[English] 日本語
Yorodumi
- PDB-7s5s: CTX-M-15 WT in complex with BLIP WT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7s5s
TitleCTX-M-15 WT in complex with BLIP WT
Components
  • Beta-lactamase
  • Beta-lactamase inhibitory protein
KeywordsPROTEIN BINDING / Beta-lactamase / antibiotic resistance / Beta-lactamase inhibitory protein / protein complex
Function / homology
Function and homology information


regulation of beta-lactamase activity / beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / extracellular region
Similarity search - Function
Beta-lactamase-inhibitor protein BLIP / Beta-lactamase-inhibitor protein BLIP domain superfamily / Beta-lactamase inhibitor (BLIP) / BamE-like / : / 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-inhibitor protein BLIP / Beta-lactamase-inhibitor protein BLIP domain superfamily / Beta-lactamase inhibitor (BLIP) / BamE-like / : / 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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Beta-lactamase / Beta-lactamase inhibitory protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Streptomyces clavuligerus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLu, S. / Palzkill, T. / Hu, L.Y. / Prasad, B.V.V. / Sankaran, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI32956 United States
CitationJournal: Nat Commun / Year: 2022
Title: An active site loop toggles between conformations to control antibiotic hydrolysis and inhibition potency for CTX-M beta-lactamase drug-resistance enzymes.
Authors: Lu, S. / Hu, L. / Lin, H. / Judge, A. / Rivera, P. / Palaniappan, M. / Sankaran, B. / Wang, J. / Prasad, B.V.V. / Palzkill, T.
History
DepositionSep 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase inhibitory protein


Theoretical massNumber of molelcules
Total (without water)45,5672
Polymers45,5672
Non-polymers00
Water13,872770
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-9 kcal/mol
Surface area16410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.480, 81.860, 129.120
Angle α, β, γ (deg.)90.000, 95.943, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-536-

HOH

21B-230-

HOH

31B-471-

HOH

-
Components

#1: Protein Beta-lactamase


Mass: 28010.697 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla, blaCTX-M-15 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C7S9T0, beta-lactamase
#2: Protein Beta-lactamase inhibitory protein / BLIP


Mass: 17556.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P35804
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 770 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 20% w/v PEG3350, 0.2 M NaF, 0.1 M Bis-Tris-propane pH 6.5

-
Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.4→33.49 Å / Num. obs: 94955 / % possible obs: 98.37 % / Redundancy: 1.9 % / Biso Wilson estimate: 9.75 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 14.8
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 0.057 / Num. unique obs: 511

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4HBT and 3GMU

4hbt

3gmu


Resolution: 1.4→33.49 Å / SU ML: 0.0994 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 14.6787
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1663 2000 2.11 %
Rwork0.1512 92955 -
obs0.1516 94955 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.27 Å2
Refinement stepCycle: LAST / Resolution: 1.4→33.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3194 0 0 770 3964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00583251
X-RAY DIFFRACTIONf_angle_d0.94664415
X-RAY DIFFRACTIONf_chiral_restr0.0856507
X-RAY DIFFRACTIONf_plane_restr0.0076575
X-RAY DIFFRACTIONf_dihedral_angle_d5.7798459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.17831410.16676549X-RAY DIFFRACTION96.8
1.43-1.470.20281400.16366516X-RAY DIFFRACTION97.22
1.47-1.520.18251410.15856547X-RAY DIFFRACTION97.44
1.52-1.570.1771400.15446542X-RAY DIFFRACTION97.69
1.57-1.620.17421430.15196597X-RAY DIFFRACTION97.94
1.62-1.690.18491420.14746602X-RAY DIFFRACTION98.07
1.69-1.760.16371430.15436655X-RAY DIFFRACTION98.45
1.76-1.860.17091430.15296644X-RAY DIFFRACTION98.55
1.86-1.970.17041430.14726644X-RAY DIFFRACTION98.88
1.97-2.130.15161430.14136690X-RAY DIFFRACTION99.04
2.13-2.340.16471450.14576700X-RAY DIFFRACTION99.36
2.34-2.680.16331450.15566749X-RAY DIFFRACTION99.58
2.68-3.370.16081450.15316767X-RAY DIFFRACTION99.75
3.37-35.990.15931460.14976753X-RAY DIFFRACTION98.18
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)
10.404593766202-0.258135272933-0.1291280854621.513087534780.3713934253730.598740265421-0.0166301750071-0.159115835571-0.1309094851060.358022241870.105267284149-0.06145731044790.2178984422570.06489033540940.006345075337510.1544348942640.00898687474007-0.02984356029230.08361660073580.02682910705650.08987027854744.54917380803-38.7732513764-15.4013465242
20.546805067018-0.1893580620790.09113653091770.348346581974-0.134060275490.576963335758-0.0111287077675-0.04532136993490.04342448795340.1278902540660.000349300960731-0.09143451888-0.1165541496150.09047680928750.028057652030.114065544769-0.0150196341094-0.01463797284790.0853756036631-0.009032681957170.08496573069865.49364141921-20.9180061835-21.186086197
30.488118040413-0.1041783420990.127817403261.935922393041.514769558072.483728542740.04567829961950.08632621865870.323924705795-0.0995212829496-0.02023581409850.106239202686-0.4281114360470.04367487902680.03222281826420.1542559617890.004888548008370.02199413272050.0673217463048-0.01607053589560.154567885556-3.91661434626-5.30688565227-38.4695492152
40.7160112478150.137370865737-0.1497082235970.703385088907-0.2224074994061.370896163560.01636923521220.09850582121260.0296438681239-0.08768663259490.02840682255680.0714446283103-0.042006412092-0.1164956150240.004707558929930.07447359080450.0144379077317-0.003711029178420.0794504276926-0.001713559274290.0910995670076-8.44281609312-14.774844332-38.2868894537
50.40994549774-0.112266538414-0.07042439005910.527706333837-0.2977317753210.3960146048830.0214774501021-0.05086117789670.04767649005840.0824424754729-0.046776323666-0.076823432739-0.05915646827650.0680877479660.02970808405050.0758588289359-0.00912242471585-0.00683032210040.06671897844540.000985868813080.08507939861977.71225866135-19.3160408993-29.3965965176
61.72493767209-0.6823024419590.5826601859541.25622613258-0.409133415071.34993935418-0.0775664172299-0.319772188323-0.03561292349990.2942055462660.1458703514080.1295254658-0.341395337317-0.175154760010.08186750840310.1787498874870.001307218947320.02511902316020.101467097607-0.02153638304290.0798338230095-3.7782079358-11.0161717269-18.871934449
70.612333021548-0.0387529926541-0.08449434129530.8045353671650.09892690859980.6938998761850.0172875450958-0.00434038282193-0.01677166657530.0187585207597-0.01411063125040.137430902576-0.0567555764928-0.206099423415-0.008588094898030.07508018748010.0008052148975760.008583634307160.09408897101920.008436642869760.0734315567553-5.86863602911-27.6113845743-21.6709875987
80.92489092225-0.480424107596-0.5362751398551.673898843621.087322569622.366080214340.113370784044-0.0226474680271-0.03616140543540.0096584476463-0.0682828589017-0.04584047326310.0130631592566-0.1935335528760.02601151643250.0822972814613-0.00129260166994-0.009785020916330.08122118191560.0157697953780.0548520879244-0.896450409307-32.1955754776-21.5702467934
91.862602906080.1172141426771.054254869391.963284018210.5337594977023.581615463210.0304438345069-0.268312775189-0.07245534230740.3215871540610.03378663519190.1035003090870.0325055867692-0.328662225430.01188084841280.135039995851-0.006981531066720.01388752519120.1038621376560.02238980282270.0750825620295-4.11164848081-35.3486296446-15.4287277224
101.63991577425-1.177880008331.815684656931.84764315110.1945238874374.484607941690.0149385808622-0.0538226255481-0.1018080360920.113578117711-0.02982106319170.1947532427970.112597778947-0.160259753943-0.0958953819190.0709553785933-0.009695971509467.01041063498E-50.06421561840090.004490629651710.105711427323-21.9861841345-32.6400922046-44.3058046939
111.098166669410.166179101506-0.4246839618160.604104132529-0.7630799235481.161930800030.05177577354460.01495846192150.05553392682690.007957814230970.06482072382570.1030172342870.0387163445701-0.0915780429295-0.04960891865210.0550666883051-0.002820121593020.002811396578750.06561605024570.01245636781780.0868712510047-28.5656678037-24.4959686174-46.7121286587
120.849052339165-0.4587756668520.02229465428150.590954845947-0.07116285916620.339322245485-0.0380782383292-0.144541897314-0.02555323341440.06561449262620.06542502109020.0495291505081-0.0433062687327-0.0299603031322-0.02228197323130.06638358885390.012887649693-0.005252679589640.0624170854841-0.0007221324587740.0698311916924-18.333500201-24.0748415877-36.2067333857
130.759104512086-0.083472932382-0.2772813675051.073571819480.05371907503170.8692131120270.0379747723340.0498400604218-0.0155821290081-0.0387458409503-0.05181573968660.04955980399910.02125846599730.0119084986462-0.02037985092490.0421957877650.003262884296270.0005042374787350.05123433130620.000580136525360.057267943977-17.2339050758-24.324820707-48.2681944262
141.19070256963-0.623568965250.7658255254951.23489060337-0.5583668713341.187897566030.0519446503420.145961780656-0.149100909485-0.195912329735-0.1324906944910.01338917114110.1404485797760.12457804873-0.005424092953320.1051589125640.0230625740620.02033135577720.194101773194-0.005164488792980.0868098862503-0.784569509847-25.6487510228-62.6057868514
150.948320649833-0.2129188318210.3690986602220.6578465426-0.3909771754020.604048961139-0.006158752514050.0685799947333-0.061951512018-0.0545088324358-0.0330877127679-0.08615136364440.03149281720940.0808698399825-0.007802655114570.06677472599340.004745430475770.008245375788140.08498609933560.004168520147240.063429746245-13.4407921617-21.8649213311-55.2903691899
160.8930769151020.2780708461710.2031462163360.09623837252250.06477888350621.81316755378-0.0400284203602-0.182950894458-0.06377295916220.0418986519077-0.0934757575767-0.1853383427390.2765482556030.319041651367-0.01219004829430.1445123548760.04562050188210.01691937230860.1768273580210.01988529063330.168323423288-2.20046383542-34.8086247504-44.8015598934
171.99723302534-0.5595820410.8009846506711.28743538634-0.7198258592471.750360004450.007381962004160.00972963392281-0.128372912270.0407858205997-0.0371914129490.01472367687420.01426511556290.2569076105410.02478585242270.05016605534880.009409211173630.006507331349950.1394067139520.006550775034670.0521456805805-1.51670619125-21.8465922817-54.588423308
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 27 through 51 )AA27 - 511 - 25
22chain 'A' and (resid 52 through 86 )AA52 - 8626 - 60
33chain 'A' and (resid 87 through 101 )AA87 - 10161 - 75
44chain 'A' and (resid 102 through 129 )AA102 - 12976 - 103
55chain 'A' and (resid 130 through 194 )AA130 - 194104 - 168
66chain 'A' and (resid 195 through 213 )AA195 - 213169 - 187
77chain 'A' and (resid 214 through 250 )AA214 - 250188 - 224
88chain 'A' and (resid 251 through 273 )AA251 - 273225 - 247
99chain 'A' and (resid 274 through 288 )AA274 - 288248 - 262
1010chain 'B' and (resid 1 through 11 )BB1 - 111 - 11
1111chain 'B' and (resid 12 through 25 )BB12 - 2512 - 25
1212chain 'B' and (resid 26 through 52 )BB26 - 5226 - 52
1313chain 'B' and (resid 53 through 84 )BB53 - 8453 - 84
1414chain 'B' and (resid 85 through 104 )BB85 - 10485 - 104
1515chain 'B' and (resid 105 through 132 )BB105 - 132105 - 132
1616chain 'B' and (resid 133 through 145 )BB133 - 145133 - 145
1717chain 'B' and (resid 146 through 165 )BB146 - 165146 - 165

+
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