[English] 日本語
Yorodumi
- PDB-9tow: Room temperature serial crystal structure of AmpC class C beta-la... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9tow
TitleRoom temperature serial crystal structure of AmpC class C beta-lactamase, drop on fixed target from PAL-XFEL, 80 ms control (avibactam)
ComponentsBeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / antibiotic resistance / beta-lactamase / inhibitor / dynamics / tr-SFX / XFEL
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
PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / FOURIER SYNTHESIS / Resolution: 2.78 Å
AuthorsHinchliffe, P. / Freeman, E.I. / Lang, P.A. / Rabe, P. / Kamps, J.G.A. / Aller, P. / Schofield, C.J. / Orville, A.M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)101021207European Union
CitationJournal: Iucrj / Year: 2026
Title: Drop-on-fixed-target reaction initiation approach for serial and time-resolved crystallography.
Authors: Kamps, J.J.A.G. / Hinchliffe, P. / Glerup, J. / Freeman, E.I. / Lang, P.A. / Tooke, C.L. / Beer, M. / Parkinson, L. / Gu, D.H. / Park, S. / Devenish, N. / Zhou, T. / Shilova, A. / Kaur, S. / ...Authors: Kamps, J.J.A.G. / Hinchliffe, P. / Glerup, J. / Freeman, E.I. / Lang, P.A. / Tooke, C.L. / Beer, M. / Parkinson, L. / Gu, D.H. / Park, S. / Devenish, N. / Zhou, T. / Shilova, A. / Kaur, S. / Rabe, P. / Schofield, C.J. / Spencer, J. / Park, J. / Owen, R.L. / Orville, A.M. / Aller, P.
History
DepositionDec 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release

-
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)79,2713
Polymers79,1762
Non-polymers951
Water1,76598
1
A: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)39,5881
Polymers39,5881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6832
Polymers39,5881
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.967, 77.599, 99.250
Angle α, β, γ (deg.)90.000, 116.660, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 4 through 8 or resid 10 through 323 or resid 325 through 361))
d_2ens_1(chain "B" and (resid 4 through 8 or resid 10 through 323 or resid 325 through 361))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ALAALAILEILEAA4 - 81 - 5
d_12ASPASPGLYGLYAA10 - 3237 - 320
d_13TYRTYRGLNGLNAA325 - 361322 - 358
d_21ALAALAILEILEBB4 - 81 - 5
d_22ASPASPGLYGLYBB10 - 3237 - 320
d_23TYRTYRGLNGLNBB325 - 361322 - 358

NCS oper: (Code: givenMatrix: (-0.997344613143, -0.0712327140985, -0.0151533189746), (-0.0728215866998, 0.977904243788, 0.19595996145), (0.000859735023973, 0.196543100676, -0.980494808978)Vector: 90. ...NCS oper: (Code: given
Matrix: (-0.997344613143, -0.0712327140985, -0.0151533189746), (-0.0728215866998, 0.977904243788, 0.19595996145), (0.000859735023973, 0.196543100676, -0.980494808978)
Vector: 90.6620833296, -0.701572355986, 41.7055837542)

-
Components

#1: Protein Beta-lactamase / Cephalosporinase / CSase


Mass: 39587.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ampC, ampA, b4150, JW4111 / Production host: Escherichia coli (E. coli) / References: UniProt: P00811, beta-lactamase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.43 %
Crystal growTemperature: 293 K / Method: batch mode
Details: Potassium phosphate (1.9 M, pH 8.8) with crystal seed

-
Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: PAL-XFEL / Beamline: NCI / Wavelength: 1.3042 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Jun 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3042 Å / Relative weight: 1
ReflectionResolution: 2.78→59.09 Å / Num. obs: 20500 / % possible obs: 99.98 % / Redundancy: 33.03 % / Biso Wilson estimate: 41.48 Å2 / CC1/2: 0.917 / R split: 0.224 / Net I/σ(I): 3.325
Reflection shellResolution: 2.78→2.8279 Å / Redundancy: 21.7 % / Mean I/σ(I) obs: 1.609 / Num. unique obs: 1026 / CC1/2: 0.381 / R split: 0.434 / % possible all: 99.9
Serial crystallography sample deliveryDescription: silicon 'Oxford' chip / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: Drop on fixed target
Serial crystallography data reductionLattices indexed: 5159

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.78→45.57 Å / SU ML: 0.2845 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.7799
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2178 1022 5.01 %
Rwork0.1567 19385 -
obs0.1598 20407 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.05 Å2
Refinement stepCycle: LAST / Resolution: 2.78→45.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5598 0 5 98 5701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00865772
X-RAY DIFFRACTIONf_angle_d0.99657889
X-RAY DIFFRACTIONf_chiral_restr0.057856
X-RAY DIFFRACTIONf_plane_restr0.00631015
X-RAY DIFFRACTIONf_dihedral_angle_d14.18572087
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.968336374942 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.78-2.930.28071450.20032723X-RAY DIFFRACTION98.96
2.93-3.110.27261440.18872752X-RAY DIFFRACTION99.28
3.11-3.350.25511450.17232734X-RAY DIFFRACTION99
3.35-3.690.23071450.15652753X-RAY DIFFRACTION99.83
3.69-4.220.21211460.13492788X-RAY DIFFRACTION99.97
4.22-5.320.17141470.13242778X-RAY DIFFRACTION100
5.32-45.570.19661500.16412857X-RAY DIFFRACTION99.87

+
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