[English] 日本語
Yorodumi
- PDB-7peh: Apo OXA-48 with fully carbamylated Lys73 at pH 7.5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7peh
TitleApo OXA-48 with fully carbamylated Lys73 at pH 7.5
ComponentsBeta-lactamase
KeywordsHYDROLASE / OXA / apo
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 / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 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 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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 1.2Mar 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 1.3Aug 6, 2025Group: Structure summary
Category: pdbx_entry_details / pdbx_modification_feature / struct
Item: _pdbx_entry_details.has_protein_modification / _struct.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)121,53511
Polymers121,0174
Non-polymers5197
Water8,197455
1
AAA: Beta-lactamase
DDD: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8056
Polymers60,5082
Non-polymers2964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Beta-lactamase
CCC: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7315
Polymers60,5082
Non-polymers2223
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.003, 106.976, 124.611
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB
32AAA
42CCC
53AAA
63DDD
74BBB
84CCC
95BBB
105DDD
116CCC
126DDD

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 24 - 265 / Label seq-ID: 19 - 260

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AAAA
21BBBB
32AAAA
42CCCC
53AAAA
63DDDD
74BBBB
84CCCC
95BBBB
105DDDD
116CCCC
126DDDD

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

-
Components

#1: Protein
Beta-lactamase


Mass: 30254.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: bla OXA-48, bla_2, blaOXA-48, G5637_27540, KPE71T_00045, SAMEA3649466_05396
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6XEC0, beta-lactamase
#2: Chemical
ChemComp-1BO / 1-BUTANOL / BUTAN-1-OL


Mass: 74.122 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / 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: 2.29 Å3/Da / Density % sol: 46.19 %
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: 0.815342 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.815342 Å / Relative weight: 1
ReflectionResolution: 1.92→53.84 Å / Num. obs: 85231 / % possible obs: 99.9 % / Redundancy: 12 % / CC1/2: 0.994 / Net I/σ(I): 5.8
Reflection shellResolution: 1.92→1.96 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 4431 / 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: 1.92→53.84 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.923 / SU ML: 0.153 / Cross valid method: FREE R-VALUE / ESU R: 0.181 / ESU R Free: 0.158
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2495 4389 5.155 %
Rwork0.2184 80758 -
all0.22 --
obs-85147 99.862 %
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: 24.047 Å2
Baniso -1Baniso -2Baniso -3
1-3.04 Å20 Å20 Å2
2---0.748 Å20 Å2
3----2.292 Å2
Refinement stepCycle: LAST / Resolution: 1.92→53.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7932 0 35 455 8422
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0138184
X-RAY DIFFRACTIONr_bond_other_d0.0010.0187677
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.63511065
X-RAY DIFFRACTIONr_angle_other_deg1.2881.58517604
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3255972
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.88922.836476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8151418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9621549
X-RAY DIFFRACTIONr_chiral_restr0.0690.21028
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029367
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022047
X-RAY DIFFRACTIONr_nbd_refined0.2140.21638
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1680.27351
X-RAY DIFFRACTIONr_nbtor_refined0.1650.23926
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.23947
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2438
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.090.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2190.214
X-RAY DIFFRACTIONr_nbd_other0.2140.293
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1850.221
X-RAY DIFFRACTIONr_mcbond_it1.5592.393876
X-RAY DIFFRACTIONr_mcbond_other1.5592.3893875
X-RAY DIFFRACTIONr_mcangle_it2.3753.5784840
X-RAY DIFFRACTIONr_mcangle_other2.3753.5784841
X-RAY DIFFRACTIONr_scbond_it2.1192.6494308
X-RAY DIFFRACTIONr_scbond_other2.1192.6494309
X-RAY DIFFRACTIONr_scangle_it3.3123.8756221
X-RAY DIFFRACTIONr_scangle_other3.3123.8756222
X-RAY DIFFRACTIONr_lrange_it4.2627.3979470
X-RAY DIFFRACTIONr_lrange_other4.21427.329390
X-RAY DIFFRACTIONr_ncsr_local_group_10.0470.058619
X-RAY DIFFRACTIONr_ncsr_local_group_20.0620.058508
X-RAY DIFFRACTIONr_ncsr_local_group_30.060.058509
X-RAY DIFFRACTIONr_ncsr_local_group_40.0650.058476
X-RAY DIFFRACTIONr_ncsr_local_group_50.0640.058460
X-RAY DIFFRACTIONr_ncsr_local_group_60.0540.058513
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.046710.0501
12BBBX-RAY DIFFRACTIONLocal ncs0.046710.0501
23AAAX-RAY DIFFRACTIONLocal ncs0.062370.05009
24CCCX-RAY DIFFRACTIONLocal ncs0.062370.05009
35AAAX-RAY DIFFRACTIONLocal ncs0.059810.05009
36DDDX-RAY DIFFRACTIONLocal ncs0.059810.05009
47BBBX-RAY DIFFRACTIONLocal ncs0.065090.05009
48CCCX-RAY DIFFRACTIONLocal ncs0.065090.05009
59BBBX-RAY DIFFRACTIONLocal ncs0.063590.05009
510DDDX-RAY DIFFRACTIONLocal ncs0.063590.05009
611CCCX-RAY DIFFRACTIONLocal ncs0.05410.0501
612DDDX-RAY DIFFRACTIONLocal ncs0.05410.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.970.3773250.3775859X-RAY DIFFRACTION99.7098
1.97-2.0240.3373410.345759X-RAY DIFFRACTION99.6244
2.024-2.0830.2953060.3085578X-RAY DIFFRACTION99.6612
2.083-2.1470.3023050.2835423X-RAY DIFFRACTION99.8083
2.147-2.2170.2992590.2645275X-RAY DIFFRACTION99.8016
2.217-2.2950.2832810.2465124X-RAY DIFFRACTION99.8153
2.295-2.3810.2672660.2354964X-RAY DIFFRACTION99.8854
2.381-2.4790.2582780.2214700X-RAY DIFFRACTION99.9398
2.479-2.5890.2882600.2234589X-RAY DIFFRACTION99.9588
2.589-2.7150.2582230.2134389X-RAY DIFFRACTION99.9783
2.715-2.8620.2762100.1974199X-RAY DIFFRACTION100
2.862-3.0350.2422190.1963949X-RAY DIFFRACTION100
3.035-3.2450.2271990.1853731X-RAY DIFFRACTION100
3.245-3.5040.2131710.1843487X-RAY DIFFRACTION100
3.504-3.8390.2031560.1773245X-RAY DIFFRACTION100
3.839-4.2910.1971710.1692911X-RAY DIFFRACTION100
4.291-4.9540.1861470.162596X-RAY DIFFRACTION99.9636
4.954-6.0650.2071290.1722201X-RAY DIFFRACTION100
6.065-8.5670.207940.1951750X-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