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- PDB-8ep6: Crystal Structure of the Beta-lactamase Class D from Chitinophaga... -

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Entry
Database: PDB / ID: 8ep6
TitleCrystal Structure of the Beta-lactamase Class D from Chitinophaga pinensis in complex with Avibactam
ComponentsBeta-lactamase Class D Cpin_0907
KeywordsHYDROLASE/INHIBITOR / beta lactamase class D / avibactam / antibiotic resistance / transpeptidase / Center for Structural Biology of Infectious Diseases / CSBID / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / HYDROLASE-INHIBITOR complex
Function / homologyACETIC ACID / Chem-NXL
Function and homology information
Biological speciesChitinophaga pinensis DSM 2588 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsMaltseva, N. / Kim, Y. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of the Beta-lactamase Class D from Chitinophaga pinensis in the complex with Avibactam.
Authors: Maltseva, N. / Kim, Y. / Endres, M. / Joachimiak, A.
History
DepositionOct 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Other / Structure summary / Category: audit_author / pdbx_SG_project

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase Class D Cpin_0907
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9353
Polymers29,6081
Non-polymers3272
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.816, 67.864, 68.698
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Beta-lactamase Class D Cpin_0907


Mass: 29607.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chitinophaga pinensis DSM 2588 (bacteria)
Strain: DSM 2588 / Gene: blaOXA, FEF09_01595 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): gold
#2: Chemical ChemComp-NXL / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide / avibactam, bound form / NXL104, bound form


Mass: 267.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H13N3O6S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
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: 1.96 Å3/Da / Density % sol: 37.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M imidazole, pH 6.5, 0.2 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 37009 / % possible obs: 99.5 % / Redundancy: 6.2 % / Biso Wilson estimate: 16.55 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.056 / Net I/σ(I): 16
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.845 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1838 / CC1/2: 0.769 / Rpim(I) all: 0.375 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→34.35 Å / SU ML: 0.1413 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 16.9991
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1867 1865 5.05 %
Rwork0.1449 35048 -
obs0.147 36913 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.61 Å2
Refinement stepCycle: LAST / Resolution: 1.5→34.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2028 0 21 95 2144
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01252177
X-RAY DIFFRACTIONf_angle_d1.24872947
X-RAY DIFFRACTIONf_chiral_restr0.0743305
X-RAY DIFFRACTIONf_plane_restr0.0108380
X-RAY DIFFRACTIONf_dihedral_angle_d13.3607823
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.24281450.16682544X-RAY DIFFRACTION95.69
1.54-1.590.22281590.15342648X-RAY DIFFRACTION99.12
1.59-1.640.21591500.13562670X-RAY DIFFRACTION99.44
1.64-1.70.20971210.13542678X-RAY DIFFRACTION99.5
1.7-1.760.20291430.13012653X-RAY DIFFRACTION99.4
1.76-1.840.17831400.12022688X-RAY DIFFRACTION99.89
1.84-1.940.18191290.11232717X-RAY DIFFRACTION99.68
1.94-2.060.15111180.11822701X-RAY DIFFRACTION99.47
2.06-2.220.17111560.12842712X-RAY DIFFRACTION99.69
2.22-2.450.17481370.1382723X-RAY DIFFRACTION99.79
2.45-2.80.20281670.15732693X-RAY DIFFRACTION99.48
2.8-3.530.20081380.16392753X-RAY DIFFRACTION98.8
3.53-34.350.17531620.15392868X-RAY DIFFRACTION99.08

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