[English] 日本語
Yorodumi
- PDB-5n55: mono-Zinc VIM-5 metallo-beta-lactamase in complex with (1-chloro-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5n55
Titlemono-Zinc VIM-5 metallo-beta-lactamase in complex with (1-chloro-4-hydroxyisoquinoline-3-carbonyl)-L-tryptophan (Compound 2)
ComponentsClass B metallo-beta-lactamase
KeywordsHYDROLASE / metallo-beta-lactamase / inhibitor / complex / antibiotic resistance
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / beta-lactamase activity / periplasmic space / response to antibiotic / 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 ...: / : / : / : / 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-8NN / beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.99 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 13, 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 31, 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_label_seq_id / _struct_conn_type.id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Class B metallo-beta-lactamase
B: Class B metallo-beta-lactamase
C: Class B metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7759
Polymers84,3493
Non-polymers1,4266
Water5,314295
1
A: Class B metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5923
Polymers28,1161
Non-polymers4752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Class B metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5923
Polymers28,1161
Non-polymers4752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Class B metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5923
Polymers28,1161
Non-polymers4752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.219, 155.191, 267.733
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-714-

HOH

21C-659-

HOH

-
Components

#1: Protein Class B metallo-beta-lactamase / Meta-beta-carbapenem / Metallo-beta-lactamase


Mass: 28116.488 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaVIM-5 / Plasmid: opinf vector based / Details (production host): plasmid derived / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): PLYSS / References: UniProt: Q8GKX2
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-8NN / (1-chloro-4-hydroxyisoquinoline-3-carbonyl)-L-tryptophan


Mass: 409.822 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H16ClN3O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.04 Å3/Da / Density % sol: 39.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium Chloride, 0.1 M 2-(N-morpholino)ethanesulfonic acid (MES), 20% (w/v) Polyethylene glycol 6000, pH=6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.99→50.68 Å / Num. all: 620570 / Num. obs: 47393 / % possible obs: 99.9 % / Redundancy: 13.1 % / Biso Wilson estimate: 23.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.028 / Rrim(I) all: 0.102 / Net I/σ(I): 15.3
Reflection shellResolution: 1.99→2.02 Å / Redundancy: 13.6 % / Rmerge(I) obs: 1.197 / Mean I/σ(I) obs: 2.1 / Num. measured obs: 31567 / Num. unique all: 2324 / Num. unique obs: 4703 / CC1/2: 0.565 / Rpim(I) all: 0.335 / Rrim(I) all: 1.244 / % possible all: 99.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.05 Å40.17 Å
Translation6.05 Å40.17 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: 5A87

5a87


Resolution: 1.99→50.683 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.66
RfactorNum. reflection% reflection
Rfree0.2526 2338 4.95 %
Rwork0.1914 --
obs0.1944 47264 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 80.82 Å2 / Biso mean: 31.2187 Å2 / Biso min: 10.58 Å2
Refinement stepCycle: final / Resolution: 1.99→50.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4969 0 90 295 5354
Biso mean--35.35 32.49 -
Num. residues----690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145217
X-RAY DIFFRACTIONf_angle_d1.0947147
X-RAY DIFFRACTIONf_chiral_restr0.061813
X-RAY DIFFRACTIONf_plane_restr0.008933
X-RAY DIFFRACTIONf_dihedral_angle_d11.5642954
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.99-2.03060.38081490.30892602275199
2.0306-2.07480.34231400.28652594273499
2.0748-2.1230.33591340.27742611274599
2.123-2.17610.3291320.26832622275499
2.1761-2.2350.26381250.25132603272899
2.235-2.30070.35431290.24832624275399
2.3007-2.3750.28961350.224626482783100
2.375-2.45990.27881390.220425942733100
2.4599-2.55840.28811510.217326422793100
2.5584-2.67480.30681270.21222608273599
2.6748-2.81580.2391400.195126452785100
2.8158-2.99220.25931280.189126552783100
2.9922-3.22320.2481370.186626402777100
3.2232-3.54750.22691270.158226742801100
3.5475-4.06060.1991390.147626942833100
4.0606-5.11520.18091400.129326892829100
5.1152-50.69920.23771660.17727812947100
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)
10.6078-0.44380.45270.3643-0.19190.8658-0.15380.34210.3708-0.34380.05780.1282-0.28620.16440.38090.3924-0.0423-0.14610.2790.18750.318-19.8881-15.586926.058
20.3328-0.3025-0.03780.2885-0.05850.64910.02130.22710.2109-0.211-0.0222-0.0794-0.25080.11020.13820.4569-0.05990.03990.34990.19080.2049-12.2673-19.522721.6651
34.01492.4261-1.64863.0769-0.1821.49570.08180.2660.175-0.3517-0.17890.0502-0.17130.00540.10480.26170.0068-0.06380.22330.08850.1763-18.4708-24.689230.4014
42.8317-0.2278-0.94942.04070.72140.5435-0.0150.147-0.0814-0.0966-0.0320.10690.1462-0.01120.08160.20790.0096-0.05180.20630.02490.0986-20.2404-32.659834.6296
55.2007-0.0425-1.30062.7313-1.37931.5998-0.1409-0.49190.28880.02680.04230.1119-0.1902-0.1920.08740.20030.0068-0.06160.17980.02240.1271-25.0731-23.703241.6329
62.7142-0.74940.86671.5642-1.21121.4499-0.16030.0440.5474-0.1936-0.01740.4837-0.0345-0.14660.13410.27150.0389-0.11710.23180.00550.3353-30.9338-15.814737.7857
74.5251-1.56870.64862.9469-0.63214.3198-0.1405-0.13790.9084-0.07180.0720.11140.0419-0.22620.03220.34790.174-0.18010.3754-0.13780.4954-40.2696-13.210837.4403
81.24810.0080.24841.66270.76662.6874-0.00060.14160.04120.0548-0.0426-0.49060.06020.31310.00840.15670.0209-0.0210.30560.15260.3156-46.9291-11.6084.9586
90.3616-0.07210.12032.3164-0.54851.11860.0389-0.05820.1260.3139-0.01670.01860.0991-0.2031-0.0610.2317-0.0154-0.03670.30570.1690.2046-59.8362-13.283214.3812
102.2067-0.25390.18652.0778-0.07462.8140.11760.0495-0.08290.284-0.0235-0.2860.36670.0153-0.06670.25990.0092-0.08320.20010.06380.2014-51.3451-27.01712.7783
112.1388-1.17811.29543.0025-0.96083.22180.1727-0.0887-0.21550.3224-0.0502-0.18750.56650.1549-0.29950.4740.0669-0.23760.20330.04430.457-45.7184-33.267918.0808
121.4021-0.22440.83190.2002-0.17021.99630.3238-0.0904-0.45050.3615-0.0274-0.46580.53150.1172-0.20980.41540.0127-0.23380.21750.03540.4148-62.1206-30.14354.9942
132.64511.32631.48973.60671.65382.5251-0.16580.4090.18790.05830.2491-0.6452-0.0490.4604-0.06570.2090.0124-0.08950.26960.05930.3798-58.7324-19.185744.9691
142.43260.56951.43730.70140.53582.1837-0.1612-0.49070.87540.1992-0.1481-0.0887-0.1944-0.24740.27960.31790.0096-0.19470.289-0.05670.4714-66.9534-13.827559.0396
150.0327-0.3199-0.04553.41461.81916.66040.1221-0.3410.20530.4498-0.2021-0.01890.0777-0.018-0.19610.43540.0984-0.13780.6132-0.24330.3161-64.3259-12.223670.987
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 88 )A32 - 88
2X-RAY DIFFRACTION2chain 'A' and (resid 89 through 102 )A89 - 102
3X-RAY DIFFRACTION3chain 'A' and (resid 103 through 122 )A103 - 122
4X-RAY DIFFRACTION4chain 'A' and (resid 123 through 163 )A123 - 163
5X-RAY DIFFRACTION5chain 'A' and (resid 164 through 184 )A164 - 184
6X-RAY DIFFRACTION6chain 'A' and (resid 185 through 245 )A185 - 245
7X-RAY DIFFRACTION7chain 'A' and (resid 246 through 261 )A246 - 261
8X-RAY DIFFRACTION8chain 'B' and (resid 32 through 102 )B32 - 102
9X-RAY DIFFRACTION9chain 'B' and (resid 103 through 184 )B103 - 184
10X-RAY DIFFRACTION10chain 'B' and (resid 185 through 245 )B185 - 245
11X-RAY DIFFRACTION11chain 'B' and (resid 246 through 261 )B246 - 261
12X-RAY DIFFRACTION12chain 'C' and (resid 32 through 102 )C32 - 102
13X-RAY DIFFRACTION13chain 'C' and (resid 103 through 156 )C103 - 156
14X-RAY DIFFRACTION14chain 'C' and (resid 157 through 245 )C157 - 245
15X-RAY DIFFRACTION15chain 'C' and (resid 246 through 261 )C246 - 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