[English] 日本語
Yorodumi
- PDB-7zo2: L1 metallo-beta-lactamase complex with hydrolysed doripenem -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zo2
TitleL1 metallo-beta-lactamase complex with hydrolysed doripenem
ComponentsMetallo-beta-lactamase L1
KeywordsANTIMICROBIAL PROTEIN / antibiotic / ligand / zinc
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / : / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Chem-DQM / Metallo-beta-lactamase L1 type 3
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsHinchliffe, P. / Spencer, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI100560 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Interactions of hydrolyzed beta-lactams with the L1 metallo-beta-lactamase: Crystallography supports stereoselective binding of cephem/carbapenem products.
Authors: Hinchliffe, P. / Calvopina, K. / Rabe, P. / Mojica, M.F. / Schofield, C.J. / Dmitrienko, G.I. / Bonomo, R.A. / Vila, A.J. / Spencer, J.
History
DepositionApr 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6927
Polymers28,8951
Non-polymers7976
Water4,071226
1
A: Metallo-beta-lactamase L1
hetero molecules

A: Metallo-beta-lactamase L1
hetero molecules

A: Metallo-beta-lactamase L1
hetero molecules

A: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,76628
Polymers115,5784
Non-polymers3,18824
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area11330 Å2
ΔGint-177 kcal/mol
Surface area38930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.435, 105.435, 98.181
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

21A-412-

HOH

31A-589-

HOH

41A-625-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Metallo-beta-lactamase L1 / Class B3 metallo-beta-lactamase L1 / Beta-lactamase type II / Penicillinase


Mass: 28894.619 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria)
Production host: Escherichia coli (E. coli) / Strain (production host): SoluBL21 / References: UniProt: P52700, beta-lactamase

-
Non-polymers , 5 types, 232 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DQM / (2~{S},3~{R},4~{S})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-3-methyl-4-[(3~{S},5~{S})-5-[(sulfamoylamino)methyl]pyrrolidin-3-yl]sulfanyl-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid / Hydrolyzed Doripenem


Mass: 438.520 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H26N4O7S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 100 mM Hepes pH 7.75, 2.0 M ammonium sulphate, 1.5% PEG400. 1 ul protein (15 mg/ml) mixed with 1 ul reservoir.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 1.49→66.86 Å / Num. obs: 52983 / % possible obs: 100 % / Redundancy: 38.4 % / CC1/2: 1 / Rpim(I) all: 0.015 / Net I/σ(I): 22.3
Reflection shellResolution: 1.49→1.52 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 2586 / CC1/2: 0.563 / Rpim(I) all: 1.425

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7O0O

7o0o


Resolution: 1.49→66.86 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2046 2599 4.92 %
Rwork0.1764 50178 -
obs0.1777 52777 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 186.85 Å2 / Biso mean: 42.9497 Å2 / Biso min: 17.06 Å2
Refinement stepCycle: final / Resolution: 1.49→66.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1992 0 65 226 2283
Biso mean--86.68 43.08 -
Num. residues----265
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.49-1.520.4521530.44642570272399
1.52-1.550.39271130.40262604271799
1.55-1.580.39161180.37052597271599
1.58-1.610.28251340.31325802714100
1.61-1.650.29411550.28062582273799
1.65-1.690.30951300.258526122742100
1.69-1.740.27431380.236125872725100
1.74-1.790.26361270.221226452772100
1.79-1.850.24281450.211325852730100
1.85-1.910.24211470.211925902737100
1.91-1.990.22211390.185526372776100
1.99-2.080.20371340.183326252759100
2.08-2.190.20371340.178426412775100
2.19-2.330.20071560.17826292785100
2.33-2.50.19471420.174926582800100
2.5-2.760.20991320.167626712803100
2.76-3.160.21111340.171427082842100
3.16-3.980.18751410.147627382879100
3.98-66.860.16121270.153729193046100
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)
10.19-0.3711-0.18011.15680.87160.5607-0.0577-0.0870.10510.35520.14660.00650.1018-0.0968-0.08420.41890.0633-0.01980.36670.02110.285429.690112.16188.7993
23.80320.79430.3574.51281.76413.2916-0.0577-0.00960.4517-0.10380.0862-0.0399-0.1513-0.13420.01760.33170.0785-0.00270.2395-0.00030.276937.586420.47547.6892
32.8518-0.20131.08392.3244-1.20471.9753-0.1195-0.04280.1397-0.02810.0551-0.3018-0.14650.02880.1050.35370.05280.00860.2435-0.04230.206243.001215.41067.1877
41.6346-0.1416-0.16860.7913-0.4840.8769-0.1071-0.09640.1207-0.00310.0997-0.01260.0706-0.00210.03270.36110.0559-0.00570.2799-0.02440.205746.87567.95349.5046
51.56310.50850.07254.2285-0.26951.0927-0.1341-0.36350.13550.23870.1060.0335-0.1195-0.07430.04890.36110.10650.01090.3577-0.03110.190341.86498.643421.9156
65.50623.66851.78693.85924.51238.3912-0.096-0.6185-0.03220.2239-0.0182-0.07790.18530.0390.05820.4520.17610.02590.47830.01010.197343.27022.56229.4911
73.28690.1472.61721.2192-0.09334.9409-0.2035-0.3790.26160.37670.21310.0039-0.1632-0.3564-0.01490.43950.14390.0290.381-0.06950.276732.668919.279223.7247
83.71552.8325-1.02272.4327-1.150.97060.0087-0.4102-0.05270.3804-0.11290.1348-0.1048-0.30470.1070.45620.1030.07870.4733-0.00030.253433.2040.784330.8648
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 32 )A3 - 32
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 70 )A33 - 70
3X-RAY DIFFRACTION3chain 'A' and (resid 71 through 92 )A71 - 92
4X-RAY DIFFRACTION4chain 'A' and (resid 93 through 156 )A93 - 156
5X-RAY DIFFRACTION5chain 'A' and (resid 157 through 201 )A157 - 201
6X-RAY DIFFRACTION6chain 'A' and (resid 202 through 215 )A202 - 215
7X-RAY DIFFRACTION7chain 'A' and (resid 216 through 245 )A216 - 245
8X-RAY DIFFRACTION8chain 'A' and (resid 246 through 267 )A246 - 267

+
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