[English] 日本語
Yorodumi
- PDB-7l8o: OXA-48 bound by Compound 4.3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7l8o
TitleOXA-48 bound by Compound 4.3
ComponentsBeta-lactamase
KeywordsHYDROLASE/INHIBITOR / beta-lactamase / carbapenemase / beta-lactamase inhibitor / complex / oxacillinase / HYDROLASE / HYDROLASE-INHIBITOR complex
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
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
9H-fluorene-2,7-disulfonate / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsTaylor, D.M. / Hu, L. / 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: Acs Infect Dis. / Year: 2021
Title: Unique Diacidic Fragments Inhibit the OXA-48 Carbapenemase and Enhance the Killing of Escherichia coli Producing OXA-48.
Authors: Taylor, D.M. / Anglin, J. / Hu, L. / Wang, L. / Sankaran, B. / Wang, J. / Matzuk, M.M. / Prasad, B.V.V. / Palzkill, T.
History
DepositionDec 31, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 22, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,18924
Polymers113,1804
Non-polymers2,00920
Water1,29772
1
A: Beta-lactamase
hetero molecules

D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,62012
Polymers56,5902
Non-polymers1,03010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_544-y,x-y-1,z-1/31
MethodPISA
2
B: Beta-lactamase
hetero molecules

C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,56912
Polymers56,5902
Non-polymers97910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z+1/31
MethodPISA
Unit cell
Length a, b, c (Å)122.039, 122.039, 160.787
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
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,z+1/2

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Beta-lactamase / Oxacillinase-48 / OXA-48


Mass: 28295.053 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: GHM residues were left behind at the N-terminus after TEV cleavage
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: bla OXA-48, bla_1, bla_2, bla_5, blaOXA-48, B6R99_29845, GJD56_28020, GJJ04_29145, KPE71T_00045, SAMEA3538918_02768, SAMEA3538961_03054, SAMEA3673128_05462
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6XEC0, beta-lactamase

-
Non-polymers , 5 types, 92 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-XV7 / 9H-fluorene-2,7-disulfonate


Mass: 326.345 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H10O6S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M TRIS 8.5 pH, 25 %v/v PEG 550 MME

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999909 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 2019
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999909 Å / Relative weight: 1
ReflectionResolution: 2.7→48.6 Å / Num. obs: 37105 / % possible obs: 99.68 % / Redundancy: 11.4 % / Biso Wilson estimate: 40.34 Å2 / Rmerge(I) obs: 0.134 / Net I/σ(I): 19.3
Reflection shellResolution: 2.702→2.798 Å / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 3638 / % possible all: 98.03

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HBR

3hbr


Resolution: 2.7→48.6 Å / SU ML: 0.2762 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.2457
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2105 1865 5.03 %
Rwork0.1684 35202 -
obs0.1706 37067 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.35 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7916 0 121 72 8109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00568225
X-RAY DIFFRACTIONf_angle_d0.738111138
X-RAY DIFFRACTIONf_chiral_restr0.04841164
X-RAY DIFFRACTIONf_plane_restr0.00341484
X-RAY DIFFRACTIONf_dihedral_angle_d26.8571131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.29351230.21962686X-RAY DIFFRACTION97.5
2.77-2.860.25861360.20652706X-RAY DIFFRACTION99.96
2.86-2.950.23261360.20222688X-RAY DIFFRACTION100
2.95-3.050.29491450.20532739X-RAY DIFFRACTION100
3.05-3.180.25261550.20262661X-RAY DIFFRACTION100
3.18-3.320.27131430.19192721X-RAY DIFFRACTION100
3.32-3.50.22561380.18282716X-RAY DIFFRACTION99.89
3.5-3.710.22721480.17372696X-RAY DIFFRACTION99.82
3.72-40.19661480.17192702X-RAY DIFFRACTION99.62
4-4.40.17361420.13582711X-RAY DIFFRACTION100
4.4-5.040.16911690.13082705X-RAY DIFFRACTION100
5.04-6.350.18651310.1622735X-RAY DIFFRACTION99.97
6.35-48.60.18481510.14832736X-RAY DIFFRACTION99.38
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)
11.707727812170.5642124268091.41885959433.436139910370.152238222631.21470326329-0.3711094405560.3737610369080.603262025201-0.1538174595390.1536101494030.63077297393-1.02840130871-0.00689358682157-0.224234671960.990826480790.0124982420641-0.2402162754590.16601999308-0.0299949734460.99483144200249.74259907067.3747901779124.397891454
22.262124911950.8607032571021.03210380962.94336585243-0.4322577726412.80491533932-0.3429276874690.2753299032840.299547518292-0.4625211324260.3251920605490.195537468459-0.6682452372820.3354514566680.01678332048830.465682256191-0.0926814879489-0.06574795942030.263829406572-0.001799671302210.34244833333457.8182209943-5.5471634350924.8482241626
37.138032977651.74947385906-0.7870728049982.73005558178-0.8016504646762.32078447981-0.028438140293-0.333455265772-0.2146573935270.3040118794580.118718313147-0.0139591177830.6943708727030.396173015443-0.0822357652720.4787855971570.053055925739-0.01057991974280.220327385733-0.06673424210010.21691628859358.2165955752-24.262329510135.2209612033
42.912831677391.090416221162.266043618852.097792794390.3924087149643.09896130165-0.2809862996390.412271458830.0148946129624-0.3070781165950.318362986801-0.258609105455-0.3014635061230.729365121431-0.07224389070850.331701835364-0.09794273925210.03308857499110.298822609646-0.08388710774030.29437707067262.9611163031-14.468091065924.9191338222
51.514875797631.234570127160.1033837638832.696972895281.181729221081.87738862563-0.39852302770.033481798990.458629096706-0.1485437585840.05546173856420.357655607782-0.652464129517-0.2388494546490.3191506954820.4435390471220.0300047732412-0.06460884647330.172026384584-0.02300084276940.38210981732848.3345353559-6.3431837811226.9207776244
61.81473120872-0.943912904797-0.7069653603235.398362004521.812438221022.31302239512-0.526652067833-0.247561866521-0.8269060807770.4347894780360.2729590443010.6885961012930.9297781099730.00427466726431-0.03621665175240.8797446948950.05107315889840.2274323677090.230629502950.02325345142640.69625460908151.6374819531-4.0107058713570.8724363706
73.72973990975-1.48112325862-0.2321075448413.264316392920.04126816587223.387616715430.01177188655320.06531825437330.236003826298-0.2172851759450.0696958388849-0.0468515257649-0.3760741939220.320090733093-0.09499254710510.371864762362-0.03497187853450.009520027490750.219866938873-0.06792959805190.201420980459.141932031720.543402846359.4984121801
83.05394549312-1.09777721668-2.263264315962.999735999410.5919096672513.33346724444-0.200806662779-0.38138282689-0.04368117581820.1809806652650.251968643757-0.2457188034360.2062125209630.607612472674-0.06216052955970.2546787148780.0682506284291-0.04167759247020.266412666354-0.07221745519090.27234397989762.957859480314.460694242767.9945479142
91.5644305102-0.86808576766-0.2560955084352.143722353280.9872423545541.22143446966-0.417265547017-0.0397583133416-0.5269966579740.15959613140.008421263260140.3049205857720.692157641564-0.1706857040150.4117180394160.470432816116-0.007423775278150.07034798322430.189211823587-0.02445433999520.41611165719848.32670585866.3267043173165.9984315575
100.1282207632290.565279320484-0.1246375000313.367942264591.132148010124.562285785250.0322220031918-0.08596487905-0.865578668301-0.57281207960.118141275569-0.08498006062141.969765754590.495212403302-0.08165604630041.26963316717-0.2100138930350.3100055249840.343216102111-0.05834138662210.74638072668780.09505402062.0211120817116.4748139077
110.2029489120150.314497736789-0.2351364268561.48965711808-0.9256994064640.960235041965-0.3289442637720.306880603823-0.2574434208-0.256907752698-0.1344791157130.3569438884150.993565663424-0.5765361089860.1638626392390.819863442505-0.2383527726840.1766052552650.217483053718-0.04578040093940.43272945264973.160985511811.461309799625.5751601032
128.6217613231-1.30037569563-0.5734036452542.965620783581.806494757361.22006546403-0.65503284409-0.829225584641-0.03335657194270.6606924987510.457517298491-0.188712693251-0.1249071402580.0009363523446870.2310407836340.550285647512-0.029333628241-0.08098661107880.228440654231-0.005090025687630.32496929066783.691336435728.676080980540.9322406556
133.69731168531-1.40152605916-0.1814488124551.53026394336-0.04077085684682.41172486824-0.19734496319-0.166008865245-0.0252119442150.3585789003170.0362951726104-0.22487024670.1722712610740.0130734301910.2227202055270.479059113148-0.1070316482280.001728246146170.1706653645440.001210515446760.29954628002977.84959983722.698722951138.591876565
141.177696450160.532214675817-1.110099491271.36177033984-1.231879188751.61678414614-0.02316157440450.155661695809-0.2838428274780.377742295312-0.05237509493160.2657365936940.373944239289-0.622853025277-0.1580202018770.544749231901-0.1624540768280.08255383730740.2098538452080.02331923089490.35644743420670.217382522117.42647235730.6321404408
152.797227772870.629547736034-0.1827518555386.71260731025-6.635274661316.63968339216-0.3401282463480.0590008714291-0.348856963401-0.35875240812-0.079143817839-0.4659227978761.24666362375-0.07833795422490.4155366062360.411501965547-0.0393684116160.0807274439180.199334286282-0.0285845306220.29662857555583.696347158519.590383505521.0782042358
161.60105737091.23982898126-1.320376525472.419387965230.6285207491622.79482841394-0.428150620152-0.045700804043-0.114589818343-0.429970156341-0.062461043142-0.3613828389811.144413472190.5144126759030.4779582731680.665654755478-0.07620637650550.1672135764920.138391788021-0.005792180305490.42175747185980.451267425210.809855171624.1547552887
172.16915829595-0.1417994800240.8589127325273.950161309561.823546047126.40078596945-0.2055084590450.39844461186-0.583967849976-0.503943523363-0.143179267706-0.4933308567760.6367409413870.8130882012820.005984489181390.8151352016510.04737352484990.4048998160370.209324638815-0.06280624423140.69843223443787.28909617539.6386262585116.999673608
180.0805793975230.512209767440.2409780862016.045013472371.169279259771.93549979213-0.1697059885960.05476535770980.8173511653560.3711781859010.0934473976479-0.226604506743-1.421019395310.540589117260.020773631861.504157730790.237251503558-0.4416212824650.143668935156-0.1243562912060.69849733616180.1171230299-2.0361158086676.3410384157
190.793654475501-0.2900558299690.08857200230122.18666391147-0.5569014302441.17128203975-0.278312501917-0.3503686825510.3352428857770.250166233164-0.1753100570710.512131572412-0.855152078898-0.5642372645580.002400944194280.785127025260.282584899966-0.2023915102080.12504698241-0.003152782242390.41838801803973.163508354-11.460293954867.3550047894
203.18750090662-0.1148144984890.5573518927642.068542983840.2747074641641.99913048228-0.3008758830340.210561484602-0.0802822363563-0.366776591630.0711718748591-0.2628917946880.07616641276110.1705722743230.277118349960.4660916711130.05813683071680.05480025763160.2023603091760.01902329643680.33519700685683.602140636-26.060008835253.3936365458
211.41608960413-0.7400123893351.001301646982.30638736782-0.8575591208183.26761408227-0.209464908404-0.08077668874610.350617528230.0578415177867-0.011179610886-0.140694871882-0.704582496682-0.07762020432890.1990237713220.5145841298080.105467107601-0.09655622465760.180377353223-0.01573226189570.34448050539376.5496552107-15.019076297666.5140168262
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 83 )
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 142 )
4X-RAY DIFFRACTION4chain 'A' and (resid 143 through 194 )
5X-RAY DIFFRACTION5chain 'A' and (resid 195 through 265 )
6X-RAY DIFFRACTION6chain 'B' and (resid 24 through 58 )
7X-RAY DIFFRACTION7chain 'B' and (resid 59 through 142 )
8X-RAY DIFFRACTION8chain 'B' and (resid 143 through 194 )
9X-RAY DIFFRACTION9chain 'B' and (resid 195 through 265 )
10X-RAY DIFFRACTION10chain 'C' and (resid 24 through 48 )
11X-RAY DIFFRACTION11chain 'C' and (resid 49 through 82 )
12X-RAY DIFFRACTION12chain 'C' and (resid 83 through 102 )
13X-RAY DIFFRACTION13chain 'C' and (resid 103 through 142 )
14X-RAY DIFFRACTION14chain 'C' and (resid 143 through 194 )
15X-RAY DIFFRACTION15chain 'C' and (resid 195 through 212 )
16X-RAY DIFFRACTION16chain 'C' and (resid 213 through 243 )
17X-RAY DIFFRACTION17chain 'C' and (resid 244 through 265 )
18X-RAY DIFFRACTION18chain 'D' and (resid 24 through 48 )
19X-RAY DIFFRACTION19chain 'D' and (resid 49 through 82 )
20X-RAY DIFFRACTION20chain 'D' and (resid 83 through 130 )
21X-RAY DIFFRACTION21chain 'D' and (resid 131 through 265 )

+
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://pdbjlvh1.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