[English] 日本語
Yorodumi
- PDB-5lca: VIM-2 metallo-beta-lactamase in complex with 3-oxo-2-(3-(trifluor... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lca
TitleVIM-2 metallo-beta-lactamase in complex with 3-oxo-2-(3-(trifluoromethyl)phenyl)isoindoline-4-carboxylic acid (compound 17)
ComponentsMetallo-beta-lactamase VIM-2
KeywordsHYDROLASE / metallo-beta-lactamase / inhibitor / complex / antibiotic resistance
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / periplasmic space / hydrolase activity / response to antibiotic / metal ion binding
Similarity search - Function
: / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-B06 / beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.93 Å
AuthorsLi, G.-B. / Brem, J. / McDonough, M.A. / Schofield, C.J.
CitationJournal: Chem Sci / Year: 2017
Title: NMR-filtered virtual screening leads to non-metal chelating metallo-beta-lactamase inhibitors.
Authors: Li, G.B. / Abboud, M.I. / Brem, J. / Someya, H. / Lohans, C.T. / Yang, S.Y. / Spencer, J. / Wareham, D.W. / McDonough, M.A. / Schofield, C.J.
History
DepositionJun 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2Jan 10, 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: Metallo-beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2659
Polymers28,3531
Non-polymers9138
Water2,684149
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-83 kcal/mol
Surface area8910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.487, 65.313, 70.716
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Metallo-beta-lactamase VIM-2 / Beta-lactamase / Beta-lactamase VIM-2 / Class B carbapenemase VIM-2 / Metallo beta lactamase VIM-2 ...Beta-lactamase / Beta-lactamase VIM-2 / Class B carbapenemase VIM-2 / Metallo beta lactamase VIM-2 / Metallo beta-lactamase / Metallo-beta-lactamase / Metallo-beta-lactamase vim-2 / VIM-2 metallo-beta-lactamase / VIM-2 protein


Mass: 28352.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: blaVIM-2, bla vim-2, bla-VIM-2, blasVIM-2, blaVIM2, blm, VIM-2, vim-2, PAERUG_P32_London_17_VIM_2_10_11_06255
Plasmid: OPINF
Details (production host): OPINF VECTOR BASED ON PTRIEX VECTOR
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): PLYSS / References: UniProt: Q9K2N0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-B06 / 3-oxidanylidene-2-[3-(trifluoromethyl)phenyl]-1~{H}-isoindole-4-carboxylic acid


Mass: 321.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H10F3NO3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 1.82 Å3/Da / Density % sol: 32.4 % / Description: rhombohedra plates
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.25 M Magnesium formate, 22.0% (v/v) Polyethylene glycol 3350, 5 mM 3-oxo-2-(3-(trifluoromethyl)phenyl)isoindoline-4-carboxylic acid, 16 mg/mL protein

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.542 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 13, 2016 / Details: OSMIC HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 14437 / % possible obs: 98.2 % / Redundancy: 7 % / Biso Wilson estimate: 15.27 Å2 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.018 / Rrim(I) all: 0.047 / Χ2: 1.07 / Net I/av σ(I): 32.62 / Net I/σ(I): 31.7 / Num. measured all: 100610
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.93-270.0932.4197.4
2-2.0870.081197.6
2.08-2.177.10.073197.1
2.17-2.297.10.068197.4
2.29-2.437.10.061198.3
2.43-2.6270.056198.8
2.62-2.8870.046198.8
2.88-3.370.041199.4
3.3-4.166.90.034199.2
4.16-506.50.03198.2

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.86 Å23.99 Å
Translation5.86 Å23.99 Å

-
Processing

Software
NameVersionClassification
PHENIXrefinement
SCALEPACKdata scaling
PHASER2.6.0phasing
PDB_EXTRACT3.2data extraction
CrystalCleardata collection
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4c1d

4c1d


Resolution: 1.93→23.99 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.11
RfactorNum. reflection% reflection
Rfree0.1697 1438 9.98 %
Rwork0.1302 --
obs0.1342 14407 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 53.6 Å2 / Biso mean: 17.3166 Å2 / Biso min: 7.1 Å2
Refinement stepCycle: final / Resolution: 1.93→23.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1654 0 55 149 1858
Biso mean--31.22 28.31 -
Num. residues----222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091751
X-RAY DIFFRACTIONf_angle_d0.6472381
X-RAY DIFFRACTIONf_chiral_restr0.049267
X-RAY DIFFRACTIONf_plane_restr0.004308
X-RAY DIFFRACTIONf_dihedral_angle_d14.762998
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.93-1.99890.15721370.11921246138397
1.9989-2.07890.16381360.11281268140498
2.0789-2.17350.15941430.11611253139697
2.1735-2.2880.15091410.12141266140797
2.288-2.43120.15481480.12351271141998
2.4312-2.61870.18561400.12561307144799
2.6187-2.88180.16711410.12911297143899
2.8818-3.29790.15731460.12531315146199
3.2979-4.15150.15731490.12441344149399
4.1515-23.99170.20621570.16121402155999
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)
14.540.9406-0.52865.7636-0.80353.61190.0596-0.30680.03440.6868-0.00160.0382-0.2506-0.0753-0.09270.1041-0.00830.01060.1452-0.00590.0353-7.020118.5302-2.3421
22.4471-0.5436-0.36413.77880.16051.85140.07260.02820.1096-0.0458-0.0374-0.0293-0.12250.0152-0.01080.0666-0.01470.00260.0538-0.00890.0405-2.904218.2775-9.0457
30.71-0.3280.42031.4563-1.29923.04030.0056-0.05860.00220.0602-0.0012-0.02730.00380.0356-0.00970.0553-0.01450.00570.0848-0.01150.09092.48717.9217-8.6523
43.27850.43450.06924.5437-0.2982.95330.06940.11120.0107-0.0534-0.1575-0.203-0.060.11510.07020.0429-0.00430.02350.09580.00290.10057.91918.2362-19.9939
52.03640.5735-0.23191.3684-0.42960.83-0.01450.18-0.2509-0.03190.018-0.01450.1259-0.0342-0.0110.1004-0.00550.00670.0903-0.02670.0855-2.71769.7714-20.669
63.9777-0.2491-1.31830.7667-0.27423.7288-0.06570.28410.4666-0.0511-0.0940.0208-0.2964-0.1146-0.00010.1255-0.0114-0.02330.14360.01630.1579-15.37823.0058-21.743
72.03030.9561-0.67673.2909-4.67057.8246-0.01450.5072-0.1901-0.51530.08850.370.5165-0.4147-0.12690.1404-0.0002-0.02630.2419-0.05110.1391-14.91710.3561-27.5574
83.55560.45650.394.85141.9594.9286-0.0271-0.0139-0.24980.3862-0.00330.2820.3194-0.1730.0390.0591-0.0050.01180.10560.00120.0857-14.494611.1105-12.7048
94.5035-0.9930.64277.3846-4.85223.40480.03090.3029-0.0122-0.28330.05250.15110.1002-0.2581-0.14020.0993-0.0036-0.00240.1394-0.010.1081-21.26116.6408-22.6871
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 39 through 52 )A39 - 52
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 88 )A53 - 88
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 122 )A89 - 122
4X-RAY DIFFRACTION4chain 'A' and (resid 123 through 146 )A123 - 146
5X-RAY DIFFRACTION5chain 'A' and (resid 147 through 199 )A147 - 199
6X-RAY DIFFRACTION6chain 'A' and (resid 200 through 215 )A200 - 215
7X-RAY DIFFRACTION7chain 'A' and (resid 216 through 229 )A216 - 229
8X-RAY DIFFRACTION8chain 'A' and (resid 230 through 245 )A230 - 245
9X-RAY DIFFRACTION9chain 'A' and (resid 246 through 260 )A246 - 260

+
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