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- PDB-6xfs: Class C beta-lactamase from Escherichia coli in complex with Tazo... -

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Basic information

Entry
Database: PDB / ID: 6xfs
TitleClass C beta-lactamase from Escherichia coli in complex with Tazobactam
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / class C beta-lactamase / Tazobactam / structural genomic / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases / HYDROLASE / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / TAZOBACTAM INTERMEDIATE / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsChang, C. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Class C beta-lactamase from Escherichia coli in complex with Tazobactam
Authors: Chang, C. / Maltseva, N. / Endres, M. / Joachimiak, A.
History
DepositionJun 16, 2020Deposition site: RCSB / Processing site: RCSB
SupersessionJul 15, 2020ID: 6WA7
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
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
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,30115
Polymers159,4374
Non-polymers1,86411
Water1,49583
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2864
Polymers39,8591
Non-polymers4263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3744
Polymers39,8591
Non-polymers5153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2683
Polymers39,8591
Non-polymers4082
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3744
Polymers39,8591
Non-polymers5153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.915, 170.299, 89.947
Angle α, β, γ (deg.)90.000, 89.980, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Beta-lactamase /


Mass: 39859.301 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla(ampc-EC31), blaEC / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q104Z6, UniProt: P00811*PLUS, beta-lactamase

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Non-polymers , 5 types, 94 molecules

#2: Chemical
ChemComp-TBE / TAZOBACTAM INTERMEDIATE


Mass: 302.307 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N4O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1M HEPES, 10% 2-propanol, 20% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 38507 / % possible obs: 99.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 43.42 Å2 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.077 / Rrim(I) all: 0.178 / Χ2: 0.889 / Net I/σ(I): 5.2 / Num. measured all: 185370
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.754.70.94419880.6870.4591.0530.645100
2.75-2.84.70.76218820.7910.3710.850.654100
2.8-2.854.70.74618750.7920.3620.8320.657100
2.85-2.914.80.61319920.8110.2970.6830.692100
2.91-2.974.80.57318920.8310.2780.6390.685100
2.97-3.044.80.53419110.8430.2560.5940.70799.9
3.04-3.124.90.38519230.9150.1830.4280.75399.8
3.12-3.24.80.3719120.9210.1790.4120.79299.8
3.2-3.34.90.31119270.9380.1470.3450.845100
3.3-3.44.80.25219450.9580.120.280.92199.8
3.4-3.524.80.21518940.9590.1030.2390.919100
3.52-3.664.90.18319270.9780.0860.2031.076100
3.66-3.834.90.15819350.9790.0760.1761.07499.9
3.83-4.034.80.13618940.9850.0650.1511.15299.7
4.03-4.294.90.11819560.9850.0560.1311.172100
4.29-4.624.90.10219270.9870.0490.1141.10999.5
4.62-5.084.80.0919240.9910.0430.11.01499.9
5.08-5.814.90.08619320.9920.0410.0960.99199.8
5.81-7.324.80.07719280.9860.0380.0860.81199.8
7.32-504.60.06919430.9910.0340.0771.07398.1

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
SCALEPACKdata scaling
SBC-Collectdata collection
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DPZ

6dpz


Resolution: 2.7→46.91 Å / SU ML: 0.3975 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.3112
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2486 1806 4.92 %
Rwork0.188 34868 -
obs0.1911 36674 95.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.52 Å2
Refinement stepCycle: LAST / Resolution: 2.7→46.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11190 0 123 83 11396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001611645
X-RAY DIFFRACTIONf_angle_d0.476815886
X-RAY DIFFRACTIONf_chiral_restr0.04131720
X-RAY DIFFRACTIONf_plane_restr0.00382030
X-RAY DIFFRACTIONf_dihedral_angle_d13.69054249
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.780.30351060.24332100X-RAY DIFFRACTION73.95
2.78-2.860.33741300.25262358X-RAY DIFFRACTION85.09
2.86-2.950.38541260.25322627X-RAY DIFFRACTION91.89
2.95-3.050.32721470.24772641X-RAY DIFFRACTION95.28
3.06-3.180.28911360.23132751X-RAY DIFFRACTION97.21
3.18-3.320.28361330.23042819X-RAY DIFFRACTION99.03
3.32-3.50.27991270.20282798X-RAY DIFFRACTION99.52
3.5-3.720.25071470.18492810X-RAY DIFFRACTION99.9
3.72-40.25961400.17492789X-RAY DIFFRACTION99.09
4-4.410.19391770.15292796X-RAY DIFFRACTION99.43
4.41-5.040.20291420.14632782X-RAY DIFFRACTION98.58
5.04-6.350.24791350.17252824X-RAY DIFFRACTION99.3
6.35-46.910.19641600.16722773X-RAY DIFFRACTION97.15
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.480521348872-0.09379165340790.02161331430690.6850273159610.1790246326150.581036613074-0.0472721997107-0.009952811479830.01401665037670.0358275225188-0.0115574354022-0.0308924682183-0.0182399469859-0.00726918929989-0.3030579990650.06327761301770.003893052871660.02421994604070.0763578728692-0.03441951567510.061795715642614.43409435690.25176058326632.8397396705
20.876380093108-0.03991820737770.05664906896291.298590567090.2059298570430.4160502245590.0512815570804-0.05063559300970.02359064986280.0472615433569-0.109938987299-0.1190534961960.03470313146390.0126944544073-0.001358387702090.153491043663-0.0237469901033-0.02878392270880.1446259247580.004044876849870.132582357175-3.42371436767-5.6281523050173.3092784318
30.691936234624-0.0786523907815-0.1055114577170.929544742861-0.3018533183460.569394078657-0.0286402987036-0.0248436460982-0.04153508132940.0541534182514-0.01999116261340.04363229189570.02169343236320.0230602423255-0.01600528717510.09555673913060.0100777735856-0.03389523017660.1019343722380.03026395765170.06899270190689.05620995583-48.02256384977.7624587394
40.8788855237550.0349157863910.04857717216121.26810982334-0.1910643892820.2969950812540.0920865616588-0.0905672952608-0.04812832145660.00140322311715-0.1051171893970.101550614808-0.007115813674970.00802712473309-0.001481971983140.113877411622-0.02255615864940.03664998095410.1452750187230.009715168795230.10527433506426.8984670386-42.125638935828.3361754461
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 32 through 388)
2X-RAY DIFFRACTION2(chain 'B' and resid 31 through 388)
3X-RAY DIFFRACTION3(chain 'C' and resid 32 through 388)
4X-RAY DIFFRACTION4(chain 'D' and resid 31 through 388)

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