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- PDB-8b3m: Millisecond cryo-trapping by the spitrobot crystal plunger, CTXM-... -

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Basic information

Entry
Database: PDB / ID: 8b3m
TitleMillisecond cryo-trapping by the spitrobot crystal plunger, CTXM-14 Avibactam complex, SSX, 1 sec
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase / CTX-M-14 / time-resolved crystallography
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
Chem-NXL / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsMehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Doepke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. ...Mehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Doepke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. / Kollewe, M. / Rohde, H. / Wilmanns, M. / Tellkamp, F. / Schulz, E.C.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Commun / Year: 2023
Title: Millisecond cryo-trapping by the spitrobot crystal plunger simplifies time-resolved crystallography.
Authors: Mehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Dopke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. / Kollewe, M. / Rohde, H. / Wilmanns, M. / ...Authors: Mehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Dopke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. / Kollewe, M. / Rohde, H. / Wilmanns, M. / Tellkamp, F. / Schulz, E.C.
History
DepositionSep 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9252
Polymers27,6581
Non-polymers2671
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.850, 41.850, 232.850
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: 27658.154 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-NXL / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide / avibactam, bound form / NXL104, bound form


Mass: 267.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H13N3O6S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.21 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 4.5 / Details: 40% PEG8000, 200 mM LiSO4, 100 mM NaOAc, pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.6→77.62 Å / Num. obs: 18275 / % possible obs: 100 % / Redundancy: 532.7 % / Biso Wilson estimate: 21.53 Å2 / CC1/2: 0.9637 / CC star: 0.9907 / Net I/σ(I): 6.37
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 369 % / Num. unique obs: 1175284 / CC1/2: 0.73 / CC star: 0.9186 / % possible all: 100
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6gth

6gth


Resolution: 1.97→77.62 Å / SU ML: 0.2825 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.669
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2898 874 4.93 %
Rwork0.2444 16871 -
obs0.2466 17745 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.14 Å2
Refinement stepCycle: LAST / Resolution: 1.97→77.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1941 0 17 240 2198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312020
X-RAY DIFFRACTIONf_angle_d0.66632761
X-RAY DIFFRACTIONf_chiral_restr0.0449328
X-RAY DIFFRACTIONf_plane_restr0.0074364
X-RAY DIFFRACTIONf_dihedral_angle_d6.1573295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.090.39561460.30542735X-RAY DIFFRACTION98.97
2.09-2.250.35641540.26372708X-RAY DIFFRACTION99.55
2.26-2.480.31561370.27962763X-RAY DIFFRACTION99.69
2.48-2.840.29121560.25832780X-RAY DIFFRACTION99.93
2.84-3.580.27241290.23422857X-RAY DIFFRACTION99.97
3.58-77.620.24341520.21523028X-RAY DIFFRACTION99.91
Refinement TLS params.Method: refined / Origin x: 4.00138942196 Å / Origin y: 3.81404587362 Å / Origin z: -19.1152137962 Å
111213212223313233
T0.120227992485 Å2-0.0310735452238 Å20.0371633362297 Å2-0.224610245616 Å2-0.0301670305861 Å2--0.140381705521 Å2
L1.48306121125 °2-0.185082801596 °20.983118463162 °2-0.718494267067 °2-0.260576459731 °2--2.34942911421 °2
S0.0194209032516 Å °0.27786974031 Å °0.00713433458962 Å °-0.102549164999 Å °-0.0283356836155 Å °-0.097712965689 Å °-0.136414482106 Å °0.404367956803 Å °0.00356831469065 Å °
Refinement TLS groupSelection details: all

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