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- PDB-5eec: Crystal structure of KPC-2 beta-lactamase in complex with the S02... -

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Basic information

Entry
Database: PDB / ID: 5eec
TitleCrystal structure of KPC-2 beta-lactamase in complex with the S02030 boronic acid inhibitor
ComponentsCarbapenem-hydrolyzing beta-lactamase KPC
KeywordsHYDROLASE/HYDROLASE INHIBITOR / transition state inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
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, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-ZXM / Carbapenem-hydrolyzing beta-lactamase KPC-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.87 Å
AuthorsNguyen, N.Q. / van den Akker, F.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2016
Title: Crystal Structures of KPC-2 and SHV-1 beta-Lactamases in Complex with the Boronic Acid Transition State Analog S02030.
Authors: Nguyen, N.Q. / Krishnan, N.P. / Rojas, L.J. / Prati, F. / Caselli, E. / Romagnoli, C. / Bonomo, R.A. / van den Akker, F.
History
DepositionOct 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbapenem-hydrolyzing beta-lactamase KPC
B: Carbapenem-hydrolyzing beta-lactamase KPC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,23310
Polymers57,0082
Non-polymers1,2258
Water7,548419
1
A: Carbapenem-hydrolyzing beta-lactamase KPC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1165
Polymers28,5041
Non-polymers6124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carbapenem-hydrolyzing beta-lactamase KPC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1165
Polymers28,5041
Non-polymers6124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.853, 77.883, 64.773
Angle α, β, γ (deg.)90.000, 108.670, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbapenem-hydrolyzing beta-lactamase KPC / Carbapenem-hydrolyzing beta-lactamase KPC-1


Mass: 28504.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla, kpc, kpc1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9F663, beta-lactamase
#2: Chemical ChemComp-ZXM / 1-{(2R)-2-(dihydroxyboranyl)-2-[(thiophen-2-ylacetyl)amino]ethyl}-1H-1,2,3-triazole-4-carboxylic acid


Mass: 324.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H13BN4O5S
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H2O
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: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 30% PEG 8000, 0.2 M lithium sulfate, and 0.1 M sodium acetate (pH 4.5) and 10:1 molar ratio with S02030 inhibitor

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.542 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 22, 2014
RadiationMonochromator: Cu filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 39177 / % possible obs: 96.7 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.107 / Χ2: 1.179 / Net I/av σ(I): 9.005 / Net I/σ(I): 9.7 / Num. measured all: 113565
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.85-1.922.30.39336131.01490.2
1.92-1.992.40.31636910.89491.5
1.99-2.082.40.26937711.10793.4
2.08-2.192.50.238430.995.3
2.19-2.332.60.18139491.10897.4
2.33-2.512.80.1440071.03299.3
2.51-2.7630.10940471.14199.9
2.76-3.163.30.08740381.172100
3.16-3.993.50.0740811.46399.9
3.99-503.90.06441371.4599.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
MOLREPphasing
RefinementResolution: 1.87→32.88 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.211 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2056 1959 5 %RANDOM
Rwork0.1657 ---
obs0.1678 37196 96.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 500 Å2 / Biso mean: 13.044 Å2 / Biso min: 2.95 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.87→32.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3960 0 83 419 4462
Biso mean--18.64 24.07 -
Num. residues----530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194184
X-RAY DIFFRACTIONr_bond_other_d0.0010.023952
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.9845701
X-RAY DIFFRACTIONr_angle_other_deg1.3623.0019057
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2625535
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.02923.494166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37815636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9881531
X-RAY DIFFRACTIONr_chiral_restr0.0830.2648
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214781
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02940
LS refinement shellResolution: 1.866→1.915 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 122 -
Rwork0.236 2437 -
all-2559 -
obs--85.9 %

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