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- PDB-5ggw: Crystal structure of Class C beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 5ggw
TitleCrystal structure of Class C beta-lactamase
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase / Class C
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.762 Å
AuthorsAn, Y.J. / Na, J.H. / Cha, S.S.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Structural basis for the extended substrate spectrum of AmpC BER and structure-guided discovery of the inhibition activity of citrate against the class C beta-lactamases AmpC BER and CMY-10.
Authors: Na, J.H. / Cha, S.S.
History
DepositionJun 16, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)81,2106
Polymers80,8282
Non-polymers3824
Water3,243180
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6053
Polymers40,4141
Non-polymers1912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6053
Polymers40,4141
Non-polymers1912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.732, 182.088, 141.881
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-510-

HOH

21B-578-

HOH

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Components

#1: Protein Beta-lactamase


Mass: 40413.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ampC / Production host: Escherichia coli (E. coli) / References: UniProt: B7SNP8, beta-lactamase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 3.45 Å3/Da / Density % sol: 64.39 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 5.5 / Details: Bis-Tris pH 5.5 Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 100735 / % possible obs: 94.7 % / Redundancy: 5.5 % / Net I/σ(I): 21.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
HKL-2000data scaling
RefinementResolution: 1.762→46.436 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 26.87
RfactorNum. reflection% reflection
Rfree0.2589 5028 4.99 %
Rwork0.2297 --
obs0.2312 100694 94.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.762→46.436 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5600 0 20 180 5800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085783
X-RAY DIFFRACTIONf_angle_d1.1487904
X-RAY DIFFRACTIONf_dihedral_angle_d13.8552075
X-RAY DIFFRACTIONf_chiral_restr0.046847
X-RAY DIFFRACTIONf_plane_restr0.0071017
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7619-1.78190.34971330.35582542X-RAY DIFFRACTION75
1.7819-1.80290.36951640.33863056X-RAY DIFFRACTION92
1.8029-1.82490.34981630.32623092X-RAY DIFFRACTION91
1.8249-1.8480.35241550.32323113X-RAY DIFFRACTION93
1.848-1.87230.30441610.32263003X-RAY DIFFRACTION90
1.8723-1.89790.35981590.33353018X-RAY DIFFRACTION90
1.8979-1.9250.43521500.43152743X-RAY DIFFRACTION82
1.925-1.95380.3531410.32682719X-RAY DIFFRACTION80
1.9538-1.98430.30061640.27683083X-RAY DIFFRACTION92
1.9843-2.01680.29591710.26423191X-RAY DIFFRACTION95
2.0168-2.05160.30231730.2833088X-RAY DIFFRACTION92
2.0516-2.08890.36941480.30273156X-RAY DIFFRACTION93
2.0889-2.12910.29771870.25013120X-RAY DIFFRACTION94
2.1291-2.17250.2531800.23683273X-RAY DIFFRACTION97
2.1725-2.21980.28051680.2473223X-RAY DIFFRACTION96
2.2198-2.27140.35681500.31852998X-RAY DIFFRACTION90
2.2714-2.32820.30511710.23883218X-RAY DIFFRACTION95
2.3282-2.39120.30841770.22333308X-RAY DIFFRACTION98
2.3912-2.46150.25781620.21723332X-RAY DIFFRACTION98
2.4615-2.5410.24061840.2153317X-RAY DIFFRACTION99
2.541-2.63180.25581700.22083335X-RAY DIFFRACTION98
2.6318-2.73710.25251770.21943308X-RAY DIFFRACTION99
2.7371-2.86170.22551610.22593391X-RAY DIFFRACTION99
2.8617-3.01260.27221680.22193378X-RAY DIFFRACTION99
3.0126-3.20130.23481750.21613386X-RAY DIFFRACTION99
3.2013-3.44840.2651830.21473405X-RAY DIFFRACTION100
3.4484-3.79520.22891890.18593395X-RAY DIFFRACTION99
3.7952-4.34410.1761850.15973420X-RAY DIFFRACTION100
4.3441-5.47170.16341700.15413475X-RAY DIFFRACTION100
5.4717-46.45230.20021890.17463580X-RAY DIFFRACTION99

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