[English] 日本語
Yorodumi
- PDB-5n4t: VIM-2 metallo-beta-lactamase in complex with ((S)-3-mercapto-2-me... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5n4t
TitleVIM-2 metallo-beta-lactamase in complex with ((S)-3-mercapto-2-methylpropanoyl)-L-tryptophan (Compound 4)
ComponentsBeta-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
BENZOIC ACID / FORMIC ACID / Chem-R59 / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.16 Å
AuthorsLi, G.-B. / Brem, J. / McDonough, M.A. / Schofield, C.J.
CitationJournal: Chem. Commun. (Camb.) / Year: 2017
Title: Crystallographic analyses of isoquinoline complexes reveal a new mode of metallo-beta-lactamase inhibition.
Authors: Li, G.B. / Brem, J. / Lesniak, R. / Abboud, M.I. / Lohans, C.T. / Clifton, I.J. / Yang, S.Y. / Jimenez-Castellanos, J.C. / Avison, M.B. / Spencer, J. / McDonough, M.A. / Schofield, C.J.
History
DepositionFeb 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Jan 17, 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_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.ptnr2_symmetry / _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.value / _struct_conn.pdbx_dist_value / _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.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)51,20915
Polymers49,8212
Non-polymers1,38813
Water11,187621
1
A: Beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6278
Polymers24,9111
Non-polymers7177
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5817
Polymers24,9111
Non-polymers6716
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.903, 80.148, 79.085
Angle α, β, γ (deg.)90.000, 139.490, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-627-

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 / Metallo-beta-lactamase VIM-2 / Metallo-beta-lactamase vim-2 / VIM-2 metallo-beta-lactamase / VIM-2 protein


Mass: 24910.648 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): OPINF VECTOR BASED / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): PLYSS / References: UniProt: Q9K2N0

-
Non-polymers , 5 types, 634 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-R59 / (2~{S})-3-(1~{H}-indol-3-yl)-2-[[(2~{S})-2-methyl-3-sulfanyl-propanoyl]amino]propanoic acid


Mass: 306.380 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H18N2O3S
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 621 / 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: 2.19 Å3/Da / Density % sol: 43.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Magnesium Formate, 21%~27% (v/v) Polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.16→56.29 Å / Num. obs: 147820 / % possible obs: 99.96 % / Observed criterion σ(F): 0.117 / Observed criterion σ(I): 1.275 / Redundancy: 10.6 % / Biso Wilson estimate: 10.98 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.03 / Rsym value: 0.063 / Net I/σ(I): 10.3
Reflection shellResolution: 1.16→1.18 Å / Redundancy: 6.51 % / Rmerge(I) obs: 0.073 / Mean I/σ(I) obs: 10.25 / CC1/2: 0.998 / % possible all: 99.96

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.01 Å56.29 Å
Translation5.01 Å56.29 Å

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.6.0phasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4c1d

4c1d


Resolution: 1.16→56.288 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.67
RfactorNum. reflection% reflection
Rfree0.1955 7266 4.97 %
Rwork0.1745 --
obs0.1755 146186 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.84 Å2 / Biso mean: 20.2636 Å2 / Biso min: 5.89 Å2
Refinement stepCycle: final / Resolution: 1.16→56.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3494 0 78 632 4204
Biso mean--25.66 32.69 -
Num. residues----467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133944
X-RAY DIFFRACTIONf_angle_d1.1785427
X-RAY DIFFRACTIONf_chiral_restr0.091606
X-RAY DIFFRACTIONf_plane_restr0.009729
X-RAY DIFFRACTIONf_dihedral_angle_d13.6911391
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.16-1.17320.40222720.38824406467895
1.1732-1.1870.4063030.39124444474796
1.187-1.20150.38242720.37224438471097
1.2015-1.21670.40932310.36224566479797
1.2167-1.23270.37882560.36474581483798
1.2327-1.24960.37712380.35794502474098
1.2496-1.26740.35822530.35154539479298
1.2674-1.28630.30092250.33964627485298
1.2863-1.30640.352220.32844619484198
1.3064-1.32790.32362200.30754644486499
1.3279-1.35080.31122350.29244596483199
1.3508-1.37530.27772510.28254643489499
1.3753-1.40180.28782500.27064603485399
1.4018-1.43040.29512270.25174665489299
1.4304-1.46150.28462110.24724685489699
1.4615-1.49550.24472390.22784634487399
1.4955-1.53290.24352030.21264694489799
1.5329-1.57440.23472530.19774649490299
1.5744-1.62070.2072390.174646734912100
1.6207-1.6730.18912710.16846504921100
1.673-1.73280.17482460.150346454891100
1.7328-1.80220.17082510.144146804931100
1.8022-1.88420.16182220.136647054927100
1.8842-1.98350.16282120.13647134925100
1.9835-2.10780.15232420.127846904932100
2.1078-2.27060.14132250.127647074932100
2.2706-2.49910.14152270.121847134940100
2.4991-2.86070.1352460.120747384984100
2.8607-3.60410.143040.122646484952100
3.6041-56.3540.15512200.134448235043100
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)
13.4614-1.0025-2.37941.68340.79964.0855-0.0361-0.04440.11040.10220.00240.0118-0.0138-0.06570.03950.07990.0121-0.01510.0552-0.00650.100466.733621.454651.7452
22.7898-1.0331-1.362.29392.16225.25150.03850.0560.3349-0.00460.0156-0.1037-0.27050.0064-0.06880.09320.0018-0.01280.03950.0140.154970.008128.376547.9702
32.3897-1.5019-0.2262.0937-0.42890.7894-0.01430.01460.3390.038-0.0133-0.4008-0.07990.1169-0.04090.0924-0.0044-0.00530.1087-0.00440.205477.836224.922347.6469
41.3666-0.3515-0.29581.41320.03181.2189-0.0577-0.19420.14240.20140.0524-0.23420.01340.13590.03410.09280.0177-0.03480.0933-0.01220.102877.446315.138854.2404
54.46464.8063-4.62045.2992-4.72536.3606-0.20290.4118-0.0773-0.3510.170.0170.3226-0.3299-0.00270.12170.0250.01750.113-0.01220.118871.46884.418242.2281
65.21490.14761.90272.68750.4517.224-0.0389-0.0438-0.03870.0850.0039-0.36750.24610.46190.00460.08350.03590.0010.07950.00970.143684.53857.442247.7967
76.35110.68773.24691.1150.45924.6782-0.0122-0.4014-0.25440.28120.0415-0.0770.197-0.1349-0.03390.13860.02340.0040.08640.01380.079472.60815.323956.7002
83.7981-0.167-1.97912.40742.24669.6070.02420.1503-0.2003-0.06320.0603-0.18960.05190.0455-0.09290.11580.01650.02440.07260.00280.158478.1589-0.282943.3621
95.4123-1.5521.48137.4344-1.86792.95590.1323-0.89450.8590.9483-0.0184-0.6319-0.8557-0.5836-0.00390.40470.01490.10770.3194-0.08430.253444.83451.314541.9397
103.1820.4840.18973.63320.1923.42490.143-0.27550.16740.2129-0.07490.1003-0.2156-0.2279-0.04080.1034-0.0180.02720.13980.0080.066543.8974-6.341133.8675
115.5563-0.5471-0.04193.3611-0.34592.65220.0487-0.44530.00250.5181-0.00030.3341-0.1708-0.1426-0.05650.2239-0.08260.01920.25810.02680.090440.9976-11.633341.6799
121.30650.3026-0.9772.0825-0.45851.94130.1183-0.1903-0.07310.1458-0.0844-0.00230.0961-0.1183-0.0070.1004-0.0286-0.01520.10820.02480.064248.1858-13.565431.3343
133.37741.2036-1.02632.8778-1.12584.04260.0652-0.2313-0.42320.1621-0.1066-0.46250.23470.15510.04910.1481-0.0107-0.03410.07780.03030.165253.5738-20.206429.6661
141.45250.5941-0.36321.9008-0.11531.064-0.02370.0782-0.0739-0.14850.0105-0.07540.0913-0.09460.00730.0846-0.00150.00150.07940.00070.055849.6741-11.295120.036
157.3933-6.1962-1.84659.2453.00251.0282-0.1707-0.40530.12450.3230.1958-0.3654-0.05090.2465-0.01410.1326-0.01190.00980.13520.03410.093558.40073.327227.3899
163.68332.15862.90073.05010.90225.1122-0.0880.43250.2042-0.36360.0831-0.0547-0.17790.09290.04470.13930.00310.03430.09270.01870.081555.3703-0.493813.7037
173.60340.31382.95841.64370.46917.3058-0.0376-0.0390.2891-0.0701-0.04240.2498-0.3184-0.30440.08520.08320.01990.01070.08790.01540.11644.44542.078323.6585
187.54752.27690.36634.61440.04154.0675-0.1120.0062-0.1079-0.11020.0889-0.1832-0.22510.20990.02460.1125-0.00520.02250.0554-0.00160.065158.39347.894420.0946
196.0516-0.63322.28885.7753-2.35437.1755-0.055-0.2477-0.69940.00140.2080.48230.4857-0.7304-0.11470.1746-0.02880.07870.22990.0120.254157.95598.159656.932
202.8324-0.2504-0.16553.42710.15342.4895-0.0412-0.0377-0.03680.09850.00620.07950.0762-0.22320.03760.07110.01010.00680.1024-0.01330.071163.366315.842154.8044
214.8388-1.0373-1.99585.6086-1.54855.1624-0.1002-0.1224-0.07830.34930.10050.35160.0307-0.3921-0.00990.09030.0150.02440.1576-0.03530.143554.944720.584757.502
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 103 through 122 )B103 - 122
2X-RAY DIFFRACTION2chain 'B' and (resid 123 through 145 )B123 - 145
3X-RAY DIFFRACTION3chain 'B' and (resid 146 through 163 )B146 - 163
4X-RAY DIFFRACTION4chain 'B' and (resid 164 through 199 )B164 - 199
5X-RAY DIFFRACTION5chain 'B' and (resid 200 through 215 )B200 - 215
6X-RAY DIFFRACTION6chain 'B' and (resid 216 through 229 )B216 - 229
7X-RAY DIFFRACTION7chain 'B' and (resid 230 through 245 )B230 - 245
8X-RAY DIFFRACTION8chain 'B' and (resid 246 through 263 )B246 - 263
9X-RAY DIFFRACTION9chain 'A' and (resid 30 through 44 )A30 - 44
10X-RAY DIFFRACTION10chain 'A' and (resid 45 through 88 )A45 - 88
11X-RAY DIFFRACTION11chain 'A' and (resid 89 through 102 )A89 - 102
12X-RAY DIFFRACTION12chain 'A' and (resid 103 through 122 )A103 - 122
13X-RAY DIFFRACTION13chain 'A' and (resid 123 through 146 )A123 - 146
14X-RAY DIFFRACTION14chain 'A' and (resid 147 through 199 )A147 - 199
15X-RAY DIFFRACTION15chain 'A' and (resid 200 through 215 )A200 - 215
16X-RAY DIFFRACTION16chain 'A' and (resid 216 through 229 )A216 - 229
17X-RAY DIFFRACTION17chain 'A' and (resid 230 through 245 )A230 - 245
18X-RAY DIFFRACTION18chain 'A' and (resid 246 through 263 )A246 - 263
19X-RAY DIFFRACTION19chain 'B' and (resid 31 through 52 )B31 - 52
20X-RAY DIFFRACTION20chain 'B' and (resid 53 through 88 )B53 - 88
21X-RAY DIFFRACTION21chain 'B' and (resid 89 through 102 )B89 - 102

+
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