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- PDB-6pxx: Class D beta-lactamase in complex with beta-lactam antibiotic -

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Basic information

Entry
Database: PDB / ID: 6pxx
TitleClass D beta-lactamase in complex with beta-lactam antibiotic
ComponentsBeta-lactamase
KeywordsHYDROLASE/Antibiotic/Inhibitor / Inhibitor / lactamase / HYDROLASE / HYDROLASE-Antibiotic-Inhibitor complex
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / plasma 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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-5R7 / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
Authorsvan den Akker, F. / Kumar, V.
CitationJournal: Antibiotics / Year: 2019
Title: Structural Analysis of The OXA-48 Carbapenemase Bound to A "Poor" Carbapenem Substrate, Doripenem.
Authors: Papp-Wallace, K.M. / Kumar, V. / Zeiser, E.T. / Becka, S.A. / van den Akker, F.
History
DepositionJul 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,14212
Polymers60,6772
Non-polymers1,46510
Water10,845602
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-3 kcal/mol
Surface area20710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.770, 125.092, 45.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-lactamase


Mass: 30338.623 Da / Num. of mol.: 2 / Mutation: K73A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla OXA-48, blaOXA-48, KPE71T_00045 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6XEC0, beta-lactamase

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Non-polymers , 5 types, 612 molecules

#2: Chemical ChemComp-5R7 / (2~{S},3~{R})-3-methyl-2-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-4-[(3~{S},5~{S})-5-[(sulfamoylamino)meth yl]pyrrolidin-3-yl]sulfanyl-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid / Doripenem(open form, pyrroline tautomer form 3, SP3 connection to Thio as R isomer)


Mass: 422.520 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H26N4O6S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 602 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.46 Å3/Da / Density % sol: 49.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES pH 7.5-8.5, 4-10% PEG4000, and 8% 1-Butanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→40.42 Å / Num. obs: 96537 / % possible obs: 99.8 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.023 / Rrim(I) all: 0.083 / Net I/σ(I): 19.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.5-1.53120.5035634047040.9550.150.525599.7
8.22-40.3812.60.0487716970.9990.0120.04240.599.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
Aimless0.7.1data scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→40 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.956 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.06
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1715 4854 5 %RANDOM
Rwork0.1512 ---
obs0.1522 91607 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 110.07 Å2 / Biso mean: 15.15 Å2 / Biso min: 6.12 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3966 0 107 602 4675
Biso mean--35.7 28.64 -
Num. residues----486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134241
X-RAY DIFFRACTIONr_bond_other_d0.0010.0183841
X-RAY DIFFRACTIONr_angle_refined_deg1.7391.6645753
X-RAY DIFFRACTIONr_angle_other_deg1.6911.6068931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1035506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.91823.109238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.57715731
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0521524
X-RAY DIFFRACTIONr_chiral_restr0.0910.2541
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024695
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02913
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 357 -
Rwork0.199 6661 -
all-7018 -
obs--99.72 %

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