[English] 日本語
Yorodumi
- PDB-5k48: VIM-2 Metallo Beta Lactamase in complex with 3-(mercaptomethyl)-[... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5k48
TitleVIM-2 Metallo Beta Lactamase in complex with 3-(mercaptomethyl)-[1,1'-biphenyl]-4-carboxylic acid
ComponentsBeta-lactamase VIM-2
KeywordsHYDROLASE / metallo beta-lactamase / antibiotic resistance / carbapenamase. inhibitor
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
FORMIC ACID / 4-phenyl-2-(sulfanylmethyl)benzoic acid / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.744 Å
AuthorsZollman, D. / McDonough, M. / Brem, J. / Schofield, C.
CitationJournal: J. Med. Chem. / Year: 2018
Title: In Silico Fragment-Based Design Identifies Subfamily B1 Metallo-beta-lactamase Inhibitors.
Authors: Cain, R. / Brem, J. / Zollman, D. / McDonough, M.A. / Johnson, R.M. / Spencer, J. / Makena, A. / Abboud, M.I. / Cahill, S. / Lee, S.Y. / McHugh, P.J. / Schofield, C.J. / Fishwick, C.W.G.
History
DepositionMay 20, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 10, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase VIM-2
B: Beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,49815
Polymers51,3872
Non-polymers1,11113
Water6,900383
1
A: Beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2728
Polymers25,6931
Non-polymers5797
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2267
Polymers25,6931
Non-polymers5336
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.888, 79.542, 67.892
Angle α, β, γ (deg.)90.000, 130.600, 90.000
Int Tables number5
Space group name H-MC121

-
Components

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


Mass: 25693.488 Da / Num. of mol.: 2
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): VECTOR BASED ON PTRIEX VECTOR / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K2N0
#2: Chemical ChemComp-S5Z / 4-phenyl-2-(sulfanylmethyl)benzoic acid


Mass: 244.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H12O2S
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: CH2O2
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.13 Å3/Da / Density % sol: 42.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M MAGNESIUM FORMATE, 20 % W/V PEG3350, 1 MM TCEP, 213 uM protein, 12.5 uM inhibitor.

-
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: May 29, 2013 / Details: Osmic HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.744→50 Å / Num. obs: 40087 / % possible obs: 95 % / Redundancy: 3.1 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.079 / Net I/av σ(I): 12.239 / Net I/σ(I): 14.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.75-1.8120.3891.875185.1
1.81-1.892.20.329189.8
1.89-1.972.60.264193.1
1.97-2.072.90.213194.9
2.07-2.23.40.2196.1
2.2-2.383.60.161197
2.38-2.613.60.117197.7
2.61-2.993.60.085198.1
2.99-3.773.60.063199.1
3.77-503.50.038199.3

-
Processing

Software
NameClassification
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C1D

4c1d


Resolution: 1.744→25.819 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.98
RfactorNum. reflection% reflection
Rfree0.1936 2015 5.03 %
Rwork0.1658 --
obs0.1673 40076 94.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.64 Å2 / Biso mean: 27.6485 Å2 / Biso min: 9.92 Å2
Refinement stepCycle: final / Resolution: 1.744→25.819 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3474 0 55 383 3912
Biso mean--30.37 34.6 -
Num. residues----463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033672
X-RAY DIFFRACTIONf_angle_d0.65029
X-RAY DIFFRACTIONf_chiral_restr0.047568
X-RAY DIFFRACTIONf_plane_restr0.004665
X-RAY DIFFRACTIONf_dihedral_angle_d14.6932145
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 (%)
1.7439-1.78750.30561210.25142269239080
1.7875-1.83580.26451350.21622529266488
1.8358-1.88980.25871480.20662567271591
1.8898-1.95080.23891360.20262656279293
1.9508-2.02050.21231440.17732701284594
2.0205-2.10130.19431490.16592757290695
2.1013-2.19690.18851480.16322727287596
2.1969-2.31270.19321440.16752783292797
2.3127-2.45750.20351410.16162791293297
2.4575-2.6470.18871490.16082806295597
2.647-2.91310.19961510.16872806295798
2.9131-3.33380.20081490.16422846299599
3.3338-4.19740.17241560.14442884304099
4.1974-25.82140.16281440.15932939308399
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)
15.54870.1686-0.68143.98220.36784.06810.0872-0.8202-0.44710.33990.0301-0.08020.27430.0729-0.03270.186-0.002-0.05070.27620.05540.2087-13.9347.782663.2223
22.41680.43480.3892.81990.58521.8636-0.0522-0.0450.0781-0.19420.0715-0.151-0.20550.16190.00510.1347-0.03550.01760.1313-0.00230.1169-17.133818.270753.1683
34.4079-3.6643.24524.3365-3.17642.5566-0.1449-0.5298-0.23190.03590.29330.24210.0589-0.5053-0.14720.18710.0027-0.01850.20030.00890.2361-27.89762.171253.1324
47.62411.1156-2.09973.4058-0.40453.7859-0.16950.8856-0.4114-0.69460.1906-0.16870.1564-0.0140.01540.2805-0.04480.01790.2027-0.06520.1469-23.54864.660239.9933
52.46471.08-0.52512.30950.18752.1764-0.00270.0745-0.3715-0.26350.1213-0.24730.04020.1694-0.0810.16780.01050.00260.1219-0.0230.1951-20.6537-0.599248.0979
63.183-0.23580.21443.11660.02632.32130.0583-0.22970.31420.1336-0.1819-0.5141-0.24170.86870.07840.1624-0.0384-0.03390.38350.03340.2583-28.6638-9.195181.2101
72.3188-0.17851.25833.4357-0.06421.503-0.0203-0.2642-0.0321-0.1434-0.0315-0.30920.24340.39320.05470.11440.06160.0150.2250.02670.1548-35.1379-16.625978.2195
82.7814-0.32050.6462.8036-1.51322.76480.03820.2261-0.3033-0.5491-0.10390.08270.61910.274-0.02060.29990.07170.01650.14980.00010.1661-37.7393-23.124772.7627
92.1573-0.59750.65383.1963-1.36822.59720.16230.062-0.3871-0.4315-0.04350.29060.2938-0.0463-0.16740.2264-0.0105-0.0470.16230.00240.1772-45.2679-21.280974.1164
102.1570.0470.60962.8638-1.27142.46380.1008-0.2103-0.01180.09570.04660.34210.003-0.1386-0.07060.13650.00520.02060.1620.01380.1689-45.92-10.819980.2647
112.39672.75722.6144.81651.99833.47930.02240.59090.0247-0.13180.1221-0.10580.00630.4712-0.14070.17190.0034-0.0210.2430.00860.2136-40.4904-0.173467.5373
124.15240.8491-2.24573.8578-2.68774.2595-0.00470.0210.20260.19280.26280.699-0.6559-0.7839-0.17260.17580.0406-0.01230.18560.03920.2524-53.4269-3.451573.0531
135.7434-0.8351-2.99742.84490.9724.2168-0.0753-0.59490.12740.42740.01580.1232-0.34140.26690.04730.23740.00570.00410.148-0.01630.1559-42.3653-1.122682.7546
143.6706-0.68760.12462.86371.77869.5462-0.10720.08130.0202-0.08560.00670.01090.1766-0.2179-0.01470.1341-0.0148-0.01660.08910.00150.1489-46.83314.819469.0847
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 76 )A32 - 76
2X-RAY DIFFRACTION2chain 'A' and (resid 77 through 199 )A77 - 199
3X-RAY DIFFRACTION3chain 'A' and (resid 200 through 215 )A200 - 215
4X-RAY DIFFRACTION4chain 'A' and (resid 216 through 229 )A216 - 229
5X-RAY DIFFRACTION5chain 'A' and (resid 230 through 262 )A230 - 262
6X-RAY DIFFRACTION6chain 'B' and (resid 32 through 102 )B32 - 102
7X-RAY DIFFRACTION7chain 'B' and (resid 103 through 122 )B103 - 122
8X-RAY DIFFRACTION8chain 'B' and (resid 123 through 146 )B123 - 146
9X-RAY DIFFRACTION9chain 'B' and (resid 147 through 163 )B147 - 163
10X-RAY DIFFRACTION10chain 'B' and (resid 164 through 199 )B164 - 199
11X-RAY DIFFRACTION11chain 'B' and (resid 200 through 215 )B200 - 215
12X-RAY DIFFRACTION12chain 'B' and (resid 216 through 229 )B216 - 229
13X-RAY DIFFRACTION13chain 'B' and (resid 230 through 245 )B230 - 245
14X-RAY DIFFRACTION14chain 'B' and (resid 246 through 263 )B246 - 263

+
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://pdbjlvh1.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