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- PDB-8b2o: Millisecond cryo-trapping by the spitrobot crystal plunger, CTX-M... -

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Basic information

Entry
Database: PDB / ID: 8b2o
TitleMillisecond cryo-trapping by the spitrobot crystal plunger, CTX-M-14 E166A, Ampicillin, 5 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-AIX / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 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 14, 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

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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)27,9522
Polymers27,6001
Non-polymers3511
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.812, 41.812, 232.962
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
Components on special symmetry positions
IDModelComponents
11A-474-

HOH

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Components

#1: Protein Beta-lactamase


Mass: 27600.119 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-AIX / (2R,4S)-2-[(1R)-1-{[(2R)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / AMPICILLIN (open form)


Mass: 351.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H21N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 42.25 %
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: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.856→77.654 Å / Num. obs: 200593 / % possible obs: 0.807 % / Redundancy: 15.3 % / Biso Wilson estimate: 18.97 Å2 / CC1/2: 0.998 / Net I/σ(I): 8.8
Reflection shellResolution: 1.856→2.094 Å / Num. unique obs: 10125 / CC1/2: 0.718 / % possible all: 37.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6gth

6gth


Resolution: 1.86→77.65 Å / SU ML: 0.1954 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.9746
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2535 654 4.99 %
Rwork0.2121 12444 -
obs0.2142 13098 61.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.91 Å2
Refinement stepCycle: LAST / Resolution: 1.86→77.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1937 0 24 146 2107
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00232021
X-RAY DIFFRACTIONf_angle_d0.54492762
X-RAY DIFFRACTIONf_chiral_restr0.04329
X-RAY DIFFRACTIONf_plane_restr0.0051363
X-RAY DIFFRACTIONf_dihedral_angle_d10.6796294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-20.387660.3436206X-RAY DIFFRACTION5.14
2-2.20.2657660.26461488X-RAY DIFFRACTION37.4
2.2-2.520.29631650.26063222X-RAY DIFFRACTION81.89
2.52-3.170.26582000.23833638X-RAY DIFFRACTION90.6
3.17-77.650.22842170.17163890X-RAY DIFFRACTION91.33
Refinement TLS params.Method: refined / Origin x: -4.13222624463 Å / Origin y: -4.32962394962 Å / Origin z: -19.0950026567 Å
111213212223313233
T-0.113091967261 Å2-0.00288014372719 Å2-0.0504025353256 Å2-0.210560428587 Å20.0261096366563 Å2--0.0825045353163 Å2
L1.4382552241 °2-0.501405280941 °2-1.30093407783 °2-1.97045814555 °20.940521453111 °2--6.57346185814 °2
S0.0813541038223 Å °0.273577328368 Å °0.0173696601891 Å °0.0239786561934 Å °-0.0267119354521 Å °0.0703469062628 Å °0.177045717606 Å °-0.953124478911 Å °-0.00564036804494 Å °
Refinement TLS groupSelection details: all

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