[English] 日本語
Yorodumi
- PDB-5le1: VIM-2 metallo-beta-lactamase in complex with 2-(2-chloro-6-fluoro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5le1
TitleVIM-2 metallo-beta-lactamase in complex with 2-(2-chloro-6-fluorobenzyl)-3-oxoisoindoline-4-carboxylic acid (compound 16)
ComponentsMetallo-beta-lactamase VIM-2
KeywordsHYDROLASE / metallo-beta-lactamase / inhibitor / complex / antibiotic resistance
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding
Similarity search - Function
: / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6UW / FORMIC ACID / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 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 29, 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)29,0347
Polymers28,3531
Non-polymers6816
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-81 kcal/mol
Surface area9340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.171, 60.720, 97.911
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-900-

HOH

21A-916-

HOH

31A-917-

HOH

41A-938-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Metallo-beta-lactamase VIM-2 / Beta-lactamase VIM-2 / Class B carbapenemase VIM-2 / Metallo beta lactamase VIM-2 / Metallo beta- ...Beta-lactamase VIM-2 / Class B carbapenemase VIM-2 / Metallo beta lactamase VIM-2 / Metallo beta-lactamase / Metallo-beta-lactamase / 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
Details: 2-(2-chloro-6-fluorobenzyl)-3-oxoisoindoline-4-carboxylic acid
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 VECTOR BASED ON PTRIEX VECTOR / Details (production host): PLASMID DERIVED NON-GENOMIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): PLYSS / References: UniProt: Q9K2N0

-
Non-polymers , 5 types, 344 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-6UW / 2-[(2-chloranyl-6-fluoranyl-phenyl)methyl]-3-oxidanylidene-1~{H}-isoindole-4-carboxylic acid


Mass: 319.715 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H11ClFNO3
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Magnesium Formate, 24.5% (v/v) Polyethylene glycol 3350, 1 mM Tris(2-carboxyethyl)phosphine, 5 mM 2-(2-chloro-6-fluorobenzyl)-3-oxoisoindoline-4-carboxylic acid, 16 mg/mL protein

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 53782 / % possible obs: 100 % / Redundancy: 11.4 % / Biso Wilson estimate: 14.12 Å2 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.028 / Rrim(I) all: 0.098 / Χ2: 1.065 / Net I/av σ(I): 25.7 / Net I/σ(I): 6.3 / Num. measured all: 614346
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.4-1.458.10.7652700.7780.280.8120.905100
1.45-1.5110.20.66953380.8610.2180.7050.93499.9
1.51-1.5811.50.54252950.9260.1670.5680.972100
1.58-1.6611.40.43152950.950.1340.4521.004100
1.66-1.7612.10.29553440.9780.0890.3081.039100
1.76-1.911.90.20553450.9880.0620.2141.134100
1.9-2.0912.50.13953730.9940.0410.1451.162100
2.09-2.3912.10.10453770.9950.0310.1081.181100
2.39-3.0212.30.07554690.9980.0220.0781.032100
3.02-50120.05156760.9970.0160.0541.184100

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.24 Å41.02 Å
Translation6.24 Å41.02 Å

-
Processing

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

4c1d


Resolution: 1.4→41.016 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1538 2000 3.72 %
Rwork0.1323 51699 -
obs0.1331 53699 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.55 Å2 / Biso mean: 19.9788 Å2 / Biso min: 8.36 Å2
Refinement stepCycle: final / Resolution: 1.4→41.016 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1719 0 39 345 2103
Biso mean--19.77 35.56 -
Num. residues----231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141877
X-RAY DIFFRACTIONf_angle_d0.9482565
X-RAY DIFFRACTIONf_chiral_restr0.076288
X-RAY DIFFRACTIONf_plane_restr0.007339
X-RAY DIFFRACTIONf_dihedral_angle_d17.385654
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3997-1.43470.2131350.21243490362596
1.4347-1.47350.23171410.188836463787100
1.4735-1.51680.21420.164236773819100
1.5168-1.56580.16751410.155736483789100
1.5658-1.62180.16961410.138636473788100
1.6218-1.68670.16441430.133836863829100
1.6867-1.76350.14761420.122336683810100
1.7635-1.85640.1531420.123936743816100
1.8564-1.97270.1321430.128236973840100
1.9727-2.1250.14411420.123736883830100
2.125-2.33890.1611440.123137283872100
2.3389-2.67730.16341460.119737373883100
2.6773-3.37280.13831450.124637773922100
3.3728-41.0340.14461530.135539364089100
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)
12.0387-0.2069-1.28831.02540.19083.28840.00570.16570.1009-0.1053-0.00220.02550.0135-0.12070.00150.0672-0.0046-0.01180.07730.01010.0854103.826583.889212.2977
22.393-4.0957-1.86428.02311.6814.97740.18330.16510.3772-0.127-0.0305-0.0361-0.2239-0.1545-0.14220.0792-0.01360.00490.09490.01340.1259108.410491.599916.4549
30.9458-0.1187-0.5313.5310.12671.3770.0011-0.1029-0.00390.0493-0.0266-0.18020.07270.10980.01560.06130.0034-0.0150.10390.00710.0829111.641278.166724.415
44.21791.72911.77071.07391.09091.28950.2395-0.4504-0.27460.1667-0.291-0.19540.2194-0.08630.06610.15850.0052-0.00850.11320.03830.1427108.582370.703428.2001
51.6654-0.0107-0.32042.38110.47762.2483-0.04320.1034-0.0919-0.18230.03250.04080.2009-0.08850.02260.1177-0.0362-0.01060.08180.00260.0974100.868669.758916.3592
64.1583-3.7592-4.2346.79882.27525.3031-0.25630.05-0.5040.03510.0740.37860.5234-0.19330.20060.2326-0.0674-0.02090.1352-0.00430.153596.81860.62416.2731
73.03120.3130.18143.841-1.10462.9967-0.04930.31010.2242-0.14180.16120.49670.0689-0.51-0.12890.134-0.0287-0.04890.1595-0.00030.141594.030874.640411.9086
89.0118-4.7408-3.08156.56832.71955.7636-0.04810.4848-0.7288-0.3365-0.10440.38950.6593-0.08030.13640.3612-0.0802-0.03130.207-0.05010.177398.170862.24516.0115
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 88 )A31 - 88
2X-RAY DIFFRACTION2chain 'A' and (resid 89 through 102 )A89 - 102
3X-RAY DIFFRACTION3chain 'A' and (resid 103 through 146 )A103 - 146
4X-RAY DIFFRACTION4chain 'A' and (resid 147 through 163 )A147 - 163
5X-RAY DIFFRACTION5chain 'A' and (resid 164 through 215 )A164 - 215
6X-RAY DIFFRACTION6chain 'A' and (resid 216 through 229 )A216 - 229
7X-RAY DIFFRACTION7chain 'A' and (resid 230 through 245 )A230 - 245
8X-RAY DIFFRACTION8chain 'A' and (resid 246 through 261 )A246 - 261

+
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