[English] 日本語
Yorodumi
- PDB-7k5v: OXA-48 bound by Compound 3.1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7k5v
TitleOXA-48 bound by Compound 3.1
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / beta-lactamase / carbapenemase / beta-lactamase inhibitor / complex / oxacillinase / HYDROLASE / 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
NAPHTHALENE-2,6-DISULFONIC ACID / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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
DepositionSep 17, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,35610
Polymers56,5902
Non-polymers7668
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-58 kcal/mol
Surface area19860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.922, 122.922, 161.143
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

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


Mass: 28295.053 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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
#2: Chemical ChemComp-BIH / NAPHTHALENE-2,6-DISULFONIC ACID / 2,6-NAPHTHALENEDISULFONIC ACID / 2,6-NAPHTHALENEDISULPHONIC ACID


Mass: 288.297 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H8O6S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.66 %
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: 0.999957 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999957 Å / Relative weight: 1
ReflectionResolution: 2.8→29.61 Å / Num. obs: 18259 / % possible obs: 99.65 % / Redundancy: 16 % / Biso Wilson estimate: 47.53 Å2 / CC1/2: 0.961 / Rmerge(I) obs: 0.138 / Net I/σ(I): 24.4
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.672 / Mean I/σ(I) obs: 5.17 / Num. unique obs: 1751

-
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: 2.8→29.61 Å / SU ML: 0.3231 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.0027
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2367 960 5.26 %
Rwork0.1923 17297 -
obs0.1946 18257 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.75 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3964 0 45 0 4009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00284103
X-RAY DIFFRACTIONf_angle_d0.58625558
X-RAY DIFFRACTIONf_chiral_restr0.0456578
X-RAY DIFFRACTIONf_plane_restr0.0025738
X-RAY DIFFRACTIONf_dihedral_angle_d26.9952557
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.950.32451260.27022382X-RAY DIFFRACTION98.51
2.95-3.130.33741450.27932410X-RAY DIFFRACTION100
3.13-3.370.30791290.2452428X-RAY DIFFRACTION100
3.37-3.710.25351530.21232432X-RAY DIFFRACTION100
3.71-4.250.20521330.17432477X-RAY DIFFRACTION100
4.25-5.350.20461380.15292504X-RAY DIFFRACTION99.92
5.35-29.610.17821360.15432664X-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)
11.02431630838-0.389750343051.450154989984.110138403370.5458071001882.71277512968-0.2371430450240.196700044045-0.113102934233-0.2243289157020.09034595041490.53455358889-0.83932411240.1464812018190.2273707522360.698638053642-0.0701366852587-0.1390725177430.375349308752-0.05590526860730.81445767763550.43803041326.61019304824-21.8781217478
23.621815193611.332158580730.04291999567884.669284126930.2761701220162.40569050931-0.493378434160.3039121853460.539718076263-0.006826374518780.2658002437650.165909221774-0.1242740524290.08819931043450.03513752202970.529711249404-0.113425882339-0.1079924716110.2781966331440.03885989438240.51922577730153.92393208790.942565407997-26.7027457304
31.71486593481.2945777210.2281236025612.65549264037-0.1830669019772.65598244763-0.102118164236-0.0195856923672-0.1520202744620.1053997675910.172126468862-0.09379990285420.404813786197-0.15825862866-0.02453956542780.3739636528890.001436930108090.005547322622980.285976092282-0.02780145812410.35312137250756.6570262384-20.5176585811-12.4445475568
45.39171545914-0.0385549200444-2.578567260424.3059116702-0.3870831555427.72850596425-0.0692313001324-0.198151475915-0.6315620224020.0138007422607-0.0218573461769-0.5306319518610.8084099752550.8367849279520.1301492075670.3808586246460.0114717463421-0.02659318740280.259028804225-0.05460255080660.33199714277867.969727309-21.9699191647-14.3210964251
51.655515906120.4592897433851.445056807632.61212168751.203841483771.72710217043-0.166011943180.1270451959240.103542249539-0.1599184327520.130416593037-0.2492709808310.09887240454250.3633637860530.05925965770.358416716164-0.06441401919540.0587562953270.269994674515-0.05639166467060.34015237349465.7574661765-11.1447967692-17.8050551772
61.10216629864-0.008459198833041.205329130891.423526821440.6229975557861.882157744970.04283054197690.1374848439360.00626616190985-0.005494209616750.129042760708-0.0458826972677-0.06152669380820.0920541640822-0.1927858723460.395796841985-0.08647448288060.06816542926690.290044471316-0.006241573056910.34315355938254.5605357639-15.7052114446-21.8883006699
71.629380028890.5359052711340.784090707063.280698229670.3126418544453.65692964896-0.2935278587460.03396889871490.195117280158-0.2039698183680.05956793719240.281087625902-0.311289044378-0.3736860450180.2242621591990.334340346329-0.0316800399979-0.01359706768540.249664838744-0.02796637842790.38990422665248.3150866677-4.74542483659-20.8858654362
83.228991806970.5762503318620.7074173728321.66061430882-0.1827431816253.475008048310.187908437208-0.4887220007150.4316891214810.5410891942570.220064826630.4446622429160.169820956533-1.16035436182-0.2409908402180.57822085008-0.4223372664090.2771903080380.761369042009-0.2102989955390.79916144630321.5077307318-35.7851080952-22.2949120024
93.252105396060.1261218890160.3491962561242.97792405233-0.09523966504681.49149491523-0.2117786800670.0417688800349-0.3507884648650.6629289100150.01550088113920.142653766670.0451747900604-0.06774356944170.09233715978110.630176237777-0.226658643970.08067130741970.4485371881-0.03764761169150.45657319253229.394923954-37.7189586176-22.5892504742
101.55282004845-0.0708220106032-0.2538258922951.54034601872-0.2535368582141.33929473854-0.05405544044280.2681423778990.0456291322757-0.1415833754740.029165703951-0.02118051229290.0434383373433-0.03062567116270.03655663072410.428237572165-0.117014810447-0.0158041691150.362548541199-0.02181634355710.3491515817240.5164443612-29.1369186401-44.4524143399
113.087322478460.5140724827270.8901048546222.289019870510.7476058421362.499169987240.21223885514-0.0358100303697-0.3827639478850.1441390543720.138005576749-0.005934953606150.191848529760.192208127233-0.3057724407820.341868637609-0.0950542066503-0.002293291406210.338031164849-0.04635971556190.32343269250142.7091630253-35.664131935-34.9479303521
122.330462050751.111452483430.7500760415452.539594211872.439724810053.45073055151-0.0435672961395-0.3139252057070.08128383823510.204199134435-0.1990231063240.3826506580610.0371055998817-0.4565528807680.1869764030960.383189000627-0.09229613403060.05475498724070.321194496438-0.005898790291790.33594943377534.3872526256-27.6266162605-29.995630435
134.85927834003-1.170692914033.106541655292.165899868280.06689062597155.53058958853-0.0537334766526-0.5527707534460.6986088899660.27929524809-0.2315917759040.36736768087-0.0907059459625-0.8659865901450.2698175867480.366354098379-0.1286500994560.1203706760220.381197372251-0.09080877043530.52510549203927.1361191823-27.894955533-26.2267224119
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 58 )
3X-RAY DIFFRACTION3chain 'A' and (resid 59 through 119 )
4X-RAY DIFFRACTION4chain 'A' and (resid 120 through 142 )
5X-RAY DIFFRACTION5chain 'A' and (resid 143 through 177 )
6X-RAY DIFFRACTION6chain 'A' and (resid 178 through 218 )
7X-RAY DIFFRACTION7chain 'A' and (resid 219 through 265 )
8X-RAY DIFFRACTION8chain 'B' and (resid 24 through 38 )
9X-RAY DIFFRACTION9chain 'B' and (resid 39 through 58 )
10X-RAY DIFFRACTION10chain 'B' and (resid 59 through 155 )
11X-RAY DIFFRACTION11chain 'B' and (resid 156 through 194 )
12X-RAY DIFFRACTION12chain 'B' and (resid 195 through 231 )
13X-RAY DIFFRACTION13chain 'B' and (resid 232 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://pdbjlc1.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