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- PDB-7qor: Structure of beta-lactamase TEM-171 -

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Basic information

Entry
Database: PDB / ID: 7qor
TitleStructure of beta-lactamase TEM-171
ComponentsBeta-lactamase TEM
KeywordsHYDROLASE / BETA-LACTAMASE
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
ACETATE ION / Beta-lactamase TEM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.999 Å
AuthorsHakanpaa, J. / Petrova, T. / Samygina, V.R. / Chojnowski, G. / Lamzin, V. / Egorov, A.M.
Funding supportEuropean Union, 3items
OrganizationGrant numberCountry
Russian Science Foundation15-14-00014-CEuropean Union
German Federal Ministry for Education and Research05K10YEAEuropean Union
European CommissionH2020-EINFRA-2015-1-675858European Union
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Crystal structures of the molecular class A beta-lactamase TEM-171 and its complexes with tazobactam.
Authors: Grigorenko, V.G. / Petrova, T.E. / Carolan, C. / Rubtsova, M.Y. / Uporov, I.V. / Pereira, J. / Chojnowski, G. / Samygina, V.R. / Lamzin, V.S. / Egorov, A.M.
History
DepositionDec 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Beta-lactamase TEM
BBB: Beta-lactamase TEM
CCC: Beta-lactamase TEM
DDD: Beta-lactamase TEM
EEE: Beta-lactamase TEM
FFF: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,22213
Polymers173,7366
Non-polymers4857
Water15,763875
1
AAA: Beta-lactamase TEM
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 29.1 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)29,1403
Polymers28,9561
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Beta-lactamase TEM


  • defined by author
  • 29 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)28,9561
Polymers28,9561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: Beta-lactamase TEM
hetero molecules


  • defined by author
  • 29.1 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)29,1394
Polymers28,9561
Non-polymers1833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
DDD: Beta-lactamase TEM
hetero molecules


  • defined by author
  • 29.1 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)29,0743
Polymers28,9561
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
EEE: Beta-lactamase TEM


  • defined by author
  • 29 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)28,9561
Polymers28,9561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
FFF: Beta-lactamase TEM


  • defined by author
  • 29 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)28,9561
Polymers28,9561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.190, 88.190, 499.323
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11EEE-487-

HOH

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Components

#1: Protein
Beta-lactamase TEM / IRT-4 / Penicillinase / TEM-1 / TEM-16/CAZ-7 / TEM-2 / TEM-24/CAZ-6 / TEM-3 / TEM-4 / TEM-5 / TEM-6 ...IRT-4 / Penicillinase / TEM-1 / TEM-16/CAZ-7 / TEM-2 / TEM-24/CAZ-6 / TEM-3 / TEM-4 / TEM-5 / TEM-6 / TEM-8/CAZ-2


Mass: 28956.021 Da / Num. of mol.: 6 / Mutation: V84I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla, blaT-3, blaT-4, blaT-5, blaT-6 / Production host: Escherichia coli (E. coli) / References: UniProt: P62593, beta-lactamase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 875 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: PEG-4000, 0.2 M calcium acetate, 0.1 M Tris-HCl, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.999→86.85 Å / Num. obs: 132474 / % possible obs: 98.6 % / Redundancy: 13.2 % / CC1/2: 0.99 / Net I/σ(I): 18.5
Reflection shellResolution: 1.999→2.05 Å / Num. unique obs: 9279 / CC1/2: 0.787

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JYI

3jyi


Resolution: 1.999→15 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 8.843 / SU ML: 0.128 / Cross valid method: FREE R-VALUE / ESU R: 0.165 / ESU R Free: 0.139
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2106 6526 4.942 %
Rwork0.1899 125525 -
all0.191 --
obs-132051 97.834 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 58.018 Å2
Baniso -1Baniso -2Baniso -3
1-1.363 Å2-0 Å2-0 Å2
2--1.363 Å2-0 Å2
3----2.727 Å2
Refinement stepCycle: LAST / Resolution: 1.999→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12168 0 32 875 13075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01312443
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711842
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.64516856
X-RAY DIFFRACTIONr_angle_other_deg1.3561.57527432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.40651582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46321.484647
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.932152211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.34515109
X-RAY DIFFRACTIONr_chiral_restr0.0770.21673
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213952
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022515
X-RAY DIFFRACTIONr_nbd_refined0.1950.22548
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.210928
X-RAY DIFFRACTIONr_nbtor_refined0.1530.26108
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.25488
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2787
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0440.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0940.216
X-RAY DIFFRACTIONr_nbd_other0.2290.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2190.229
X-RAY DIFFRACTIONr_mcbond_it1.171.8496323
X-RAY DIFFRACTIONr_mcbond_other1.171.8486321
X-RAY DIFFRACTIONr_mcangle_it1.9012.7617892
X-RAY DIFFRACTIONr_mcangle_other1.9012.7627893
X-RAY DIFFRACTIONr_scbond_it1.4482.1136120
X-RAY DIFFRACTIONr_scbond_other1.4482.1146121
X-RAY DIFFRACTIONr_scangle_it2.4183.0878960
X-RAY DIFFRACTIONr_scangle_other2.4183.0888961
X-RAY DIFFRACTIONr_lrange_it7.31422.93314110
X-RAY DIFFRACTIONr_lrange_other7.25722.26413889
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.999-2.050.3234380.31688410.31696770.6770.6895.88720.28
2.05-2.1050.324450.29186980.29293750.7560.77597.52530.256
2.105-2.1650.2554250.26185200.26191630.8640.85697.62090.226
2.165-2.230.2544230.24982650.24989010.8850.88397.6070.211
2.23-2.3010.2544310.22480120.22686340.8950.91297.78780.188
2.301-2.380.234110.21378400.21484180.9270.92998.01620.18
2.38-2.4680.2383900.19875640.281060.9310.94398.12480.165
2.468-2.5660.2093770.18773070.18878150.9420.94898.32370.157
2.566-2.6760.2073560.18370860.18475650.9430.94898.37410.157
2.676-2.8020.2343660.18666970.18971880.9360.94798.2610.163
2.802-2.9480.2233530.18465060.18669520.9450.95398.66230.163
2.948-3.1190.2193350.19661130.19765580.9440.94998.32270.18
3.119-3.3250.2013130.20257920.20261770.9540.95498.83440.191
3.325-3.5760.2122940.20154780.20158350.9610.9698.92030.195
3.576-3.8960.2212530.18751020.18854050.950.9699.07490.185
3.896-4.3190.1892450.15746600.15949420.9650.9799.25130.161
4.319-4.920.1442400.14442090.14444770.9790.97899.37460.151
4.92-5.870.1781760.16836830.16838860.9750.97899.30520.172
5.87-7.730.2291430.19730280.19831810.9550.96799.68560.206
7.73-150.181120.14521240.14622780.9730.98298.15630.164
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)
11.1981-0.09880.70940.04790.06381.53450.22010.19840.02640.0093-0.127-0.0084-0.06490.1366-0.09310.2698-0.02010.04940.66190.02670.2995-5.629-17.34461.632
21.8747-0.06811.61040.2265-0.35222.460.5218-0.1598-0.09150.0728-0.2654-0.0423-0.07890.0252-0.25640.41280.06130.11141.05450.2060.1135-18.47427.05761.128
30.83450.5108-0.55050.3285-0.30471.56940.03120.08890.00830.0767-0.0268-0.01190.0518-0.0573-0.00440.3488-0.16530.03160.5195-0.01880.333-24.315-20.772103.035
41.1710.64330.98180.37550.50922.48170.08690.13910.0590.09790.01640.09250.07530.1149-0.10330.4113-0.2164-0.010.45880.03040.30249.15210.395105.85
50.87050.16770.55910.1451-0.32542.06420.1181-0.0596-0.05740.0180.0320.02680.0977-0.3396-0.15020.3096-0.2384-0.00140.70210.0820.292221.713-36.095104.767
62.78631.1432-3.29290.7305-1.62534.29460.8994-0.525-0.07880.4613-0.63160.1389-1.30230.8337-0.26780.6073-0.3710.13751.2642-0.01190.2709-37.34925.102102.528
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA26 - 501
2X-RAY DIFFRACTION2ALLBBB26 - 290
3X-RAY DIFFRACTION3ALLCCC26 - 501
4X-RAY DIFFRACTION4ALLDDD26 - 501
5X-RAY DIFFRACTION5ALLEEE26 - 501
6X-RAY DIFFRACTION6ALLFFF26 - 290

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