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- PDB-8rs1: CTX-M-14 measured via serial crystallography from a kapton HARE-c... -

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Basic information

Entry
Database: PDB / ID: 8rs1
TitleCTX-M-14 measured via serial crystallography from a kapton HARE-chip (125 micron)
ComponentsBeta-lactamase
KeywordsHYDROLASE / Lysozyme / enzyme / muramidase
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: 1.63 Å
AuthorsBosman, R. / Prester, A. / von Soosten, L. / Dibenedetto, S. / Bartels, K. / Sung, S. / von Stetten, D. / Mehrabi, P. / Schulz, E.C.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)458246365 Germany
German Research Foundation (DFG)451079909 Germany
German Federal Ministry for Economic Affairs and Energy01KI2114 Germany
CitationJournal: To Be Published
Title: Kapton-based HARE chips for fixed-target serial crystallography
Authors: Bosman, R. / Prester, A. / von Soosten, L. / Dibenedetto, S. / Bartels, K. / Sung, S. / von Stetten, D. / Mehrabi, P. / Blatter, G. / Lu, G. / Bernhard, S. / Osbild, M. / Schulz, E.C.
History
DepositionJan 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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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)27,8672
Polymers27,7711
Non-polymers961
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-17 kcal/mol
Surface area10670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.150, 42.150, 234.200
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: 27771.314 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ctx-m-14 / Production host: Escherichia coli (E. coli) / References: UniProt: D2D9A0, beta-lactamase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 43.12 %
Crystal growTemperature: 293 K / Method: batch mode
Details: CTX-M-14 solution (22 mg/ml) was mixed with 45% precipitant solution (40% PEG8000, 200mM lithium sulfate, 100mM sodium acetate, pH 4.5) and with 5% undiluted seed stock in batch crystallization

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.63→78.07 Å / Num. obs: 31624 / % possible obs: 100 % / Redundancy: 212.6 % / Biso Wilson estimate: 21.66 Å2 / CC1/2: 0.971 / CC star: 0.993 / R split: 0.137 / Net I/σ(I): 5.34
Reflection shellResolution: 1.63→1.68 Å / Mean I/σ(I) obs: 0.95 / Num. unique obs: 2675 / CC1/2: 0.551 / CC star: 0.843 / R split: 0.107 / % possible all: 100
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetSample holding: HARE-chip, Kapton

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrystFEL0.10.2data reduction
CrystFEL0.10.2data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→78.07 Å / SU ML: 0.1733 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.4565
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1954 1550 4.93 %
Rwork0.1647 29887 -
obs0.1662 31437 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.89 Å2
Refinement stepCycle: LAST / Resolution: 1.63→78.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1941 0 5 164 2110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00532132
X-RAY DIFFRACTIONf_angle_d0.77512926
X-RAY DIFFRACTIONf_chiral_restr0.049342
X-RAY DIFFRACTIONf_plane_restr0.0071393
X-RAY DIFFRACTIONf_dihedral_angle_d13.0127803
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.680.3147980.31812637X-RAY DIFFRACTION96.85
1.68-1.740.3381240.26132673X-RAY DIFFRACTION99.75
1.74-1.810.2771620.24052607X-RAY DIFFRACTION99.75
1.81-1.890.26411490.21262657X-RAY DIFFRACTION99.79
1.89-1.990.18621350.16682703X-RAY DIFFRACTION99.93
1.99-2.120.18091670.15992653X-RAY DIFFRACTION99.86
2.12-2.280.16961460.15632706X-RAY DIFFRACTION100
2.28-2.510.17091420.16342724X-RAY DIFFRACTION99.97
2.51-2.880.19961050.16532769X-RAY DIFFRACTION100
2.88-3.620.20741600.15522785X-RAY DIFFRACTION100
3.62-78.070.17061620.1372973X-RAY DIFFRACTION99.94
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)
14.9092123706-2.61515052612-1.289471672884.677109998831.03854261782.63655378559-0.1750367705140.289643702275-0.0766416676188-0.1010605094490.03098886593840.3585540422720.0886131544668-0.8810365680120.1456802321820.165883196871-0.00236523972712-0.02152082812080.2975332334750.01646669808360.161933556956-12.6033221531-11.11282805467.17083442969
2-0.143642097044-0.05026276462820.2943457705852.80435215860.8208990228771.86471104005-0.00986520694643-0.02813841924920.00957829136655-0.0427533826526-0.1565447480460.306485098956-0.221835492526-0.663596722890.0872943960770.1831978890390.06542765695470.003076463098230.260122269238-0.01080174364820.203802297283-11.2163425945-0.73932085088222.14348435
38.96945018004-1.72645864946-3.793673102831.435254884691.141710120885.28892074714-0.0753264028276-0.8871303443980.864896104790.08131327003190.234864923696-0.244103078638-0.9274717799570.240247843301-0.05515813820720.527318939328-0.0122089852960.008607220118990.22248984203-0.0352304196680.2580268766352.4595806919616.075585292434.4498227188
40.3280544648540.06504670537950.4752536649321.858894758060.382756733083.25820989513-0.0770646129312-0.03150127827640.0621072991665-0.1721149867330.110094214047-0.168181646729-0.7222602952710.127556899433-0.0143215911560.304612658018-0.01715767881450.02726255074710.118280951149-0.004719505007760.1994606622662.679034568148.7277302189327.6007551207
53.11478501604-2.221623048570.3769771116844.24703319841.502386448924.351812599780.178978622925-0.0511391602878-0.3119349510320.0846939730435-0.029476194530.007217813194930.124685143586-0.0698147365183-0.110468699860.140404045898-0.00291170230941-0.0261715275020.08812501906350.01457392419470.163990188197-1.27200807563-7.5682844435327.4260016014
64.04988090937-3.61400987080.88231866993.21133705401-0.6626051043291.818140964390.006562014239770.00113350060109-0.09727846991590.00647638600083-0.1135265664120.13178916679-0.179745894625-0.7220272012260.1270875803640.1652733584830.0654117964642-0.009780076184140.337829975529-0.02643432498530.204418955397-15.1077257215-1.0695811911222.2143944725
70.955221743913-0.4535279304880.4405269280711.566502149850.832983309382.08831010773-0.0505656200861-0.00874067991610.130646681972-0.5951650475210.03112874192210.105885338933-0.963073315816-0.329893192325-0.0008025384076960.4820313066090.188122599933-0.04195435580420.1818346944440.02997190899450.216181272167-9.073861924787.114598108915.412052993
84.70696329933-1.085825704371.360747253011.0599363506-0.3563598887570.753722006345-0.01540580728270.4852848960730.356996192899-0.509985351137-0.2887097767980.220179783385-0.532159884364-0.594570638763-0.1251004675420.3515520232190.223243785123-0.1047483656460.3586489176640.008813121736750.277618524574-13.43447789110.23926713310911.709687145
95.79572154199-3.866484899913.13075689086.60331195984-1.489397478837.678391117310.05154013035590.295565078988-0.0325058359883-0.32908034591-0.0702568363185-0.33620168088-0.149871037470.1092941849540.03216767059570.2169432445550.01377705660370.03739887324720.147702260707-0.01481458082970.162527303409-1.67336734622-7.188507230767.49125935797
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 28 through 51 )28 - 511 - 24
22chain 'A' and (resid 52 through 85 )52 - 8525 - 58
33chain 'A' and (resid 86 through 101 )86 - 10159 - 74
44chain 'A' and (resid 102 through 155 )102 - 15575 - 128
55chain 'A' and (resid 156 through 179 )156 - 179129 - 152
66chain 'A' and (resid 180 through 194 )180 - 194153 - 167
77chain 'A' and (resid 195 through 250 )195 - 250168 - 223
88chain 'A' and (resid 251 through 264 )251 - 264224 - 237
99chain 'A' and (resid 265 through 287 )265 - 287238 - 260

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