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- PDB-5za2: Fox-4 beta-lactamase complexed with avibactam -

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Basic information

Entry
Database: PDB / ID: 5za2
TitleFox-4 beta-lactamase complexed with avibactam
Components(Beta-lactamase) x 2
KeywordsHYDROLASE / beta-lactamase drug resistance
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic / metal ion binding
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NXL / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.503 Å
AuthorsNukaga, M. / Hoshino, T. / Papp-Wallace, K.M. / Bonomo, R.A.
Funding support Japan, United States, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science26460534 Japan
United States Departtment of Veterans AffairsBX002872; BX001974 United States
National Institutes of HealthR21AI114508, R01AI100560, R01AI063517, and R01AI072219 United States
CitationJournal: Antimicrob. Agents Chemother. / Year: 2018
Title: Probing the Mechanism of Inactivation of the FOX-4 Cephamycinase by Avibactam
Authors: Nukaga, M. / Papp-Wallace, K.M. / Hoshino, T. / Lefurgy, S.T. / Bethel, C.R. / Barnes, M.D. / Zeiser, E.T. / Johnson, J.K. / Bonomo, R.A.
History
DepositionFeb 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume

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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)77,3068
Polymers76,2572
Non-polymers1,0496
Water9,548530
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8226
Polymers38,0401
Non-polymers7825
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint1 kcal/mol
Surface area13500 Å2
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4842
Polymers38,2171
Non-polymers2671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.391, 85.908, 144.227
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Beta-lactamase /


Mass: 38039.973 Da / Num. of mol.: 1 / Fragment: UNP residues 29-382
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fox-4 / Plasmid: pET50b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q9L387, beta-lactamase
#2: Protein Beta-lactamase /


Mass: 38217.066 Da / Num. of mol.: 1 / Fragment: UNP residues 28-382
Source method: isolated from a genetically manipulated source
Details: In molB of the structure, Ser58 was partially phosphorilated. And partially inhibited(cobalently bonded to avibactam(NXL))
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fox-4 / Plasmid: pET50b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)plys / References: UniProt: Q9L387, beta-lactamase

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Non-polymers , 4 types, 536 molecules

#3: Chemical ChemComp-NXL / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide / avibactam, bound form, NXL104, bound form / Avibactam


Mass: 267.260 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H13N3O6S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic, inhibitor*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


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


Mass: 18.015 Da / Num. of mol.: 530 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsThere are both SEP and Ser at the same position in the chain B. The Ser64 is linked to NXL.

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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: 2.08 Å3/Da / Density % sol: 40.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG8000, MOPS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 101610 / % possible obs: 99.2 % / Redundancy: 7.5 % / Net I/σ(I): 14.95
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5036 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIX(1.10.1_2155)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.503→37.624 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.02
RfactorNum. reflection% reflection
Rfree0.2137 1999 1.97 %
Rwork0.1893 --
obs0.1898 101496 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.503→37.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5362 0 67 530 5959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055641
X-RAY DIFFRACTIONf_angle_d0.8467682
X-RAY DIFFRACTIONf_dihedral_angle_d12.1023338
X-RAY DIFFRACTIONf_chiral_restr0.052835
X-RAY DIFFRACTIONf_plane_restr0.006996
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5027-1.54030.29721400.26357002X-RAY DIFFRACTION99
1.5403-1.5820.25711420.23597051X-RAY DIFFRACTION100
1.582-1.62850.22371430.21827103X-RAY DIFFRACTION100
1.6285-1.68110.2261430.20267101X-RAY DIFFRACTION100
1.6811-1.74120.20331420.19777094X-RAY DIFFRACTION100
1.7412-1.81090.23791430.18877108X-RAY DIFFRACTION100
1.8109-1.89330.20171440.18467132X-RAY DIFFRACTION100
1.8933-1.99310.21081430.17687139X-RAY DIFFRACTION100
1.9931-2.1180.21381430.17797121X-RAY DIFFRACTION100
2.118-2.28150.20251440.17577167X-RAY DIFFRACTION100
2.2815-2.5110.20381440.18787173X-RAY DIFFRACTION100
2.511-2.87420.20281440.18867219X-RAY DIFFRACTION100
2.8742-3.62080.21381450.18497149X-RAY DIFFRACTION98
3.6208-37.63580.21511390.19066938X-RAY DIFFRACTION92

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