[English] 日本語
Yorodumi
- PDB-8af8: Room temperature SSX crystal structure of CTX-M-14 (5K dataset) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8af8
TitleRoom temperature SSX crystal structure of CTX-M-14 (5K dataset)
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase / serial crystallography / SSX / TapeDrive
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
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/transpeptidase-like
Similarity search - Domain/homology
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsOberthuer, D. / Perbandt, M. / Prester, A. / Rohde, H. / Betzel, C. / Yefanov, O.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Iucrj / Year: 2022
Title: Rapid and efficient room-temperature serial synchrotron crystallography using the CFEL TapeDrive.
Authors: Zielinski, K.A. / Prester, A. / Andaleeb, H. / Bui, S. / Yefanov, O. / Catapano, L. / Henkel, A. / Wiedorn, M.O. / Lorbeer, O. / Crosas, E. / Meyer, J. / Mariani, V. / Domaracky, M. / White, ...Authors: Zielinski, K.A. / Prester, A. / Andaleeb, H. / Bui, S. / Yefanov, O. / Catapano, L. / Henkel, A. / Wiedorn, M.O. / Lorbeer, O. / Crosas, E. / Meyer, J. / Mariani, V. / Domaracky, M. / White, T.A. / Fleckenstein, H. / Sarrou, I. / Werner, N. / Betzel, C. / Rohde, H. / Aepfelbacher, M. / Chapman, H.N. / Perbandt, M. / Steiner, R.A. / Oberthuer, D.
History
DepositionJul 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Apr 3, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0754
Polymers27,7871
Non-polymers2883
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint-28 kcal/mol
Surface area10770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.160, 42.160, 234.350
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

-
Components

#1: Protein Beta-lactamase /


Mass: 27787.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: blaCTX-M-14, bla_2, SAMEA3512100_05103, SAMEA3727679_05436
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7BGE9, beta-lactamase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.15 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 4.5
Details: CTX-M-14 was produced, purified and crystallized as before, with a slight modification in crystallization conditions to obtain slightly bigger crystals which roughly match the X-ray focal ...Details: CTX-M-14 was produced, purified and crystallized as before, with a slight modification in crystallization conditions to obtain slightly bigger crystals which roughly match the X-ray focal spot. For this purpose, a 50% CTX-M-14 solution (22 mg/ml) was mixed with a 45% precipitant solution (40% PEG8000, 200 mM lithium sulfate, 100 mM sodium acetate, pH 4.5) and with a 5% undiluted seed stock in batch crystallization setups, resulting in crystals with a homogeneous size distribution of 11-15 um after 90 minutes. The crystals were centrifuged at 200xg for 5 min and the supernatant was replaced with a stabilization buffer (28% PEG8000, 140 mM lithium sulfate, 70 mM sodium acetate, pH 4.5) to stop further crystal growth.

-
Data collection

DiffractionMean temperature: 295 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.55→17.77 Å / Num. obs: 36495 / % possible obs: 99.98 % / Redundancy: 149 % / Biso Wilson estimate: 23.14 Å2 / CC1/2: 0.907 / CC star: 0.975 / R split: 0.23 / Net I/σ(I): 3.75
Reflection shellResolution: 1.55→1.58 Å / Mean I/σ(I) obs: 0.63 / Num. unique obs: 3514 / CC1/2: 0.262 / CC star: 0.644 / R split: 1.7
Serial crystallography sample deliveryDescription: TapeDrive / Method: injection
Serial crystallography sample delivery injectionDescription: TapeDrive / Flow rate: 1 µL/min / Injector diameter: 180 µm
Serial crystallography data reductionFrames total: 5000 / Lattices indexed: 5109

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GTH

6gth


Resolution: 1.55→14.98 Å / SU ML: 0.2082 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.0439
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1988 765 2.1 %
Rwork0.1758 35697 -
obs0.1763 36462 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.56 Å2
Refinement stepCycle: LAST / Resolution: 1.55→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1940 0 15 209 2164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01132048
X-RAY DIFFRACTIONf_angle_d1.17612801
X-RAY DIFFRACTIONf_chiral_restr0.0604328
X-RAY DIFFRACTIONf_plane_restr0.0079370
X-RAY DIFFRACTIONf_dihedral_angle_d11.9532295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.670.32951500.35276968X-RAY DIFFRACTION99.61
1.67-1.840.28781500.28237026X-RAY DIFFRACTION100
1.84-2.10.21981530.1897054X-RAY DIFFRACTION100
2.1-2.650.18431510.16817166X-RAY DIFFRACTION100
2.65-14.980.17561610.14667483X-RAY DIFFRACTION99.9
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)
12.1969295884-1.32796157054-0.1845806448874.842333174191.118098746045.22616676242-0.00321170641422-0.04892089608270.229526972155-0.0875965801410.101540152165-0.656175024091-0.2831303647760.945382625314-0.08387029185930.245356129856-0.07458944076750.001814160901880.371973628591-0.00806702240880.28580802949813.344497694213.41106187914.0747807324
22.41952831339-0.5919116645030.2602292138362.077236168520.1374984949181.18686887945-0.08259652072530.174527997138-0.0611763967791-0.222736174337-0.0956601576944-0.4356475742310.1085587006570.5223544208150.07125923320420.2597336439120.07279023408440.08075769500580.3820934354680.04549609204270.33291635752614.91713028245.8085988662111.9875220936
36.95359144546-3.725906962461.024259862565.87358933111-0.1015720756323.95323135531-0.07114278526630.2151926737580.1283610769540.172358018966-0.220833089064-1.10496315785-0.2883528965491.030890637940.1787700288470.262108093836-0.04216270079180.009372120542920.4274651083240.04749967803510.37161077225218.71452150878.3243523289213.4156673368
40.251497813274-0.541451597269-0.02475469993352.67165579518-1.037382440522.08379755842-0.000674544915823-0.0406175716218-0.08593137782040.00992764147611-0.03671689392970.003094362645360.2184616551610.321661146298-0.02138033758770.2098796629870.0462422800794-0.009912698133370.197319683911-0.002012499415480.1965241161767.78971091521-1.9983690376226.6726064221
52.9282292834-1.087252602282.940848547952.05422387613-0.1997535668694.637682791650.00941663508837-0.577041263912-0.7149101328240.8896587812380.717247340526-0.196988038620.4115768914850.256736137698-0.03667757964830.6630057537940.201503087013-0.07053564451730.309109584791-0.009407494228710.379037656287.13536988367-19.028157587935.6080349517
63.01535154685-2.814894427823.854187059794.86029537543-3.034106428025.07438625546-0.396735770819-0.856788178031-0.1694518389170.5554851195560.3389957732670.05867169758780.571834428089-0.4887795268790.1978728064110.425096130598-0.0335477673360.003002804309550.2726960668120.06199793258580.370545295545-7.29439258066-15.882054270933.5475886868
71.420219816240.704182098027-0.7969337257022.89566708659-0.903887555422.46781039324-0.09370072302680.2351675282130.0926447388757-0.4025070025460.3785624607990.6765656856890.437947351539-0.598043608641-0.2666765129880.377486508054-0.0753365341461-0.07243070373270.3270692102760.02410208885260.393837956936-12.0396625122-10.892062193524.6410640458
81.19534357480.182471963298-0.4718893822372.11957106885-1.298118093931.989794628-0.0326747376699-0.0583596979648-0.0372355411865-0.2366914705330.1751782336020.06318191269550.733687614377-0.0254194026853-0.1157524398110.469501077711-0.0109064578971-0.03718508939870.1783713342650.003471005810690.280677009641-1.59896966496-13.771411551724.3181622565
92.63736772970.04636242165320.8870041338092.026147027150.1362442517163.884671093790.04125132477460.0676189400015-0.0822535017440.005150492441270.1545853290840.1481777518250.17207324101-0.206549329981-0.1416160860930.261148207571-0.0157023410127-0.04145319584970.1728292618290.007551786931710.247170138099-4.35547650586-6.774195245727.8946572231
102.623431900560.433676223625-0.8418590740931.60162415916-0.4823942085532.11378441308-0.128927273748-0.2047276666790.0855177346659-0.0469717470.0838494285675-0.04111513869850.2379402670260.389494534040.04774577738110.2184102786870.041995219964-0.02645228981890.247224238892-0.01690367180550.216834308437.7245603074-1.4642508308333.9237092905
119.795855163110.0248116523929-6.040635315248.85079786112-0.4908166140234.73803249384-0.0356470585997-0.4202000627350.3519357411960.1176682516960.070161018645-0.202845143098-0.1722780447220.404047092723-0.006173556134110.240011650621-0.00957990794903-0.02756564821080.249916753329-0.02531718676610.1819537149927.728665846996.3932683671530.2791131242
121.26483527879-0.105524598472-0.3758494484332.04184441197-0.935026529572.074069868060.1457701852530.1272257344270.01629824614720.1637116629360.1742621188230.106735825848-0.121850393752-0.206922814133-0.2436833865070.2350396689930.02337720184170.02870831838960.1789033040970.01232941982760.299558632824-4.220338699587.0952931297525.4651463689
134.01594018919-1.4413127373-1.868750518842.94719162620.676026581844.408376512860.233760997988-0.1404374228830.196422537994-0.0303466588546-0.0862276266049-0.0768229100489-0.4097433332720.293482450309-0.1614965353590.224264856922-0.03531797636040.01575957782060.189043397662-0.007082946714860.1964294992857.16113306349.3108537083824.518943704
145.75867164222-5.73633629398-1.498827931847.55735913837-0.5531856558953.45429769492-0.164308252741-0.0135204732447-0.03756790146260.1347889291010.0831254147896-0.3831151754790.5549500016460.7634028919380.05477999916010.2567630809230.1183674569370.01175788964020.3880508832420.01617756986070.25071552771616.8118596517-3.2492481562621.8339348984
151.3858080414-0.8200069056160.2429939610472.53712327594-1.273931950762.024391189050.106033355778-0.121962947607-0.271568316189-0.4390528789310.01691954243810.05183977944810.9330517608990.396098789808-0.08702289232330.4808306913130.1613044038380.01125026873260.269869144682-0.01342959418790.25773307484810.6725649125-12.69873402620.7438889723
160.449654297507-0.1762459477240.326319887491.927040031160.5247723304540.4905689115980.1674841056410.377377892585-0.165942265149-0.588508944164-0.100688792707-0.0345805477420.7144679577440.1434832217480.08060856714620.551144325960.1469988341560.02872096950470.289593201237-0.024775369450.2367220080638.0290637801-5.513668561198.0758088448
172.67861202557-0.962255713662-0.2836861212872.17411871977-0.710742302342.71279535334-0.08875057564440.135238124011-0.0137249006543-0.202746564498-0.0343392800847-0.1583403278110.3474033295180.3720216565890.01048931108120.2768413447770.06286584939070.03769218963940.240566594685-0.0185319503260.2355728002778.878191878851.0553730947412.8268771473
182.00194525782.364086356150.09308621307241.283253656392.473456443867.862314428450.2001282099960.3550461427780.2961364169380.04768468805890.1146452987281.15310390322-1.17539456258-1.02171280645-0.1873376035180.3246847749280.135510953503-0.0001169940014090.4250332632670.06545659790210.387422932845-8.3150264936513.717344738413.3912597309
192.00470116364-5.11939866526-2.587606180283.192749099252.285415504912.95496123144-0.08092314981640.238282639411-0.358041321697-0.5455943847820.1045450813180.933970936430.0802797565927-0.943020803819-0.09065216812540.2977141396360.0396096031053-0.08473611991150.39943711316-0.001753991009260.369954083108-4.246191034175.955005995227.77919644992
209.32274717706-1.00422311479-0.1813376904186.193086831120.5866243842294.758403285960.07875239134250.4187411192030.123982587909-0.577069683061-0.157051625542-0.3743854143070.3738575554750.7356909785850.04006924113090.3609002092360.08571642050320.04764502459390.3101882791470.03037179976740.19974703477410.63402746453.550810148783.27403293234
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 27:39)
2X-RAY DIFFRACTION2(chain A and resid 40:53)
3X-RAY DIFFRACTION3(chain A and resid 54:61)
4X-RAY DIFFRACTION4(chain A and resid 62:86)
5X-RAY DIFFRACTION5(chain A and resid 87:91)
6X-RAY DIFFRACTION6(chain A and resid 92:99)
7X-RAY DIFFRACTION7(chain A and resid 100:115)
8X-RAY DIFFRACTION8(chain A and resid 116:130)
9X-RAY DIFFRACTION9(chain A and resid 131:138)
10X-RAY DIFFRACTION10(chain A and resid 139:157)
11X-RAY DIFFRACTION11(chain A and resid 158:163)
12X-RAY DIFFRACTION12(chain A and resid 164:175)
13X-RAY DIFFRACTION13(chain A and resid 176:185)
14X-RAY DIFFRACTION14(chain A and resid 186:196)
15X-RAY DIFFRACTION15(chain A and resid 197:218)
16X-RAY DIFFRACTION16(chain A and resid 219:237)
17X-RAY DIFFRACTION17(chain A and resid 238:267)
18X-RAY DIFFRACTION18(chain A and resid 268:271)
19X-RAY DIFFRACTION19(chain A and resid 272:275)
20X-RAY DIFFRACTION20(chain A and resid 276:289)

+
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