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- PDB-8af8: Room temperature SSX crystal structure of CTX-M-14 (5K dataset) -

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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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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


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


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

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Experimental details

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Experiment

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

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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.

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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

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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)

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