[English] 日本語
Yorodumi
- PDB-9h15: Crystal structure of OXA-163 in complex with nacubactam -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9h15
TitleCrystal structure of OXA-163 in complex with nacubactam
ComponentsBeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / antibiotic resistance / beta lactamase / class D / apo
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding / 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
Chem-OP0 / DI(HYDROXYETHYL)ETHER / Beta-lactamase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsHoff, J.F. / Goudar, K.E. / Hinchliffe, P. / Spencer, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)R102376-101 United Kingdom
CitationJournal: Rsc Med Chem / Year: 2025
Title: Electrostatic interactions influence diazabicyclooctane inhibitor potency against OXA-48-like beta-lactamases.
Authors: Hoff, J.F. / Goudar, K.E. / Calvopina, K. / Beer, M. / Hinchliffe, P. / Shaw, J.M. / Tooke, C.L. / Takebayashi, Y. / Cadzow, A.F. / Harmer, N.J. / Mulholland, A.J. / Schofield, C.J. / Spencer, J.
History
DepositionOct 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2025Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
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)57,29516
Polymers55,7392
Non-polymers1,55614
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-10 kcal/mol
Surface area19260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.623, 79.043, 126.250
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

-
Protein , 1 types, 2 molecules AB

#1: Protein Beta-lactamase


Mass: 27869.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: blaOXA-163 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F6KZJ2, beta-lactamase

-
Non-polymers , 7 types, 205 molecules

#2: Chemical ChemComp-OP0 / (2S,5R)-N-(2-aminoethoxy)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide


Mass: 326.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H18N4O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.09 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 8.8 / Details: 0.1 M Tris pH 8.8, 40% PEG 400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.18→52.66 Å / Num. obs: 37053 / % possible obs: 98.7 % / Redundancy: 14.1 % / Biso Wilson estimate: 34.99 Å2 / CC1/2: 0.987 / Rpim(I) all: 0.141 / Net I/σ(I): 5.1
Reflection shellResolution: 2.18→2.22 Å / Redundancy: 14.6 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 3661 / CC1/2: 0.327 / Rpim(I) all: 1.171 / % possible all: 98.1

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.18→52.66 Å / SU ML: 0.2778 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.0944
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.243 1881 5.08 %
Rwork0.1963 35172 -
obs0.1987 37053 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.61 Å2
Refinement stepCycle: LAST / Resolution: 2.18→52.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3910 0 96 191 4197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00734131
X-RAY DIFFRACTIONf_angle_d0.84235570
X-RAY DIFFRACTIONf_chiral_restr0.0521579
X-RAY DIFFRACTIONf_plane_restr0.0074707
X-RAY DIFFRACTIONf_dihedral_angle_d14.60641524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.240.33321450.31642647X-RAY DIFFRACTION98.03
2.24-2.310.33941290.29032685X-RAY DIFFRACTION98.32
2.31-2.380.32461670.27192626X-RAY DIFFRACTION98.35
2.38-2.460.31161390.25812694X-RAY DIFFRACTION98.75
2.46-2.560.30881540.23232641X-RAY DIFFRACTION98.73
2.56-2.680.25971330.22922692X-RAY DIFFRACTION98.74
2.68-2.820.25791460.20962703X-RAY DIFFRACTION98.85
2.82-30.26651620.19762687X-RAY DIFFRACTION99.2
3-3.230.24131330.18962728X-RAY DIFFRACTION99.24
3.23-3.550.23861400.16862728X-RAY DIFFRACTION99.31
3.55-4.070.21731440.16742603X-RAY DIFFRACTION94.4
4.07-5.130.19451430.15262807X-RAY DIFFRACTION99.7
5.13-52.660.20831460.19222931X-RAY DIFFRACTION99.58
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)
18.7612514827-1.5516475270.433683023865.357638213921.209547372896.70643076499-0.0296725824620.543411255274-0.932231847414-0.0204133170813-0.1158079958330.3527987901810.854685932274-0.1308419133480.1324310514080.491278175077-0.0922919032932-0.01578884864770.295828288796-0.04323406206950.236476985211-27.6757195505-12.9698315788-10.1584762468
28.6958994484-0.6294425095112.489762072454.218272909530.561813066895.14228095891-0.09223432955090.26320621891-0.414648257097-0.3866733910750.09258978153560.06268210764790.702746906410.1381739739210.04932473727170.455447228937-0.02162888458950.03664044487350.3038710572760.03150868443810.218636740992-22.1553790339-8.89530896398-6.94186333441
31.968124071251.48947140082.443176497995.310430603442.584920544415.63630981786-0.3298530676050.1352264910150.139581183652-0.6749878998090.296412241825-0.06072236056-0.95413078316-0.0164152430470.05494252737420.256210653755-0.008116676745430.05244660258430.2441202400830.01452435748540.206932968722-24.78396634376.60515029275-4.17322622219
43.76295081150.1497403291692.614510838151.793313830721.03389981963.23702921523-0.505679815958-0.7720982787810.5876459268460.05798452597580.08645548636470.172753510432-0.6086821106-0.8214986929980.4587491898220.5335306861820.161798001031-0.001585449299340.387953663972-0.04083608074170.367842041957-31.881297870116.332484400713.5965642734
54.01093167648-4.53258090264-0.7969801057047.050855235331.361220680330.2677787760830.0424948893621-0.5222424341720.0710290892108-0.239871098236-0.3602508335990.348752867788-0.380412328827-1.194850156740.2442813313610.2786594892790.09195772308250.02555616531780.563775594788-0.05360906234430.256469779297-31.126200110410.093351311713.257287286
66.22083015772-0.735802006176-0.7556209659125.235455677220.1246103327723.05257653922-0.1941402999240.1774354378910.839957705706-0.2120419047530.17949503997-0.117059305887-1.24058194901-0.108635320870.007058920143720.6544025777580.0236890795764-0.1283528543610.2585033408880.01550261395630.299869719714-22.932325588919.30002046010.909807346455
70.9755612451291.018786061610.5098317561081.591326149620.5767762336384.22571970256-0.1014402749520.1404021634610.104803838187-0.2166034281010.0840973395347-0.0413562382304-0.602179533021-0.04602885275630.01701717899560.312422903070.0149493215613-0.008824401573130.248529589297-0.004024508414570.247735315892-19.79265809449.22112223541-1.52916932893
82.123894001390.390462871569-0.1615525216842.489995397341.158850406914.117640709630.03137550863830.0862716105738-0.02950208538860.0976242359942-0.08799818111630.1971806286110.365144353678-0.5333605591720.02943642085980.262234477686-0.04572722605330.01223813846070.2762835813360.02935268705140.240844265671-27.7869798383-5.57746480771.8391634727
94.28775228988-2.42302554698-0.7246786087928.656571850411.534367298876.23030455860.206602728495-0.291643608094-0.2325771002260.934174293148-0.3539755928530.3740071269940.000146982452283-0.5499412731020.1512009524510.310069016982-0.1321357473030.03248461893090.6138732797770.01661680257450.283646813087-28.9797177825-5.67133119341.886145887
104.27007525453-0.455717060351-1.165580327080.782389622981-0.8588018228135.19155643558-0.1587534716-0.37710630727-0.00766209850260.1490954350610.1649695586580.03789440306430.104618098892-0.0448141727994-0.01674283235960.299880714994-0.0395730002512-0.02650062790950.17145825597-0.08503802901850.237324610337-16.3466742847-3.0500710422135.3330521113
113.85151139452-0.374079687962-0.2676979385055.59117531676-0.6676996437333.848278366880.2434415792960.0925023500795-0.253493602732-0.123495739189-0.346846563733-0.2385341417060.7744499235450.6923645208280.09827647413690.3556481686320.115867808390.00554973645990.404957254227-0.02239177113740.209930421307-4.65329549951-13.30971047416.2844883313
122.002951068530.274232629144-0.3918168040571.39381815584-0.5746543681813.664332983410.114587536751-0.209264953202-0.09999216523320.0516630061889-0.0461235868195-0.1060267107730.1151493234770.226045711955-0.07399583303450.260186450844-0.00248576928021-0.02321901983650.213596004008-0.0229267491240.233248230208-13.1033265127-4.3037958547629.3692713445
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 23 through 38 )AA23 - 381 - 16
22chain 'A' and (resid 39 through 56 )AA39 - 5617 - 34
33chain 'A' and (resid 57 through 83 )AA57 - 8335 - 61
44chain 'A' and (resid 84 through 105 )AA84 - 10562 - 83
55chain 'A' and (resid 106 through 119 )AA106 - 11984 - 97
66chain 'A' and (resid 120 through 142 )AA120 - 14298 - 120
77chain 'A' and (resid 143 through 194 )AA143 - 194121 - 172
88chain 'A' and (resid 195 through 261 )AA195 - 261173 - 239
99chain 'B' and (resid 23 through 38 )BG23 - 381 - 16
1010chain 'B' and (resid 39 through 83 )BG39 - 8317 - 61
1111chain 'B' and (resid 84 through 119 )BG84 - 11962 - 97
1212chain 'B' and (resid 120 through 261 )BG120 - 26198 - 239

+
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