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- PDB-6edm: Structure of apo-CDD-1 beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 6edm
TitleStructure of apo-CDD-1 beta-lactamase
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase / class D / apo protein / ANTIMICROBIAL PROTEIN
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
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 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
DepositionAug 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Dec 4, 2019Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Mar 25, 2020Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last

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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)29,1696
Polymers28,6881
Non-polymers4805
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.201, 123.201, 123.201
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-606-

HOH

21A-662-

HOH

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Components

#1: Protein Beta-lactamase /


Mass: 28688.312 Da / Num. of mol.: 1
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
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O

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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: 2.72 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES, pH 7.0, 3.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.4→39 Å / Num. obs: 63142 / % possible obs: 99.9 % / Redundancy: 12.8 % / Biso Wilson estimate: 18.4 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.02 / Rrim(I) all: 0.071 / Net I/σ(I): 19.3
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 12.4 % / Mean I/σ(I) obs: 2.7 / CC1/2: 0.841 / Rpim(I) all: 0.265 / Rrim(I) all: 0.949 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→38.96 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1812 3100 4.92 %
Rwork0.1536 59971 -
obs0.155 63071 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.77 Å2 / Biso mean: 22.6843 Å2 / Biso min: 12 Å2
Refinement stepCycle: final / Resolution: 1.4→38.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2016 0 25 295 2336
Biso mean--63.81 31.74 -
Num. residues----251
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.42190.241490.18932617276699
1.4219-1.44520.19131400.157626652805100
1.4452-1.47010.19351350.150226942829100
1.4701-1.49690.19941410.144726762817100
1.4969-1.52560.17631370.139726962833100
1.5256-1.55680.1681310.137427072838100
1.5568-1.59060.19921440.137126682812100
1.5906-1.62760.20321440.130226912835100
1.6276-1.66830.16671210.133127002821100
1.6683-1.71350.18351370.132427132850100
1.7135-1.76390.16011290.134827072836100
1.7639-1.82080.17211410.136627032844100
1.8208-1.88590.17651330.147927142847100
1.8859-1.96140.16831470.150527122859100
1.9614-2.05070.18571420.143927202862100
2.0507-2.15880.1611410.151527232864100
2.1588-2.2940.19451200.148427742894100
2.294-2.47110.17381550.161427222877100
2.4711-2.71970.19571420.164127682910100
2.7197-3.11310.19811590.173427702929100
3.1131-3.92160.16381710.152928042975100
3.9216-38.97470.18661410.156930273168100

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