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- PDB-8rei: CTX-M-14 measured via serial crystallography from a silicon HARE-chip. -

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Basic information

Entry
Database: PDB / ID: 8rei
TitleCTX-M-14 measured via serial crystallography from a silicon HARE-chip.
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: 1.62 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: Cell Rep Phys Sci / Year: 2024
Title: A systematic comparison of Kapton-based HARE chips for fixed-target serial crystallography
Authors: Bosman, R. / Prester, A. / Sung, S. / von Soosten, L. / Dibenedetto, S. / Bartels, K. / von Stetten, D. / Mehrabi, P. / Blatter, M. / Lu, G. / Suer, B. / Wilmanns, M. / Osbild, M. / Schulz, E.C.
History
DepositionDec 11, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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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
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-17 kcal/mol
Surface area10650 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.: 165 / 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 / pH: 4.5
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 ...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 setups Matthews Coefficient: 2.07 Percentage Solvent: 40.54

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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: 1.62→78.07 Å / Num. obs: 31752 / % possible obs: 95.05 % / Redundancy: 422.6 % / Biso Wilson estimate: 20.83 Å2 / CC1/2: 0.993 / CC star: 0.993 / R split: 0.1132 / Net I/σ(I): 7.48
Reflection shellResolution: 1.62→1.68 Å / Redundancy: 186.2 % / Mean I/σ(I) obs: 1.31 / Num. unique obs: 2803 / CC1/2: 0.019 / CC star: 0.019 / R split: 4.13 / % possible all: 87.27
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetSample holding: Hare-Chip , silicon
Serial crystallography data reductionCrystal hits: 27740 / Frames indexed: 39483

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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: 1.62→78.07 Å / SU ML: 0.1496 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.3306
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.188 1550 4.97 %
Rwork0.1553 29646 -
obs0.1569 31196 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.9 Å2
Refinement stepCycle: LAST / Resolution: 1.62→78.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1941 0 5 165 2111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01042123
X-RAY DIFFRACTIONf_angle_d1.04142913
X-RAY DIFFRACTIONf_chiral_restr0.0631341
X-RAY DIFFRACTIONf_plane_restr0.0102391
X-RAY DIFFRACTIONf_dihedral_angle_d13.2136796
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.680.3231850.29232139X-RAY DIFFRACTION79.43
1.68-1.740.25621230.2152707X-RAY DIFFRACTION99.75
1.74-1.810.2371580.20772643X-RAY DIFFRACTION99.86
1.81-1.890.24971550.19282682X-RAY DIFFRACTION99.79
1.89-1.990.17531360.1542710X-RAY DIFFRACTION99.82
1.99-2.110.17421700.14662719X-RAY DIFFRACTION99.9
2.11-2.280.16791420.15022694X-RAY DIFFRACTION99.96
2.28-2.510.16661510.16182742X-RAY DIFFRACTION99.93
2.51-2.870.20331070.15972805X-RAY DIFFRACTION99.97
2.87-3.610.20851600.15172804X-RAY DIFFRACTION100
3.61-78.070.16311630.13093001X-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)
13.56482968764-2.17551941341-1.340827257043.819469424970.8279439842422.40126022916-0.1681142948310.293853578353-0.0984726624493-0.2029694728710.03290699538760.3271236446020.141269080162-1.043172856270.1432811189270.164911449865-0.00365741596951-0.03317746418040.3289439321260.00790336618330.17507593102-12.6126878228-11.13149870647.18251625011
20.126990569191-0.1173857023380.2414771714492.817102048260.8242343813721.69771013774-0.00234519081968-0.0193777729340.0404007393338-0.023638642119-0.1228025722410.252328080441-0.215332788715-0.6328649742210.04386351502650.168809499070.057851912120.003560966386010.2498319992790.000732892915330.188698681873-11.2276868584-0.74080743061822.1400093288
33.85997408282-1.64989968125-3.403219815572.542826029441.304780882934.84381907049-0.113012352998-0.7946042527260.7552007052630.07466904216260.26298619119-0.23514483673-1.055478595120.178505395611-0.13084958610.5663698397980.01034409500910.00738171758610.259547729442-0.02454972226080.2584699808782.4287809608216.055641423634.4354125168
40.1738348401830.138425436780.5284626794111.637669895880.5309052609733.22170931374-0.0521549841174-0.02099061590640.0571451562312-0.1585900864030.094677262835-0.167947980327-0.7860874942820.111177500793-0.01336153126760.299613597985-0.0162474316730.03082744221660.105416260766-0.004169731514790.1898961396832.660782042998.6995934113227.5963136917
52.9118889915-2.059778236930.5703550006653.44413074031.555257311243.982554782950.169624476858-0.0425475479778-0.2886057023730.0863076185416-0.0164104877884-0.02137699354260.161081997503-0.0791464657271-0.1313673070010.145028802109-0.00142948492023-0.01903101749760.08362513950270.01607796285570.157195748159-1.29642791414-7.5912511750327.428320131
62.62466834606-3.82419991560.6790905071867.64247257234-0.8481320304641.18723668597-0.00475219054147-0.0111909594722-0.00807310852169-0.0188829256474-0.130989816060.235533674692-0.150139407444-0.7964566663440.05802441986450.1491131523330.0803370105087-0.01181856180890.361879640091-0.01739212593930.183943159103-15.1217233251-1.0734869535522.2000391105
71.0169363824-0.3026211089460.3762184999651.746131903820.7131585129271.77315663159-0.0509367116698-0.03097794197810.183879122278-0.6412005562410.1079425406070.040046670881-1.07294644575-0.2473477864720.02853445255840.5040604137240.226152757157-0.04408447676290.132930955550.05213381686880.174731430422-9.078039552117.1016978128915.4082246779
85.63120055834-1.626106405951.275444029491.91501902719-0.6852181642230.463157545144-0.1460154945320.3989919071660.22850784944-0.53813413176-0.237871684570.234896473196-0.700679760008-0.728484389064-0.06282823290690.3779559951390.294702255508-0.1435091311470.380967597815-0.008349119007490.255076718196-13.41781252730.24803679123911.7024338104
98.13200871491-4.241459617213.185095434196.05149153408-1.368212956546.67361742514-0.02629444498410.2926016909140.137797462366-0.246206975423-0.044833070473-0.421033278228-0.1652332651120.1560394866880.08966748154160.1906477099440.02300546272550.03047720772440.134194469248-0.02250299927280.125435800584-1.41173638902-7.404932942697.79300624452
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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