[English] 日本語
Yorodumi
- PDB-3g35: CTX-M-9 class A beta-lactamase complexed with compound 12 (F13) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3g35
TitleCTX-M-9 class A beta-lactamase complexed with compound 12 (F13)
ComponentsBeta-lactamase CTX-M-9a
KeywordsHYDROLASE/HYDROLASE INHIBITOR / CTX-M / beta-lactamase / molecular docking / fragment / inhibitor / Antibiotic resistance / Hydrolase / Plasmid / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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 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
3-fluoro-N-[3-(1H-tetrazol-5-yl)phenyl]benzamide / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsChen, Y. / Shoichet, B.K.
CitationJournal: Nat.Chem.Biol. / Year: 2009
Title: Molecular docking and ligand specificity in fragment-based inhibitor discovery
Authors: Chen, Y. / Shoichet, B.K.
History
DepositionFeb 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase CTX-M-9a
B: Beta-lactamase CTX-M-9a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,80110
Polymers55,9452
Non-polymers1,8568
Water10,935607
1
A: Beta-lactamase CTX-M-9a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5393
Polymers27,9721
Non-polymers5672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase CTX-M-9a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2627
Polymers27,9721
Non-polymers1,2896
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.265, 107.243, 47.727
Angle α, β, γ (deg.)90.000, 99.930, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 27972.494 Da / Num. of mol.: 2 / Fragment: sequence database residues 29-291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaCTX-M-9, blaCTX-M-9a, CTX-M / Plasmid: PET-9a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9L5C8, beta-lactamase
#2: Chemical
ChemComp-F13 / 3-fluoro-N-[3-(1H-tetrazol-5-yl)phenyl]benzamide


Mass: 283.261 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H10FN5O
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 607 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.69 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: Potassium Phosphate, pH 8.7, vapor diffusion, hanging drop, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM Q315r / Detector: CCD / Date: Jul 28, 2008 / Details: mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.41→50 Å / Num. obs: 84626 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Rmerge(I) obs: 0.053 / Χ2: 1.024
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.41-1.462.20.33480570.95894
1.46-1.522.50.26683191.00597.7
1.52-1.592.50.20284511.01198.3
1.59-1.672.50.15384531.02698.8
1.67-1.782.50.11884621.03799
1.78-1.912.60.08885451.0299.3
1.91-2.112.60.06985081.04799.5
2.11-2.412.60.0785810.9899.9
2.41-3.042.60.05886051.00499.8
3.04-502.60.03186451.1399.5

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YLJ

1ylj


Resolution: 1.41→35.36 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.199 / WRfactor Rwork: 0.166 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.903 / SU B: 1.991 / SU ML: 0.036 / SU R Cruickshank DPI: 0.079 / SU Rfree: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.182 4258 5 %RANDOM
Rwork0.155 ---
obs0.156 84588 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.73 Å2 / Biso mean: 16.826 Å2 / Biso min: 8.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20.04 Å2
2--0.05 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.41→35.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3996 0 134 607 4737
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224216
X-RAY DIFFRACTIONr_angle_refined_deg1.1642.0025758
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5755555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.72324.713174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.93215693
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8131532
X-RAY DIFFRACTIONr_chiral_restr0.0730.2658
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023256
X-RAY DIFFRACTIONr_nbd_refined0.1910.22075
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22986
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.2492
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.2115
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.286
X-RAY DIFFRACTIONr_mcbond_it0.7221.52719
X-RAY DIFFRACTIONr_mcangle_it1.11424264
X-RAY DIFFRACTIONr_scbond_it3.54931692
X-RAY DIFFRACTIONr_scangle_it3.1944.51477
X-RAY DIFFRACTIONr_rigid_bond_restr3.8134411
X-RAY DIFFRACTIONr_sphericity_free2.5143607
X-RAY DIFFRACTIONr_sphericity_bonded2.11934130
LS refinement shellResolution: 1.41→1.447 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 298 -
Rwork0.242 5368 -
all-5666 -
obs--89.2 %

+
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