[English] 日本語
Yorodumi
- PDB-9h18: Crystal structure of OXA-405 in complex with nacubactam -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9h18
TitleCrystal structure of OXA-405 in complex with nacubactam
ComponentsBeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / antibiotic resistance / beta lactamase / class D / DBO
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
: / Chem-OP0 / DI(HYDROXYETHYL)ETHER / Beta-lactamase
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 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

-
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)57,50912
Polymers55,6752
Non-polymers1,83410
Water9,944552
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-34 kcal/mol
Surface area21190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.692, 123.692, 159.347
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-664-

HOH

21B-430-

HOH

31B-628-

HOH

41B-643-

HOH

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Beta-lactamase


Mass: 27837.545 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: blaOXA-405 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F6P2I5, beta-lactamase

-
Non-polymers , 7 types, 562 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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-A1IYS / (2S,5R)-N-(2-azanylethoxy)-1-methanoyl-5-(oxidanylamino)piperidine-2-carboxamide / nacubactam, reacted form


Mass: 246.264 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H18N4O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C18H38O10 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 552 / 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: 61.08 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M Tris pH 9.0, 20% 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 EIGER2 X 16M / Detector: PIXEL / Date: Feb 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.33→57.66 Å / Num. obs: 163547 / % possible obs: 100 % / Redundancy: 39.9 % / CC1/2: 0.999 / Rpim(I) all: 0.027 / Net I/σ(I): 8.9
Reflection shellResolution: 1.33→1.35 Å / Redundancy: 40.5 % / Mean I/σ(I) obs: 0.1 / Num. unique obs: 7912 / CC1/2: 0.297 / Rpim(I) all: 1.319 / % possible all: 98.1

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→57.66 Å / SU ML: 0.2102 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.7906
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.199 1739 1.25 %
Rwork0.1833 136943 -
obs0.1835 138682 84.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.03 Å2
Refinement stepCycle: LAST / Resolution: 1.33→57.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3896 0 118 552 4566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00584235
X-RAY DIFFRACTIONf_angle_d0.81445726
X-RAY DIFFRACTIONf_chiral_restr0.0794590
X-RAY DIFFRACTIONf_plane_restr0.0066734
X-RAY DIFFRACTIONf_dihedral_angle_d14.37041590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.370.2834250.42962022X-RAY DIFFRACTION15.27
1.37-1.410.4076670.40146139X-RAY DIFFRACTION46.22
1.41-1.460.38581290.38799285X-RAY DIFFRACTION69.92
1.46-1.520.43371380.381111445X-RAY DIFFRACTION86
1.52-1.590.33471810.331513229X-RAY DIFFRACTION99.45
1.59-1.680.25941690.265313337X-RAY DIFFRACTION99.99
1.68-1.780.26321690.219613344X-RAY DIFFRACTION99.94
1.78-1.920.2391630.22513410X-RAY DIFFRACTION99.99
1.92-2.110.21871910.184313397X-RAY DIFFRACTION99.95
2.11-2.420.20051900.169913500X-RAY DIFFRACTION99.99
2.42-3.050.18341590.1713648X-RAY DIFFRACTION100
3.05-57.660.14261580.141514187X-RAY DIFFRACTION99.94
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)
13.48884876585-0.8031962295550.8312542549946.98769553752-2.492594583214.50977404418-0.0007427661076830.204070079858-0.589147842189-0.1430806635620.000610010327730.09697321581320.393742158033-0.2556763854950.001495832857540.150910486863-0.0649824472710.02477730297190.226900732959-0.07019453088610.248224076296-19.80709188141.6843946597-5.0428807919
21.832862677050.00684900095215-0.1468837351081.133737797450.1864579715721.756272443540.0092626534558-0.248229188435-0.09209967289880.176431568532-0.0168363840744-0.061969067880.1190679594060.115887060740.003606286447290.17794333956-0.04089667376520.006436171179240.226854642740.02406727867960.164990064844-4.8467686729750.14718801317.22199189
31.992529825490.43418630879-0.7471396203071.136061048380.09537381670691.857229285280.028282314697-0.0685030874807-0.0956819487930.0594828292084-0.03572381892060.04659979703330.0709151591583-0.05095463027010.005838554147380.125028461303-0.0236479321874-0.003787811569080.184057514951-0.0003108686353580.165867930894-7.620649900451.8685359945.98195594728
44.328857246181.40047363547-1.268188559423.74926950957-0.5705365778344.93093936446-0.05422327959770.0530391123482-0.5072564626310.14151600782-0.0812910460189-0.09021398225410.394546225836-0.02495659833210.1406896021790.111401774991-0.01159612603330.005635819236720.146043672881-0.03130280796040.234801598139-10.286633045140.3466453325-0.837456039916
52.21496916103-0.3933247518430.009209568019176.90101824115.002562975217.55310222982-0.03412631323960.21701210598-0.491862026882-0.02598677491890.0354476438590.1438633496590.3181235282870.300352060349-0.01639537231210.1365065750620.04483524857380.01236975826420.2245627850060.006467915018250.29977737590731.79531485741.4445595618-3.38336984881
64.87528223786-0.728560216283-0.9269027182213.346261389372.335828468989.068070642090.1403679215580.0499582338841-0.36326017265-0.0532010074416-0.0818603356662-0.02124376665260.339643601622-0.167221850802-0.03353129439370.1214639145880.0186526883884-0.0166340442130.1612918889190.04760064480210.19573510263627.95384025546.4266001768-0.583258961886
74.55030436469-4.072994368710.9947979512185.03411054243-0.7641819293110.7658254242680.01631127448940.01458126368050.161172992190.00746245879875-0.0539286053448-0.1044727002820.06545077533780.08783777157550.04094550689520.1262250421520.003933204072320.004207087409510.1878190931660.0009001991193260.13200547325521.965793727359.4496530428-9.40639332516
80.7212532890981.562145931431.404751711773.992971239613.005178568038.778753482120.0551126504320.3405108202360.0548595595454-0.4106631685440.136437728967-0.0819392196397-0.036285427074-0.0538813525041-0.1564272247210.1675253595530.05250988518580.001665853066980.2928897492110.005149757228050.215147235573.3919823586962.9447867812-18.0791253251
93.62630961914-2.25650409014-4.51768822497.05319669653-0.711469964127.933267499610.04186102944680.13025785047-0.116157959277-0.218570565241-0.0995126567625-0.069549608640.141756394049-0.06187029933670.06212052338860.0889896590326-0.00920996062326-0.01781499535490.179967035019-0.02576042181050.1586725133484.9843213305556.1362007248-16.9179011657
106.55537172942.558766359556.466815183043.582264393822.468934361849.29921372048-0.2351258526710.02624756823750.334531165511-0.1882552761180.07622178021230.0502605782035-0.6578504772530.09872315439710.1519207761860.1489930736210.03071937070540.06424182738870.1753432785050.004189588245380.1717455681315.151399592870.1827713078-12.4000286711
117.74236912715-3.375025316966.511673988245.25164086853-4.576948317727.22443697445-0.05609924212290.3827575885420.6129328388350.0579834559796-0.306757862759-0.344266726626-0.3647565614260.5571269942210.3901543753480.1596128983510.01077141693560.02119335820720.2333207766380.005068189290120.23887047488124.130303849768.0152108433-12.1199185772
125.608011018661.21901288954-3.337932621293.32312713075-2.171790153712.677946546360.1132098998350.0138289961790.0304188768249-0.137009585867-0.0945089802412-0.02170212750940.08800114711790.177000802128-0.01969269290850.117207608310.00339182436901-0.03034626737350.16155086936-0.01741277682130.13969136160123.096369720460.0000596719-7.45054575295
132.0311150532-1.540081140680.991600305848.326459868081.722935679997.075831530510.0149074100747-0.2073521662120.1218421731330.1009827883290.0186028823338-0.118780444216-0.4202507973840.0967881156302-0.02320795726020.0977457090058-0.02236589447330.03849772990280.1817485691180.001373916440660.13415055468510.621086785562.91785590351.55387784305
147.048877992614.26941781158-5.073680632235.06638773782-5.002843119439.43467303719-0.366983785140.112897124839-0.536904644876-0.390224288793-0.0812066477671-0.3221244649210.5273076426330.06351061379860.467687242420.1226055039040.02300870862140.006091973284990.158238492671-0.01373972129990.22537847272813.406217616848.3879175545-7.5985327344
156.662056924711.08480717119-3.190583541114.55665437693-2.289366246267.270995630120.00531056483998-0.250239201865-0.256839631315-0.0157938989448-0.0864826608366-0.007603699858620.2658822008020.1987353762930.08019351231030.05881026443460.0223083980067-0.03907828668770.142637436660.002225117630290.18638134233418.34033796348.8349144333-3.20975535326
167.41771527049-0.0982542518051-0.4941569998434.85680817371-0.3299635486140.05559247030160.04425899691990.514494244197-0.375407278056-0.4801481486820.05617241654860.106835736010.2566925824160.162781857422-0.1036499233870.1650982875790.0249956250027-0.04023983542320.149469744938-0.008828436787790.19812102315722.2810967246.9478952038-9.30549148507
178.35702345328-3.566548382764.512344095255.86874624205-3.555775669666.649526946930.180504709134-0.275502877906-0.865656455603-0.0715211356513-0.02181831784930.3721808144910.480553110854-0.288990409349-0.1456330791620.1784879063960.009617308530560.004730491682280.195754675592-0.00810735787370.34354432240620.344100496139.060685528-4.4794629497
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 21 through 58 )AA21 - 581 - 38
22chain 'A' and (resid 59 through 155 )AA59 - 15539 - 135
33chain 'A' and (resid 156 through 213 )AA156 - 213136 - 193
44chain 'A' and (resid 214 through 261 )AA214 - 261194 - 241
55chain 'B' and (resid 21 through 38 )BF21 - 381 - 18
66chain 'B' and (resid 39 through 58 )BF39 - 5819 - 38
77chain 'B' and (resid 59 through 82 )BF59 - 8239 - 62
88chain 'B' and (resid 83 through 102 )BF83 - 10263 - 82
99chain 'B' and (resid 103 through 119 )BF103 - 11983 - 99
1010chain 'B' and (resid 120 through 142 )BF120 - 142100 - 122
1111chain 'B' and (resid 143 through 155 )BF143 - 155123 - 135
1212chain 'B' and (resid 156 through 177 )BF156 - 177136 - 157
1313chain 'B' and (resid 178 through 194 )BF178 - 194158 - 174
1414chain 'B' and (resid 195 through 213 )BF195 - 213175 - 193
1515chain 'B' and (resid 214 through 227 )BF214 - 227194 - 207
1616chain 'B' and (resid 228 through 245 )BF228 - 245208 - 220
1717chain 'B' and (resid 246 through 261 )BF246 - 261221 - 236

+
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