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)56,4414
Polymers55,9452
Non-polymers4962
Water13,944774
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2212
Polymers27,9721
Non-polymers2481
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2212
Polymers27,9721
Non-polymers2481
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.116, 106.595, 47.680
Angle α, β, γ (deg.)90.00, 102.03, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Beta-lactamase / Beta-lactamase CTX-M / Beta-lactamase CTX-M-9a / Betalactamase CTX-M-9 / CTX-M-9 beta-lactamase / ...Beta-lactamase CTX-M / Beta-lactamase CTX-M-9a / Betalactamase CTX-M-9 / CTX-M-9 beta-lactamase / CTX-M-9 extended-spectrum beta-lactamase


Mass: 27972.494 Da / Num. of mol.: 2 / Fragment: CTX-M9 / Mutation: none
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12
Gene: blaCTX-M-9, blaCTX-M-9a, blaCTX-M-9a blaCTX-M-9 blaCTX-M-9b, blaCTX-M-9b
Plasmid: pET-9a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9L5C8, beta-lactamase
#2: Chemical ChemComp-2GK / (2E)-3-[2-(dihydroxyboranyl)-1-benzothiophen-3-yl]prop-2-enoic acid


Mass: 248.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H9BO4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 774 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE STARTING MATERIAL USED FOR CHEMICAL REACTION CORRESPONDS TO THE COMPUND: 3-[2-(4,4,5,5- ...THE STARTING MATERIAL USED FOR CHEMICAL REACTION CORRESPONDS TO THE COMPUND: 3-[2-(4,4,5,5-TETRAMETHYL-[1,3,2]DIOXABOROLAN-2-YL)-BENZO[B]THIOPHEN-3-YL]-ACRYLIC ACID. SEE ALSO LINK RECORDS.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 1.4 M potassium phosphate buffer using microseeding techniques, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 8.8

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 1, 2004 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.35→20 Å / Num. all: 82707 / Num. obs: 82595 / % possible obs: 85.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1YM1

1ym1


Resolution: 1.5→19.39 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.114 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18174 3455 5 %RANDOM
Rwork0.15935 ---
obs0.16048 65055 97.48 %-
all-82707 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.214 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3907 0 34 774 4715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0194097
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.9775589
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8165545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.08524.578166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.68615683
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.0061531
X-RAY DIFFRACTIONr_chiral_restr0.0850.2662
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213089
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4140.7692133
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.7531.1482665
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.4480.8581964
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 223 -
Rwork0.18 4329 -
obs--88.22 %

+
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