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- PDB-6pqc: Structure of cefotaxime-CDD-1 beta-lactamase complex -

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Basic information

Entry
Database: PDB / ID: 6pqc
TitleStructure of cefotaxime-CDD-1 beta-lactamase complex
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE Inhibitor / beta-lactamase / class D / Gram-positive / cefotaxime / HYDROLASE / HYDROLASE-HYDROLASE Inhibitor complex
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / membrane
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
CEFOTAXIME, C3' cleaved, open, bound form / Beta-lactamase
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSmith, C.A. / Vakulenko, S.B.
CitationJournal: J.Struct.Biol. / Year: 2019
Title: The crystal structures of CDD-1, the intrinsic class D beta-lactamase from the pathogenic Gram-positive bacterium Clostridioides difficile, and its complex with cefotaxime.
Authors: Stewart, N.K. / Smith, C.A. / Toth, M. / Stasyuk, A. / Vakulenko, S.B.
History
DepositionJul 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Mar 25, 2020Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)30,26212
Polymers28,7601
Non-polymers1,50111
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.513, 123.513, 123.513
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-402-

SO4

21A-579-

HOH

31A-593-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-lactamase


Mass: 28760.443 Da / Num. of mol.: 1 / Mutation: K238A, K244A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: blaR1_1, BGU81_18485, SAMEA3374989_01677 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A160YKM3, beta-lactamase

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Non-polymers , 5 types, 108 molecules

#2: Chemical ChemComp-CEF / CEFOTAXIME, C3' cleaved, open, bound form


Mass: 397.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15N5O5S2 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.73 Å3/Da / Density % sol: 55.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES, pH 7.0, 3.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.195 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.195 Å / Relative weight: 1
ReflectionResolution: 2.1→39.1 Å / Num. obs: 19410 / % possible obs: 99.9 % / Redundancy: 10.6 % / Rpim(I) all: 0.056 / Rrim(I) all: 0.175 / Net I/σ(I): 10.4
Reflection shellResolution: 2.1→2.16 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1542 / CC1/2: 0.568 / Rpim(I) all: 0.49

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EDM

6edm


Resolution: 2.1→39.058 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.06
RfactorNum. reflection% reflection
Rfree0.2187 1062 5.49 %
Rwork0.1733 --
obs0.1758 19360 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.91 Å2 / Biso mean: 37.3432 Å2 / Biso min: 19.21 Å2
Refinement stepCycle: final / Resolution: 2.1→39.058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2021 0 89 97 2207
Biso mean--71.82 38.75 -
Num. residues----252
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1001-2.19570.30271370.2506220099
2.1957-2.31140.28721200.212243100
2.3114-2.45620.25341140.20522268100
2.4562-2.64580.23481210.18422256100
2.6458-2.9120.22451430.18632261100
2.912-3.33320.21721400.17762273100
3.3332-4.19870.20531420.14022323100
4.1987-39.0580.18961450.16232474100
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)
10.8065-0.1667-0.12550.4619-0.55290.82030.10550.27650.1305-0.1686-0.0635-0.0199-0.0481-0.0830.00120.4093-0.02680.07440.3780.00670.354916.864126.8827-30.5682
20.7979-0.1861-0.11460.54760.21611.61250.04840.06630.02920.0043-0.019-0.01220.0354-0.029100.2331-0.0168-0.00680.2163-0.00130.223411.288714.0573-9.8027
30.11490.1717-0.2470.7744-0.09930.7842-0.03850.07270.1151-0.1072-0.0316-0.1734-0.23590.11960.00030.3424-0.01310.02550.3184-0.02530.370911.559627.5936-16.608
41.1354-0.5223-0.96551.5817-0.3441.28670.1560.13250.3468-0.1297-0.01040.1291-0.3618-0.0750.00040.29180.01590.03280.27170.00290.350812.407629.0845-22.2142
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 59 through 94 )A59 - 94
2X-RAY DIFFRACTION2chain 'A' and (resid 95 through 237 )A95 - 237
3X-RAY DIFFRACTION3chain 'A' and (resid 238 through 261 )A238 - 261
4X-RAY DIFFRACTION4chain 'A' and (resid 262 through 310 )A262 - 310

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