[English] 日本語
Yorodumi
- PDB-6rpn: Structure of metallo beta lactamase VIM-2 with cyclic boronate APC308. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rpn
TitleStructure of metallo beta lactamase VIM-2 with cyclic boronate APC308.
ComponentsBeta-lactamase VIM-2
KeywordsANTIMICROBIAL PROTEIN / beta lactamases / antimicrobial resistance / cyclic boronate
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding
Similarity search - Function
: / : / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Chem-KDZ / Chem-KL8 / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.409 Å
AuthorsParkova, A. / Lucic, A. / Brem, J. / McDonough, M.A. / Langley, G.W. / Schofield, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
CitationJournal: Acs Infect Dis. / Year: 2020
Title: Broad Spectrum beta-Lactamase Inhibition by a Thioether Substituted Bicyclic Boronate.
Authors: Parkova, A. / Lucic, A. / Krajnc, A. / Brem, J. / Calvopina, K. / Langley, G.W. / McDonough, M.A. / Trapencieris, P. / Schofield, C.J.
History
DepositionMay 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 2.0Apr 15, 2020Group: Non-polymer description / Refinement description / Category: chem_comp / refine / Item: _chem_comp.formula / _refine.pdbx_diffrn_id
Revision 2.1Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.2Jan 24, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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)53,38719
Polymers51,3872
Non-polymers2,00017
Water12,520695
1
A: Beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6238
Polymers25,6931
Non-polymers9297
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,76411
Polymers25,6931
Non-polymers1,07010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.081, 79.155, 67.746
Angle α, β, γ (deg.)90.000, 130.030, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-460-

HOH

21A-742-

HOH

31B-763-

HOH

41B-896-

HOH

-
Components

-
Protein , 1 types, 2 molecules AB

#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: pOPINF / Production host: Escherichia coli (E. coli) / Variant (production host): Lemo21 / References: UniProt: Q9K2N0

-
Non-polymers , 7 types, 712 molecules

#2: Chemical ChemComp-KDZ / (3~{R})-2,2-bis(oxidanyl)-3-(phenylmethylsulfanyl)-3,4-dihydro-1,2-benzoxaborinin-2-ium-8-carboxylic acid


Mass: 331.171 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C16H16BO5S
#3: Chemical ChemComp-KL8 / (3~{S})-2,2-bis(oxidanyl)-3-(phenylmethylsulfanyl)-3,4-dihydro-1,2-benzoxaborinin-2-ium-8-carboxylic acid


Mass: 331.171 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C16H16BO5S
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 695 / 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: 2.07 Å3/Da / Density % sol: 40.52 % / Description: Rod shaped crystal about 100 microns big.
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.25
Details: 0.2M Magnesium Chloride, 25% PEG 8000, 0.1M Tris Buffer

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 8, 2019 / Details: OSMIC VARIMAX HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.41→50 Å / Num. obs: 75121 / % possible obs: 95.5 % / Redundancy: 2 % / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.063 / Rrim(I) all: 0.106 / Χ2: 1.097 / Net I/σ(I): 14.4 / Num. measured all: 147264
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.41-1.461.40.36566820.7250.3650.5171.15285.1
1.46-1.521.50.28768850.7980.2870.4061.1588.1
1.52-1.591.50.22971460.8670.2290.3241.16391.2
1.59-1.671.60.18773870.9010.1870.2641.10394.4
1.67-1.781.60.14676730.9350.1460.2061.13797.4
1.78-1.911.70.10877550.9650.1080.1521.04699.1
1.91-2.111.80.09178650.9710.0840.1251.38999.9
2.11-2.412.20.10578630.9690.0850.1361.007100
2.41-3.042.50.09578760.9720.0720.1191.028100
3.04-503.50.06979890.990.0440.0821.05399.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.7 Å29.19 Å
Translation5.7 Å29.19 Å

-
Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-20002.3.10data reduction
HKL-20002.3.10data scaling
PHASER2.7.16phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BZ3

4bz3


Resolution: 1.409→31.336 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1556 1843 2.45 %
Rwork0.1288 73271 -
obs0.1294 75114 95.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.95 Å2 / Biso mean: 15.495 Å2 / Biso min: 3.26 Å2
Refinement stepCycle: final / Resolution: 1.409→31.336 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3487 0 110 718 4315
Biso mean--21.82 28.36 -
Num. residues----466
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4093-1.44740.27741170.23114944506184
1.4474-1.490.23551380.2075126526487
1.49-1.53810.24081250.18495266539190
1.5381-1.59310.18251370.16945361549892
1.5931-1.65690.19691500.15325558570894
1.6569-1.73230.15761380.13885717585597
1.7323-1.82360.17311470.1295804595198
1.8236-1.93780.16431500.12355866601699
1.9378-2.08740.15061470.111558656012100
2.0874-2.29740.13771460.112259166062100
2.2974-2.62970.14811490.109558976046100
2.6297-3.31260.1251490.111859356084100
3.3126-31.34360.13441500.122160166166100
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)
14.3871-0.2706-3.68392.17690.49034.2020.1271-0.30570.51250.0467-0.01150.0469-0.35610.2504-0.18650.1236-0.0058-0.03140.1386-0.06010.1629-26.9112-5.152483.9696
22.44330.6336-0.42412.8738-0.64392.2767-0.0623-0.07380.0930.00580.0759-0.01170.04650.0719-0.01040.04160.017-0.01180.0497-0.00910.0582-31.1817-12.984980.2241
31.9906-1.14761.00434.8361.03252.3942-0.1051-0.13850.13270.16450.0498-0.2302-0.09350.32950.01540.06160.0026-0.01540.1028-0.01020.0987-22.9482-16.93783.771
42.4402-0.65922.17111.3681-0.41884.5167-0.0547-0.0618-0.01090.04530.0338-0.02320.0091-0.00680.03250.06150.01130.01730.0416-0.00660.0648-34.1858-19.320978.7419
54.7189-0.42731.19271.46580.64372.8255-0.05410.1338-0.1341-0.04650.0189-0.03280.09470.03910.01430.0874-0.00870.02510.02350.00170.0744-36.5748-25.958573.0572
62.5994-2.6201-0.15972.9370.60871.2339-0.01520.0407-0.3131-0.02580.01810.20610.0622-0.0178-0.00350.0699-0.016-0.00030.0611-0.00750.0611-44.7247-24.055474.4383
70.8093-0.1590.27721.4812-0.30551.45880.0016-0.01230.03380.0004-0.00330.0794-0.0423-0.0724-0.00060.04960.00380.01150.0548-0.00580.0608-45.7306-9.871275.9409
87.24841.381-3.97930.3816-1.12933.48820.0485-0.26140.19420.0863-0.03060.042-0.08560.0747-0.03590.09220.00920.00910.0656-0.01550.0796-41.6428-4.1183.0994
93.50780.3271.95563.7933-1.8982.80120.00480.24330.1731-0.1598-0.00850.0401-0.1195-0.10760.01460.07120.0187-0.00170.06980.01190.1006-46.61411.338869.2592
104.53752.1296-1.64726.8449-3.21216.67770.0703-0.3242-0.41360.1043-0.1201-0.06240.28220.22290.03070.0890.0272-0.05510.10930.02440.121-10.32811.400865.3354
117.00511.3205-3.36822.1307-0.88363.70950.0235-0.12-0.05320.06590.0530.11170.117-0.1034-0.01440.0772-0.0072-0.01750.05950.02280.0548-17.81065.625762.6319
121.09550.07980.46860.7260.10831.4746-0.00760.01580.0301-0.0022-0.0086-0.0614-0.06580.06640.01850.0627-0.00370.01090.04930.0020.0591-16.873514.485353.2017
132.5003-1.07221.18873.0032-0.36171.23520.1066-0.0072-0.19680.09220.00070.06410.1651-0.1611-0.08970.0989-0.022-0.02220.0632-0.01910.0751-25.346-0.60247.7236
141.520.8289-0.2891.75290.17682.29770.04080.0683-0.0636-0.00350.0126-0.04890.21960.0157-0.04360.12420.0236-0.01660.0428-0.00630.079-20.6028-4.188748.7201
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 52 )A31 - 52
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 88 )A53 - 88
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 102 )A89 - 102
4X-RAY DIFFRACTION4chain 'A' and (resid 103 through 122 )A103 - 122
5X-RAY DIFFRACTION5chain 'A' and (resid 123 through 146 )A123 - 146
6X-RAY DIFFRACTION6chain 'A' and (resid 147 through 163 )A147 - 163
7X-RAY DIFFRACTION7chain 'A' and (resid 164 through 229 )A164 - 229
8X-RAY DIFFRACTION8chain 'A' and (resid 230 through 245 )A230 - 245
9X-RAY DIFFRACTION9chain 'A' and (resid 246 through 263 )A246 - 263
10X-RAY DIFFRACTION10chain 'B' and (resid 31 through 52 )B31 - 52
11X-RAY DIFFRACTION11chain 'B' and (resid 53 through 76 )B53 - 76
12X-RAY DIFFRACTION12chain 'B' and (resid 77 through 199 )B77 - 199
13X-RAY DIFFRACTION13chain 'B' and (resid 200 through 229 )B200 - 229
14X-RAY DIFFRACTION14chain 'B' and (resid 230 through 263 )B230 - 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://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