[English] 日本語
Yorodumi
- PDB-9q0b: CTX-M-15 WT in complex with BLIP E73W -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9q0b
TitleCTX-M-15 WT in complex with BLIP E73W
Components
  • Beta-lactamase CTX-M-15
  • Beta-lactamase inhibitory protein
KeywordsHYDROLASE/PROTEIN BINDING / beta-lactamase / BLIP / beta-lactamase inhibitory protein / PROTEIN BINDING / HYDROLASE-PROTEIN BINDING complex
Function / homology
Function and homology information


regulation of beta-lactamase activity / beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / extracellular region
Similarity search - Function
Beta-lactamase-inhibitor protein BLIP / Beta-lactamase-inhibitor protein BLIP domain superfamily / Beta-lactamase inhibitor (BLIP) / BamE-like / Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Beta-lactamase CTX-M-15 / Beta-lactamase inhibitory protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Streptomyces clavuligerus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsRivera, P. / Lu, S. / Sankaran, B. / Prasad, B.V.V. / Palzkill, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: J.Biol.Chem. / Year: 2025
Title: A beta-lactamase inhibitory protein mutant displays high potency and a broad inhibition profile due to an altered binding mode with beta-lactamases.
Authors: Rivera, P. / Lu, S. / Ngango, D. / Sankaran, B. / Venkataram Prasad, B. / Palzkill, T.
History
DepositionAug 12, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2025Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase CTX-M-15
B: Beta-lactamase inhibitory protein


Theoretical massNumber of molelcules
Total (without water)45,4522
Polymers45,4522
Non-polymers00
Water9,044502
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-9 kcal/mol
Surface area16380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.460, 81.960, 129.074
Angle α, β, γ (deg.)90.000, 96.145, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-543-

HOH

21B-228-

HOH

-
Components

#1: Protein Beta-lactamase CTX-M-15 / Cefotaximase 15


Mass: 27909.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla, blaCTX-M-15, EWT59_27045 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5R8T042, beta-lactamase
#2: Protein Beta-lactamase inhibitory protein / BLIP


Mass: 17542.510 Da / Num. of mol.: 1 / Mutation: E73W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Production host: Komagataella pastoris (fungus) / References: UniProt: P35804
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES pH 6.5, 25% (w/v) PEG 4000

-
Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.58→40.98 Å / Num. obs: 65474 / % possible obs: 96.89 % / Redundancy: 4.8 % / Biso Wilson estimate: 11.27 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.05857 / Net I/σ(I): 15.43
Reflection shellResolution: 1.58→1.6 Å / Num. unique obs: 2804 / CC1/2: 0.977 / % possible all: 97.97

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→40.98 Å / SU ML: 0.1288 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.2297
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1816 3159 4.85 %
Rwork0.1631 61955 -
obs0.164 65114 96.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.59 Å2
Refinement stepCycle: LAST / Resolution: 1.58→40.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3191 0 0 502 3693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00523250
X-RAY DIFFRACTIONf_angle_d0.82434414
X-RAY DIFFRACTIONf_chiral_restr0.0514504
X-RAY DIFFRACTIONf_plane_restr0.0076574
X-RAY DIFFRACTIONf_dihedral_angle_d12.24681162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.60.20221390.16142665X-RAY DIFFRACTION97.97
1.6-1.630.21031370.15892767X-RAY DIFFRACTION98.21
1.63-1.660.17631390.1522702X-RAY DIFFRACTION98.24
1.66-1.680.16361390.14912702X-RAY DIFFRACTION98.3
1.68-1.710.17261440.152741X-RAY DIFFRACTION98.84
1.71-1.750.18691510.16062742X-RAY DIFFRACTION98.4
1.75-1.780.17781420.15732707X-RAY DIFFRACTION98.41
1.78-1.820.21051480.15952725X-RAY DIFFRACTION98.19
1.82-1.860.21161590.1682639X-RAY DIFFRACTION96.98
1.86-1.910.19171270.19132614X-RAY DIFFRACTION92.95
1.91-1.960.22521140.21212464X-RAY DIFFRACTION89.39
1.96-2.020.18731110.16142594X-RAY DIFFRACTION93.08
2.02-2.090.17961380.18812696X-RAY DIFFRACTION97.39
2.09-2.160.18891430.1632764X-RAY DIFFRACTION97.94
2.16-2.250.20941270.18652665X-RAY DIFFRACTION96.71
2.25-2.350.26871290.19412693X-RAY DIFFRACTION96.68
2.35-2.470.1641390.16162728X-RAY DIFFRACTION98.08
2.47-2.630.15571630.15912723X-RAY DIFFRACTION98.06
2.63-2.830.17441200.16012739X-RAY DIFFRACTION97.71
2.83-3.120.19171410.16052720X-RAY DIFFRACTION97.98
3.12-3.560.14541370.15672668X-RAY DIFFRACTION94.67
3.57-4.490.15881380.13712631X-RAY DIFFRACTION94.34
4.49-40.980.17261340.1532866X-RAY DIFFRACTION99.9

+
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