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- PDB-7vqn: Crystal structure of KPC-2 beta-lactamase complexed with hydrolyz... -

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Basic information

Entry
Database: PDB / ID: 7vqn
TitleCrystal structure of KPC-2 beta-lactamase complexed with hydrolyzed EXW-1
ComponentsCarbapenem-hydrolyzing beta-lactamase KPC
KeywordsHYDROLASE / KPC-2 beta-lactamase
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-7TC / Carbapenem-hydrolyzing beta-lactamase KPC-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsXie, H.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of KPC-2 beta-lactamase complexed with hydrolyzed EXW-1
Authors: Xie, H.X.
History
DepositionOct 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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: Carbapenem-hydrolyzing beta-lactamase KPC
B: Carbapenem-hydrolyzing beta-lactamase KPC
C: Carbapenem-hydrolyzing beta-lactamase KPC
D: Carbapenem-hydrolyzing beta-lactamase KPC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,15925
Polymers112,8834
Non-polymers2,27621
Water9,782543
1
A: Carbapenem-hydrolyzing beta-lactamase KPC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6055
Polymers28,2211
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carbapenem-hydrolyzing beta-lactamase KPC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7016
Polymers28,2211
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Carbapenem-hydrolyzing beta-lactamase KPC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0228
Polymers28,2211
Non-polymers8027
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Carbapenem-hydrolyzing beta-lactamase KPC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8306
Polymers28,2211
Non-polymers6095
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.193, 127.539, 76.303
Angle α, β, γ (deg.)90.000, 104.288, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 28220.750 Da / Num. of mol.: 4
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-7TC / (2R,3S)-3-methyl-4-methylidene-2-[(2S,3R)-3-oxidanyl-1-oxidanylidene-butan-2-yl]-2,3-dihydropyrrole-5-carboxylic acid


Mass: 225.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 543 / Source method: isolated from a natural source / Formula: H2O
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: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.34→50 Å / Num. obs: 50057 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 31.32 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.095 / Net I/σ(I): 10
Reflection shellResolution: 2.34→2.38 Å / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 2.72 / Num. unique obs: 2522 / CC1/2: 0.809 / Rpim(I) all: 0.284 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UJ4

5uj4


Resolution: 2.34→48.29 Å / SU ML: 0.2646 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.7782
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2059 2506 5.02 %
Rwork0.1696 47460 -
obs0.1714 49966 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.31 Å2
Refinement stepCycle: LAST / Resolution: 2.34→48.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7952 0 127 543 8622
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01378301
X-RAY DIFFRACTIONf_angle_d1.743111323
X-RAY DIFFRACTIONf_chiral_restr0.16641291
X-RAY DIFFRACTIONf_plane_restr0.00721460
X-RAY DIFFRACTIONf_dihedral_angle_d17.80882959
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.380.28431160.21842446X-RAY DIFFRACTION90.75
2.38-2.430.23891470.20762564X-RAY DIFFRACTION99.45
2.43-2.480.25861390.19562679X-RAY DIFFRACTION99.47
2.48-2.540.24441560.19242604X-RAY DIFFRACTION99.5
2.54-2.610.29591490.19542603X-RAY DIFFRACTION99.71
2.61-2.680.25751130.18582677X-RAY DIFFRACTION99.86
2.68-2.750.24971390.17432632X-RAY DIFFRACTION99.82
2.75-2.840.20951430.17972635X-RAY DIFFRACTION99.86
2.84-2.950.24551370.18952664X-RAY DIFFRACTION99.86
2.95-3.060.24341430.19012662X-RAY DIFFRACTION99.96
3.06-3.20.22941330.18272668X-RAY DIFFRACTION100
3.2-3.370.23151450.18162640X-RAY DIFFRACTION100
3.37-3.580.19551420.15952646X-RAY DIFFRACTION100
3.58-3.860.17381600.15292633X-RAY DIFFRACTION100
3.86-4.250.17631240.1482677X-RAY DIFFRACTION100
4.25-4.860.15021280.13572673X-RAY DIFFRACTION100
4.86-6.120.1951530.16882653X-RAY DIFFRACTION99.93
6.12-48.290.16411390.16282704X-RAY DIFFRACTION99.44

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