[English] 日本語
Yorodumi
- PDB-9to1: Room temperature serial crystal structure of CTX-M-15 class A bet... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9to1
TitleRoom temperature serial crystal structure of CTX-M-15 class A beta-lactamase uncomplexed resting state from PAL-XFEL
ComponentsBeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / antibiotic resistance / beta-lactamase / inhibitor / dynamics / tr-SFX / XFEL
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
: / 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
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsHinchliffe, P. / Tooke, C.L. / Spencer, J.
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 16, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4474
Polymers28,2931
Non-polymers1553
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint-38 kcal/mol
Surface area11050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.288, 45.941, 118.453
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Beta-lactamase


Mass: 28292.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaCTX-M-15 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Solu / References: UniProt: G3G192, beta-lactamase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.18 Å3/Da / Density % sol: 43.52 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 2.0 M ammonium sulphate, 0.1 M Tris 8.0, with crystal seed

-
Data collection

DiffractionMean temperature: 295 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: PAL-XFEL / Beamline: NCI / Wavelength: 1.30419 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Dec 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.30419 Å / Relative weight: 1
ReflectionResolution: 1.6→59.23 Å / Num. obs: 33457 / % possible obs: 99.99 % / Redundancy: 78.89 % / Biso Wilson estimate: 15.12 Å2 / CC1/2: 0.969 / R split: 0.149 / Net I/σ(I): 4.286
Reflection shellResolution: 1.6→1.6276 Å / Mean I/σ(I) obs: 1.044 / Num. unique obs: 1653 / CC1/2: 0.689 / R split: 0.383
Serial crystallography measurementPulse energy: 650 µJ
Serial crystallography sample deliveryDescription: Silicon 'Oxford' chip / Method: fixed target
Serial crystallography sample delivery fixed targetSample dehydration prevention: Mylar film

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.6→42.83 Å / SU ML: 0.146 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.5509
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1648 1665 4.98 %
Rwork0.1398 31788 -
obs0.1411 33453 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.91 Å2
Refinement stepCycle: LAST / Resolution: 1.6→42.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1943 0 7 208 2158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00792053
X-RAY DIFFRACTIONf_angle_d0.99422800
X-RAY DIFFRACTIONf_chiral_restr0.0582324
X-RAY DIFFRACTIONf_plane_restr0.0073373
X-RAY DIFFRACTIONf_dihedral_angle_d16.9651775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.650.26231410.24162611X-RAY DIFFRACTION99.89
1.65-1.70.19351380.19322601X-RAY DIFFRACTION99.93
1.7-1.760.2291400.1762582X-RAY DIFFRACTION100
1.76-1.830.17331360.14522610X-RAY DIFFRACTION100
1.83-1.910.14951330.12842633X-RAY DIFFRACTION100
1.91-2.020.1651360.12032626X-RAY DIFFRACTION100
2.02-2.140.15171330.12112629X-RAY DIFFRACTION100
2.14-2.310.15811420.12352649X-RAY DIFFRACTION100
2.31-2.540.15581350.12642652X-RAY DIFFRACTION100
2.54-2.910.17061430.13662651X-RAY DIFFRACTION100
2.91-3.660.1561410.13782698X-RAY DIFFRACTION100
3.66-42.830.15091470.14242846X-RAY DIFFRACTION100
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)
11.992802139770.862835284645-0.6537229283982.02369727061-0.970513462762.13175857974-0.1564241887490.181683401462-0.314075730509-0.3300539929210.0811428428359-0.2728442243540.3389084365040.0921434508010.07169887402720.1515099975940.008022455742780.03970791493960.134613687502-0.01978096158740.1423030636794.84849533757-20.86433700788.58985805481
22.40401206434-0.32542304421-0.6456709550013.46087581186-0.890005146722.0621800834-0.0728858953801-0.3331895273740.06776574833890.4253143158430.1274371727490.2751871553370.0335279008919-0.0149839914486-0.01999621817570.137024349058-0.02210371047130.005775805303290.124111688137-0.02614074583070.122830855877-12.5326035105-6.1175332602530.1141810442
37.68160320298-2.02532490203-2.929254938196.936104775693.207324372873.81167230233-0.01107450546550.3536107236250.393065232681-0.379285469211-0.01107966634040.544512934732-0.403603795109-0.2041755354040.008969673180980.1931004358680.0153124008928-0.04210368030430.1135074668950.05199878203820.20777092324-15.84435521917.7887099650218.6478257525
40.978543760345-0.217327423465-0.1718659893991.583304554690.2037396436330.8242966995270.00846703112839-0.03878721496280.013153808470.02790137456950.004576948109020.0174717118217-0.02025626824770.0320017645796-0.01177345987580.10289228725-0.00851037577891-0.0007920190946070.0993788022211-0.002587826888450.0828924965244-3.06450039894-6.5169639490523.0611560184
55.71081133744-2.68743202281.176343891882.53506676552-0.3886391692164.13441955535-0.00454554205802-0.142555713663-0.2776499707670.1708307803810.0723748101030.3248247507950.121273771402-0.180156103757-0.1143679833770.103638574627-0.03993931393460.01400284813420.07698721335550.01498789890930.120034726572-14.5126582148-17.277996814425.8109317963
62.175761988540.8344147569650.09495267433661.782283443650.3790107670581.961745471020.0462081889880.0659204387368-0.0150387136566-0.161987286492-0.04026986313950.09819368436860.0210202273651-0.1173422354170.00961693412160.08882178745540.00693710699228-0.01723607088070.08406266118770.004394456081030.0763430082318-9.06254061557-14.81758714789.75006758522
76.027442889752.50002588074-2.68119097192.93216002933-2.361951876712.50023259369-0.1058015128020.213502707982-0.21775958583-0.369367613110.1923632264290.1784886259870.312915559961-0.0862781901112-0.07619855825030.172842006213-0.00659838121158-0.03201055940770.101647245117-0.0163330329580.0890435420098-5.97340829496-22.506096751111.9815943494
86.438999083915.03616282453-0.6696517012087.43617129742-2.00821928223.65579531721-0.1005251165790.3400701056470.150162702418-0.4072166031230.2039367108960.1983509486930.0883918921801-0.0730469877422-0.1246774089280.131886775680.01341804897630.02618792560720.143738371523-0.01918756921250.0564215266546-0.757193001108-12.73253903092.30369271506
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 28 through 68 )28 - 681 - 43
22chain 'A' and (resid 69 through 96 )69 - 9644 - 73
33chain 'A' and (resid 97 through 115 )97 - 11574 - 92
44chain 'A' and (resid 116 through 194 )116 - 19493 - 176
55chain 'A' and (resid 195 through 213 )195 - 213177 - 195
66chain 'A' and (resid 214 through 250 )214 - 250196 - 234
77chain 'A' and (resid 251 through 264 )251 - 264235 - 248
88chain 'A' and (resid 265 through 287 )265 - 287249 - 271

+
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