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- PDB-4kzb: Crystal structure of AmpC beta-lactamase in complex with fragment... -

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Basic information

Entry
Database: PDB / ID: 4kzb
TitleCrystal structure of AmpC beta-lactamase in complex with fragment 50 (N-(methylsulfonyl)-N-phenyl-alanine)
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / AMPC beta-lactamase / class C / hydrolase / cephalosporinase / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
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
N-(methylsulfonyl)-N-phenyl-L-alanine / N-(methylsulfonyl)-N-phenyl-D-alanine / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsEidam, O. / Barelier, S. / Fish, I. / Shoichet, B.K.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Increasing chemical space coverage by combining empirical and computational fragment screens.
Authors: Barelier, S. / Eidam, O. / Fish, I. / Hollander, J. / Figaroa, F. / Nachane, R. / Irwin, J.J. / Shoichet, B.K. / Siegal, G.
History
DepositionMay 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)80,8799
Polymers79,1762
Non-polymers1,7037
Water17,276959
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5615
Polymers39,5881
Non-polymers9734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3184
Polymers39,5881
Non-polymers7303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.600, 77.440, 97.500
Angle α, β, γ (deg.)90.000, 116.180, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-778-

HOH

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Components

#1: Protein Beta-lactamase / AmpC beta-lactamase / Cephalosporinase


Mass: 39587.922 Da / Num. of mol.: 2 / Fragment: UNP residues 20-377
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ampA, ampC, b4150, JW4111 / Plasmid: POGO295 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase
#2: Chemical
ChemComp-NZ2 / N-(methylsulfonyl)-N-phenyl-L-alanine


Mass: 243.280 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H13NO4S
#3: Chemical ChemComp-NZ3 / N-(methylsulfonyl)-N-phenyl-D-alanine


Mass: 243.280 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13NO4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 959 / Source method: isolated from a natural source / Formula: H2O

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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: 2.52 Å3/Da / Density % sol: 51.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 1.7 M potassium phosphate, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 3, 2012
RadiationMonochromator: KHOZU Double flat crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 1.37→29.547 Å / Num. obs: 163137 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.339 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 19.69
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.37-1.410.4872.37349281203899
1.41-1.440.383.03342121171599.3
1.44-1.490.3023.78334721142499.5
1.49-1.530.2374.77329271118399.6
1.53-1.580.186.13316181070999.6
1.58-1.640.1457.73311981047299.5
1.64-1.70.1159.52299261003499.5
1.7-1.770.09111.9829072970999.5
1.77-1.850.06915.2527897929899.4
1.85-1.940.05418.8626771887699.5
1.94-2.040.04124.2625458843399.2
2.04-2.170.03330.0424173800699.2
2.17-2.320.02834.4222615749399
2.32-2.50.02537.8221045702199
2.5-2.740.02241.8618934640799.1
2.74-3.060.01947.7217387584999.3
3.06-3.540.01656.7616020516599.3
3.54-4.330.01561.7613365436298.7
4.33-6.130.01562.0610051333297.1
6.130.01560.84677161183.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KE4

1ke4


Resolution: 1.37→29.547 Å / Occupancy max: 1 / Occupancy min: 0.15 / FOM work R set: 0.9122 / SU ML: 0.12 / σ(F): 1.99 / Phase error: 15.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1677 6201 3.8 %
Rwork0.1389 --
obs0.14 163131 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 53.65 Å2 / Biso mean: 14.7869 Å2 / Biso min: 2.57 Å2
Refinement stepCycle: LAST / Resolution: 1.37→29.547 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5557 0 112 959 6628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095931
X-RAY DIFFRACTIONf_angle_d1.3018134
X-RAY DIFFRACTIONf_chiral_restr0.086874
X-RAY DIFFRACTIONf_plane_restr0.0071045
X-RAY DIFFRACTIONf_dihedral_angle_d13.2652202
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.37-1.38550.28492180.22265239545799
1.3855-1.40180.22392150.25150536599
1.4018-1.41890.23962160.18985178539499
1.4189-1.43690.21582180.185233545199
1.4369-1.45580.22242160.167551815397100
1.4558-1.47570.21052180.16655246546499
1.4757-1.49680.2192180.162152245442100
1.4968-1.51910.21532180.152452265444100
1.5191-1.54290.17782180.144852295447100
1.5429-1.56820.17942180.13252455463100
1.5682-1.59520.17292170.124352055422100
1.5952-1.62420.17382170.124752185435100
1.6242-1.65540.16172160.122151815397100
1.6554-1.68920.16692200.119852645484100
1.6892-1.7260.15991440.12585313545799
1.726-1.76610.16931900.129152605450100
1.7661-1.81030.15752130.122152405453100
1.8103-1.85920.16061930.125752525445100
1.8592-1.91390.16911490.125153005449100
1.9139-1.97570.16571980.12625233543199
1.9757-2.04630.16021900.12365242543299
2.0463-2.12820.13052160.11865254547099
2.1282-2.2250.16452140.12115208542299
2.225-2.34230.15261960.12845279547599
2.3423-2.48890.161900.13255249543999
2.4889-2.6810.17512090.14145231544099
2.681-2.95060.16352310.14995269550099
2.9506-3.3770.17312080.14652705478100
3.377-4.25260.13792190.13025268548799
4.2526-29.55380.17191980.15975043524193

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