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- PDB-9ryd: Room temperature serial structure of CTX-M-15 collected on tape d... -

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Basic information

Entry
Database: PDB / ID: 9ryd
TitleRoom temperature serial structure of CTX-M-15 collected on tape drive at Diamond Light Source VMXi
ComponentsBeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / beta-lactamase / antibiotics / serial / room temperature / microcrystals
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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 / FOURIER SYNTHESIS / Resolution: 1.83 Å
AuthorsHinchliffe, P. / Tooke, C.L. / Spencer, J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)101021207European Union
CitationJournal: To Be Published
Title: Room temperature serial structure of CTX-M-15 collected on tape drive at Diamond Light Source VMXi
Authors: Hinchliffe, P. / Tooke, C.L. / Spencer, J.
History
DepositionJul 15, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2026Provider: 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)28,5445
Polymers28,2931
Non-polymers2514
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.908, 45.553, 117.446
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Beta-lactamase


Mass: 28292.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaCTX-M-15 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Solu / References: UniProt: G3G192, beta-lactamase
#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.12 Å3/Da / Density % sol: 42.06 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 2.0 M ammonium sulphate, 0.1 M Tris 8.0

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Data collection

DiffractionMean temperature: 294 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: VMXi / Wavelength: 0.7749 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Jan 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.83→58.72 Å / Num. obs: 21932 / % possible obs: 99.8 % / Redundancy: 91.9 % / Biso Wilson estimate: 17.62 Å2 / CC1/2: 0.966 / R split: 0.117 / Net I/σ(I): 9.2
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 11.1 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1038 / CC1/2: 0.305 / R split: 1.087 / % possible all: 98.2
Serial crystallography sample deliveryDescription: Tape drive / Method: injection
Serial crystallography data reductionLattices indexed: 20556

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.83→58.72 Å / SU ML: 0.2419 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.05
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1994 1144 5.23 %
Rwork0.1658 20721 -
obs0.1676 21865 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.39 Å2
Refinement stepCycle: LAST / Resolution: 1.83→58.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1943 0 12 191 2146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512017
X-RAY DIFFRACTIONf_angle_d0.75492746
X-RAY DIFFRACTIONf_chiral_restr0.0486319
X-RAY DIFFRACTIONf_plane_restr0.0072362
X-RAY DIFFRACTIONf_dihedral_angle_d12.5694755
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.910.36521340.31082444X-RAY DIFFRACTION96.27
1.91-2.010.24921630.20362521X-RAY DIFFRACTION99.81
2.01-2.140.2531220.1782588X-RAY DIFFRACTION99.96
2.14-2.310.18141290.12992591X-RAY DIFFRACTION100
2.31-2.540.16671410.13482590X-RAY DIFFRACTION100
2.54-2.90.17721350.14672607X-RAY DIFFRACTION100
2.91-3.660.17981610.14632606X-RAY DIFFRACTION100
3.66-58.720.19221590.18052774X-RAY DIFFRACTION99.97
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)
11.964846052981.03774927068-1.016134935282.39057407399-1.327900162972.51945641142-0.2042961964730.295569838899-0.278196815748-0.3474624443250.09246395836-0.2223241186360.4298764861540.03522534864970.1108192357130.168557958621-0.002014675728310.01780765134080.162969675378-0.01714631013370.144188186354.91526415895-20.52893155948.7309068734
22.07555389445-0.2472955427720.01379189706133.87024936036-1.51004865671.75994651672-0.0724611360484-0.383434151480.09316037763110.4718917973320.1401461891140.309136273925-0.0472946678389-0.0688390434178-0.07364231252350.147332700552-0.0248190968550.006652482204770.128054670789-0.0345082336320.16002078935-12.1400929945-6.0671292388729.5812806189
38.75001476124-1.8202413223-2.470949129868.12753501472.523167140465.10742025295-0.1253663298670.4737487948780.334248486931-0.4311335845040.0488442866010.591209935339-0.324204046511-0.1603679707240.0996226489910.19021423044-0.0117892993786-0.04731477336670.1100656351740.03087475616340.185677924582-15.68017793947.7414837127618.4871088356
41.02300993011-0.345671462907-0.3986666860651.363352857840.1357900131991.022978510550.0241945057993-0.03883180393870.028086896767-0.003030905397260.01696410427110.0680450602624-0.0116329052520.0482157954995-0.04275926610.0930494576195-0.0086061847252-0.007016284162950.0935142447183-0.007762519774470.0930622232806-3.00480345152-6.1186276675122.8660501155
56.01174056926-3.256605939121.2686502261.93413053757-0.4689177096473.67632726242-0.00220861060869-0.0979537536854-0.3265690249560.1490179119070.07872039459530.2745288076620.0998186336487-0.0715079979219-0.09418885243010.134305731179-0.04349257063990.007055666286610.087279664160.004477408197320.15401456649-14.3876663684-17.136096174225.5804880963
62.395176837711.139952203590.1044858530462.163713727680.3317456910991.967731172350.0009466305768390.0314878122450.00595640444102-0.112024897449-0.04913657126080.1826500857310.0447048287057-0.108611975530.05445970854420.09376927558010.00720853489805-0.008598044227590.095182878392-0.005845499178150.077945228467-8.96252256813-14.6755344499.66136275261
75.032780131131.95675074953-2.168350715332.35163510227-2.068471306871.99808719717-0.1325596837190.218288385133-0.144567048104-0.315974672290.2969548273690.2768182731410.387325557471-0.0589608905032-0.1403891090550.221000978929-0.0166937511094-0.04362011842240.119140881151-0.01604780138220.0949786144282-5.88133251047-22.300291490911.8659138244
85.491973137764.03790122337-0.659589856786.62292523899-1.766085915873.65932074858-0.07135912222660.2899936202080.160494222224-0.2982355016190.1591393044880.2834205610770.0431733549299-0.16296859533-0.0694243221170.1301758529260.01898841623050.02709770332780.149891460561-0.02793492356060.049868682712-0.689084400338-12.56993159762.26229589295
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 68 )28 - 681 - 41
22chain 'A' and (resid 69 through 96 )69 - 9642 - 69
33chain 'A' and (resid 97 through 115 )97 - 11570 - 88
44chain 'A' and (resid 116 through 194 )116 - 19489 - 167
55chain 'A' and (resid 195 through 213 )195 - 213168 - 186
66chain 'A' and (resid 214 through 250 )214 - 250187 - 223
77chain 'A' and (resid 251 through 264 )251 - 264224 - 237
88chain 'A' and (resid 265 through 287 )265 - 287238 - 260

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