[English] 日本語
Yorodumi
- PDB-6rtn: Crystal structure of OXA-10 with VNRX-5133 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rtn
TitleCrystal structure of OXA-10 with VNRX-5133
ComponentsBeta-lactamase OXA-10
KeywordsANTIMICROBIAL PROTEIN / beta lactamase / antibiotic resistance / boronates
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / periplasmic space / 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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-KJK / Beta-lactamase OXA-10
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.17 Å
AuthorsBrem, J. / Schofield, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
CitationJournal: J.Med.Chem. / Year: 2019
Title: Bicyclic Boronate VNRX-5133 Inhibits Metallo- and Serine-beta-Lactamases.
Authors: Krajnc, A. / Brem, J. / Hinchliffe, P. / Calvopina, K. / Panduwawala, T.D. / Lang, P.A. / Kamps, J.J.A.G. / Tyrrell, J.M. / Widlake, E. / Saward, B.G. / Walsh, T.R. / Spencer, J. / Schofield, C.J.
History
DepositionMay 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Jan 24, 2024Group: 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 OXA-10
B: Beta-lactamase OXA-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,60116
Polymers55,3972
Non-polymers1,20414
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-130 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.879, 95.620, 126.269
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Beta-lactamase OXA-10 / Beta-lactamase PSE-2


Mass: 27698.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: bla, oxa10, pse2 / Production host: Escherichia coli (E. coli) / References: UniProt: P14489, beta-lactamase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-KJK / (3~{R})-3-[2-[4-(2-azanylethylamino)cyclohexyl]ethanoylamino]-2-oxidanyl-3,4-dihydro-1,2-benzoxaborinine-8-carboxylic acid


Mass: 389.254 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H28BN3O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.68 Å3/Da / Density % sol: 54.02 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M MES, pH = 6.0, 20 % w/v PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97872 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 18, 2018 / Details: mirror
RadiationMonochromator: Double mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.17→76.25 Å / Num. obs: 32199 / % possible obs: 100 % / Redundancy: 12.5 % / Biso Wilson estimate: 18.55 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.073 / Rrim(I) all: 0.259 / Net I/σ(I): 7.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.17-2.2312.60.823540.8830.2610.931100
9.7-76.2510.30.14290.9970.0320.10699.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.28 Å76.23 Å
Translation4.28 Å76.23 Å

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.3data scaling
PHASER2.8.1phasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FQ9

5fq9


Resolution: 2.17→63.134 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.64
RfactorNum. reflection% reflection
Rfree0.2236 1614 5.02 %
Rwork0.1948 --
obs0.1962 32125 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 68.74 Å2 / Biso mean: 22.4515 Å2 / Biso min: 3.07 Å2
Refinement stepCycle: final / Resolution: 2.17→63.134 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3758 0 68 304 4130
Biso mean--25.49 28.59 -
Num. residues----491
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1691-2.23290.23891270.22092486261399
2.2329-2.3050.30431250.24624952620100
2.305-2.38730.23361220.209125222644100
2.3873-2.48290.24261030.20925262629100
2.4829-2.59590.20251340.202525282662100
2.5959-2.73280.22671470.200825122659100
2.7328-2.9040.24871360.206225272663100
2.904-3.12820.25641540.201724922646100
3.1282-3.4430.20631280.183225612689100
3.443-3.94120.211390.165825492688100
3.9412-4.96520.15721450.148325952740100
4.9652-63.16120.2561540.228527182872100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.873-3.2685-1.43374.49070.41774.17920.10810.42030.9734-0.3299-0.321-0.7598-0.59110.56330.04530.3091-0.04890.04830.24170.08670.306822.05734.5198-15.4682
20.81930.4888-0.57382.1778-0.66052.7524-0.01680.02340.06240.00630.00610.0528-0.0599-0.03770.03380.06320.0361-0.02320.143-0.01840.145911.954-7.3586-2.8715
35.6379-3.41240.7182.6494-1.76256.0369-0.1571-0.0183-0.02770.41430.16-0.2793-0.18420.2801-0.03770.16690.0122-0.00220.1528-0.04060.152519.3304-17.718212.4067
43.46410.58322.24173.1724-1.51025.00660.0355-0.1562-0.08990.09460.12590.06230.2071-0.1652-0.14970.1030.01270.02070.0709-0.02670.1054.8276-20.24012.4356
52.4320.69010.79573.9122-1.55785.14630.02670.1009-0.2887-0.3087-0.0195-0.00170.38470.31340.01030.1598-0.00330.0130.1702-0.00450.10719.283-18.5213-6.7337
62.1035-0.8363-0.87521.83660.07942.551-0.0495-0.1010.10090.12710.06750.0655-0.2232-0.0677-0.0020.17890.0199-0.02060.11960.01130.13188.8151-1.71673.0913
74.1339-1.8021-0.4365.66441.03912.9322-0.05130.14290.1321-0.02510.0103-0.344-0.05340.0489-0.0040.1022-0.0255-0.02220.13340.03930.057719.0578-4.1586-5.7827
86.0926-5.0760.96474.4379-1.08933.40520.09050.0690.14830.1869-0.1917-0.5651-0.29810.06310.08690.1606-0.0518-0.00420.1885-0.01510.196825.44961.8151-4.2857
91.3896-0.07140.87511.3857-0.00292.98020.0193-0.0520.09810.0646-0.0382-0.0752-0.01880.26020.00670.1115-0.01650.02730.1581-0.02350.132813.23598.011730.0973
105.48921.78071.32292.1121-2.21667.74690.0730.2910.19-0.3079-0.1941-0.2024-0.24290.14650.05520.24940.0343-0.00180.19470.01240.17597.78121.05511.773
113.8178-0.2346-0.50782.0233-2.03874.64790.04970.1650.173-0.08950.11550.3941-0.2642-0.3593-0.1090.13960.0261-0.01170.1602-0.03970.1906-4.172215.203124.2809
123.6446-1.28140.8151.3265-0.31393.4786-0.2248-0.27680.29020.22220.27930.2776-0.6381-0.25690.07390.21280.01970.02520.1855-0.05950.24711.77317.599932.6212
134.24490.22242.39493.01851.32474.56630.2033-0.1597-0.21630.2018-0.11270.30070.3525-0.1508-0.13070.1178-0.01440.01360.12690.00770.12615.19910.906127.9737
142.96180.4056-0.06752.6564-0.12082.42030.06270.26690.0351-0.3064-0.00550.02710.20430.2449-0.02910.20630.0393-0.00220.1439-0.00560.101511.62093.909817.6025
153.16521.30070.29247.13821.03792.93750.00720.01120.20750.13720.0716-0.1775-0.10840.19040.02490.0778-0.00810.01960.17630.03950.119717.377910.252928.9732
164.5595-1.4445-0.85599.51740.9543.256-0.15530.31240.0476-0.11430.2314-0.76140.04350.3212-0.02150.1023-0.0030.02640.30680.00670.164525.32348.561426.4148
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 35 )A20 - 35
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 89 )A36 - 89
3X-RAY DIFFRACTION3chain 'A' and (resid 90 through 116 )A90 - 116
4X-RAY DIFFRACTION4chain 'A' and (resid 117 through 138 )A117 - 138
5X-RAY DIFFRACTION5chain 'A' and (resid 139 through 162 )A139 - 162
6X-RAY DIFFRACTION6chain 'A' and (resid 163 through 208 )A163 - 208
7X-RAY DIFFRACTION7chain 'A' and (resid 209 through 243 )A209 - 243
8X-RAY DIFFRACTION8chain 'A' and (resid 244 through 264 )A244 - 264
9X-RAY DIFFRACTION9chain 'B' and (resid 19 through 89 )B19 - 89
10X-RAY DIFFRACTION10chain 'B' and (resid 90 through 116 )B90 - 116
11X-RAY DIFFRACTION11chain 'B' and (resid 117 through 139 )B117 - 139
12X-RAY DIFFRACTION12chain 'B' and (resid 140 through 162 )B140 - 162
13X-RAY DIFFRACTION13chain 'B' and (resid 163 through 181 )B163 - 181
14X-RAY DIFFRACTION14chain 'B' and (resid 182 through 208 )B182 - 208
15X-RAY DIFFRACTION15chain 'B' and (resid 209 through 243 )B209 - 243
16X-RAY DIFFRACTION16chain 'B' and (resid 244 through 264 )B244 - 264

+
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