[English] 日本語
Yorodumi
- PDB-7pfn: Acetyllysine73-incorporated OXA-48 complexed with imipenem in bot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pfn
TitleAcetyllysine73-incorporated OXA-48 complexed with imipenem in both active and inactive acyl-enzyme intermediates
ComponentsBeta-lactamase
KeywordsHYDROLASE / OXA / Imipenem
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / plasma membrane
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
1-BUTANOL / Imipenem / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZhou, Q. / He, Y. / Jin, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31400663 China
CitationJournal: Acs Cent.Sci. / Year: 2023
Title: An Ion-Pair Induced Intermediate Complex Captured in Class D Carbapenemase Reveals Chloride Ion as a Janus Effector Modulating Activity
Authors: Zhou, Q. / Catalan, P. / Bell, H. / Baumann, P. / Cooke, R. / Evans, R. / Yang, J. / Zhang, Z. / Zappala, D. / Zhang, Y. / Blackburn, G.M. / He, Y. / Jin, Y.
History
DepositionAug 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Mar 6, 2024Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 2.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 2.4Aug 6, 2025Group: Structure summary / Category: struct / Item: _struct.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Beta-lactamase
BBB: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,57310
Polymers60,5042
Non-polymers1,0688
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint19 kcal/mol
Surface area20360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.799, 104.995, 124.745
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ILE / End label comp-ID: ILE / Auth seq-ID: 24 - 264 / Label seq-ID: 19 - 259

Dom-IDAuth asym-IDLabel asym-ID
1AAAA
2BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

#1: Protein Beta-lactamase


Mass: 30252.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaOXA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A482LRD5, beta-lactamase
#2: Chemical ChemComp-ID1 / Imipenem


Mass: 301.362 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-1BO / 1-BUTANOL / BUTAN-1-OL


Mass: 74.122 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 11.6% PEG8000, 8% 1-BuOH, mixed with the 10 mg/mL protein stock at 1:1 ratio.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976292 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976292 Å / Relative weight: 1
ReflectionResolution: 1.8→62.37 Å / Num. obs: 55552 / % possible obs: 100 % / Redundancy: 11.4 % / CC1/2: 0.997 / Net I/σ(I): 9.9
Reflection shellResolution: 1.8→1.84 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3253 / CC1/2: 0.588

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S2P

4s2p


Resolution: 1.8→62.37 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.117 / SU ML: 0.09 / Cross valid method: FREE R-VALUE / ESU R: 0.116 / ESU R Free: 0.113
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2137 2745 4.947 %
Rwork0.1778 52742 -
all0.18 --
obs-55487 99.993 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.438 Å2
Baniso -1Baniso -2Baniso -3
1-1.471 Å20 Å20 Å2
2--0.782 Å2-0 Å2
3----2.252 Å2
Refinement stepCycle: LAST / Resolution: 1.8→62.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3975 0 70 365 4410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134169
X-RAY DIFFRACTIONr_bond_other_d0.0010.0183929
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.6425636
X-RAY DIFFRACTIONr_angle_other_deg1.3951.5859016
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3015493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.52922.459244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43415722
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2641525
X-RAY DIFFRACTIONr_chiral_restr0.080.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024739
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021031
X-RAY DIFFRACTIONr_nbd_refined0.2130.2838
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1710.23741
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21992
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21928
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2286
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1220.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1190.213
X-RAY DIFFRACTIONr_nbd_other0.1640.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0960.212
X-RAY DIFFRACTIONr_mcbond_it2.0222.4261948
X-RAY DIFFRACTIONr_mcbond_other2.0182.4251947
X-RAY DIFFRACTIONr_mcangle_it2.873.6282434
X-RAY DIFFRACTIONr_mcangle_other2.873.6292435
X-RAY DIFFRACTIONr_scbond_it3.0692.8012221
X-RAY DIFFRACTIONr_scbond_other3.0632.82218
X-RAY DIFFRACTIONr_scangle_it4.7284.063197
X-RAY DIFFRACTIONr_scangle_other4.7174.0573192
X-RAY DIFFRACTIONr_lrange_it5.7528.7224884
X-RAY DIFFRACTIONr_lrange_other5.69328.4654813
X-RAY DIFFRACTIONr_ncsr_local_group_10.1060.058070
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.106270.05008
12BBBX-RAY DIFFRACTIONLocal ncs0.106270.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.3281940.2983839X-RAY DIFFRACTION100
1.847-1.8970.311820.2823782X-RAY DIFFRACTION99.9748
1.897-1.9520.2511830.2533659X-RAY DIFFRACTION100
1.952-2.0120.2831790.2333522X-RAY DIFFRACTION100
2.012-2.0780.2411860.2113431X-RAY DIFFRACTION100
2.078-2.1510.2451910.1963334X-RAY DIFFRACTION100
2.151-2.2330.211570.1743237X-RAY DIFFRACTION100
2.233-2.3240.2321740.1793089X-RAY DIFFRACTION100
2.324-2.4270.2021640.162940X-RAY DIFFRACTION100
2.427-2.5450.1761510.1572874X-RAY DIFFRACTION100
2.545-2.6830.2031510.162696X-RAY DIFFRACTION100
2.683-2.8460.1981230.1622604X-RAY DIFFRACTION100
2.846-3.0420.2131160.1622437X-RAY DIFFRACTION100
3.042-3.2860.2141180.1812273X-RAY DIFFRACTION99.9164
3.286-3.5990.2171190.1752094X-RAY DIFFRACTION100
3.599-4.0230.1721090.1481913X-RAY DIFFRACTION100
4.023-4.6450.185870.1381697X-RAY DIFFRACTION100
4.645-5.6870.166630.1491483X-RAY DIFFRACTION100
5.687-8.0340.232620.1681147X-RAY DIFFRACTION100

+
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