[English] 日本語
Yorodumi
- PDB-9mtw: Crystal structure of ADC-1-ertapenem complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9mtw
TitleCrystal structure of ADC-1-ertapenem complex
ComponentsBeta-lactamase
KeywordsHYDROLASE/INHIBITOR / ANTIBIOTIC / beta-lactamase / class C / ertapenem / acyl-enzyme complex / HYDROLASE / HYDROLASE-INHIBITOR / ANTIBIOTIC complex
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Chem-1RG / : / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsSmith, C.A. / Stewart, N.K. / Vakulenko, S.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI155723 United States
CitationJournal: Mbio / Year: 2025
Title: Evolution of carbapenemase activity in the class C beta-lactamase ADC-1.
Authors: Stewart, N.K. / Toth, M. / Bhattacharya, M. / Smith, C.A. / Vakulenko, S.B.
History
DepositionJan 12, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 1.1May 14, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 18, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)82,2686
Polymers81,1892
Non-polymers1,0794
Water7,116395
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1343
Polymers40,5941
Non-polymers5402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1343
Polymers40,5941
Non-polymers5402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.994, 183.065, 50.451
Angle α, β, γ (deg.)90.00, 98.48, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Beta-lactamase


Mass: 40594.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ADC-1 beta-lactamase / Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: ampC / Production host: Escherichia coli (E. coli) / References: UniProt: Q9L4R5, beta-lactamase
#2: Chemical ChemComp-1RG / (4R,5S)-3-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid / ERTAPENEM, bound form PRE-ISOMERIZED


Mass: 477.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H27N3O7S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-A1B93 / (2S,3R,4R)-4-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid / ertapenem, bound form, post-isomerized, delta-1(R) isomer


Mass: 477.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H27N3O7S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M lithium chloride, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.6→38.63 Å / Num. obs: 99666 / % possible obs: 98.6 % / Redundancy: 4 % / CC1/2: 0.997 / Rpim(I) all: 0.039 / Rrim(I) all: 0.08 / Net I/σ(I): 9.8
Reflection shellResolution: 1.6→1.63 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4852 / CC1/2: 0.491 / Rpim(I) all: 0.577

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.6→38.63 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2069 4946 4.97 %
Rwork0.1825 --
obs0.1837 99491 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→38.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5573 0 74 395 6042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065835
X-RAY DIFFRACTIONf_angle_d0.9827914
X-RAY DIFFRACTIONf_dihedral_angle_d16.7612235
X-RAY DIFFRACTIONf_chiral_restr0.062868
X-RAY DIFFRACTIONf_plane_restr0.0071020
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.28151520.27453024X-RAY DIFFRACTION94
1.62-1.640.27561620.24563156X-RAY DIFFRACTION99
1.64-1.660.23161600.23283214X-RAY DIFFRACTION99
1.66-1.680.23291610.22663136X-RAY DIFFRACTION99
1.68-1.70.24371730.22943155X-RAY DIFFRACTION99
1.7-1.720.23341720.22263156X-RAY DIFFRACTION98
1.72-1.750.2781510.22923124X-RAY DIFFRACTION98
1.75-1.770.28091720.24483113X-RAY DIFFRACTION97
1.77-1.80.27551910.25163097X-RAY DIFFRACTION97
1.8-1.830.24641880.23242907X-RAY DIFFRACTION94
1.83-1.860.24841730.21743241X-RAY DIFFRACTION100
1.86-1.90.2951800.23493096X-RAY DIFFRACTION99
1.9-1.930.24051600.19923208X-RAY DIFFRACTION99
1.93-1.970.22681690.19363155X-RAY DIFFRACTION99
1.97-2.020.21781460.18613217X-RAY DIFFRACTION99
2.02-2.060.21381690.19383153X-RAY DIFFRACTION99
2.06-2.110.22571390.19553153X-RAY DIFFRACTION98
2.11-2.170.2561530.19723097X-RAY DIFFRACTION97
2.17-2.240.20851670.1933097X-RAY DIFFRACTION97
2.24-2.310.22661440.19373224X-RAY DIFFRACTION99
2.31-2.390.21581730.18983196X-RAY DIFFRACTION99
2.39-2.490.19871660.18143149X-RAY DIFFRACTION100
2.49-2.60.21191470.18473198X-RAY DIFFRACTION99
2.6-2.740.23011710.19313182X-RAY DIFFRACTION99
2.74-2.910.2431730.19053118X-RAY DIFFRACTION98
2.91-3.130.21941870.18823188X-RAY DIFFRACTION100
3.13-3.450.20341640.18313197X-RAY DIFFRACTION99
3.45-3.940.17351700.16663191X-RAY DIFFRACTION99
3.95-4.970.141390.13393171X-RAY DIFFRACTION98
4.97-38.630.15991740.14453232X-RAY DIFFRACTION99
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)
10.8978-0.61150.44221.0757-0.00090.6808-0.0959-0.14380.18260.31320.00780.1786-0.3585-0.099-0.00650.260.03160.03290.19760.01390.222313.278-8.423511.6112
21.2963-0.1755-0.06410.7869-0.02380.9174-0.01070.06880.005-0.11410.03470.0389-0.0313-0.05170.00070.1289-0.001-0.01660.16210.01940.113223.5278-28.3548-8.1662
31.0339-0.14010.22140.9766-0.06361.20250.008-0.06170.02810.0749-0.0056-0.0188-0.07290.0016-0.00050.1339-0.00750.00640.18010.02310.128521.3284-24.97038.9669
40.5352-0.1695-0.1950.2268-0.13060.2870.25380.4005-0.5572-0.4904-0.1612-0.38530.45950.01370.0030.36380.0299-0.00980.2823-0.0260.41356.43799.677-5.1117
50.3479-0.1668-0.39940.94040.23990.5827-0.04860.017-0.29690.00890.01620.17710.1208-0.00610.00020.2330.0009-0.04870.18990.01260.35252.63817.97445.7822
60.0750.2008-0.09461.6739-0.1790.15030.1298-0.32280.01371.4387-0.20640.1925-0.0246-0.0119-0.07020.643-0.08710.12040.244-0.00880.2288-5.12536.364421.5875
70.6807-0.1562-0.34781.15850.38530.2852-0.1472-0.1878-0.24340.929-0.00410.31540.08950.0941-0.01090.4585-0.0220.0570.23250.04720.3108-5.333915.480217.4124
80.4976-0.9421-0.21462.10410.34420.51560.06680.03150.0081-0.1701-0.11530.2495-0.1012-0.1017-0.00360.18980.0108-0.00670.2074-0.00730.265-6.89432.20712.7631
90.8208-0.0466-0.6781.95140.31260.7570.08290.105-0.0464-0.2517-0.0853-0.11770.0065-0.017300.17440.0067-0.01340.18180.00950.23621.965320.80460.4391
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 64 )
2X-RAY DIFFRACTION2chain 'A' and (resid 65 through 210 )
3X-RAY DIFFRACTION3chain 'A' and (resid 211 through 361 )
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 28 )
5X-RAY DIFFRACTION5chain 'B' and (resid 29 through 64 )
6X-RAY DIFFRACTION6chain 'B' and (resid 65 through 168 )
7X-RAY DIFFRACTION7chain 'B' and (resid 169 through 241 )
8X-RAY DIFFRACTION8chain 'B' and (resid 242 through 309 )
9X-RAY DIFFRACTION9chain 'B' and (resid 310 through 360 )

+
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