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- PDB-7qnk: Structure of beta-lactamase TEM-171 complexed with tazobactam int... -

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Basic information

Entry
Database: PDB / ID: 7qnk
TitleStructure of beta-lactamase TEM-171 complexed with tazobactam intermediate at 2.5 A resolution
ComponentsBeta-lactamase TEM
KeywordsHYDROLASE / BETA-LACTAMASE / BETA-LACTAMASE INHIBITOR / HYDROLASE-INHIBITOR COMPLEX
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 / TAZOBACTAM INTERMEDIATE / Beta-lactamase TEM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHakanpaa, J. / Petrova, T. / Samygina, V.R. / Lamzin, V.S. / 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 21, 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase TEM
B: Beta-lactamase TEM
C: Beta-lactamase TEM
D: Beta-lactamase TEM
E: Beta-lactamase TEM
F: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,36613
Polymers173,7366
Non-polymers1,6307
Water13,691760
1
A: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3173
Polymers28,9561
Non-polymers3612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2582
Polymers28,9561
Non-polymers3021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2582
Polymers28,9561
Non-polymers3021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3173
Polymers28,9561
Non-polymers3612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2582
Polymers28,9561
Non-polymers3021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Beta-lactamase TEM


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)89.501, 89.501, 500.895
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: TRP / End label comp-ID: TRP / Refine code: _ / Auth seq-ID: 26 - 288 / Label seq-ID: 1 - 263

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16BB
26CC
17BB
27DD
18BB
28EE
19BB
29FF
110CC
210DD
111CC
211EE
112CC
212FF
113DD
213EE
114DD
214FF
115EE
215FF

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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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-TBE / TAZOBACTAM INTERMEDIATE


Mass: 302.307 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H14N4O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 760 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.89 Å3/Da / Density % sol: 57.39 %
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: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.5→112 Å / Num. obs: 71685 / % possible obs: 99.8 % / Redundancy: 5.8 % / CC1/2: 0.99 / Net I/σ(I): 7
Reflection shellResolution: 2.5→2.56 Å / Mean I/σ(I) obs: 1.56 / Num. unique obs: 4915 / CC1/2: 0.986

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JYI

3jyi


Resolution: 2.5→10 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.92 / SU B: 17.214 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.498 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24829 3575 5 %RANDOM
Rwork0.20936 ---
obs0.21133 67269 98.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.997 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20 Å2
2--0.53 Å20 Å2
3----1.05 Å2
Refinement stepCycle: 1 / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12168 0 108 760 13036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01312489
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711848
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.64916911
X-RAY DIFFRACTIONr_angle_other_deg1.241.57627432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.60951572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.69121.233657
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.277152202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.11515108
X-RAY DIFFRACTIONr_chiral_restr0.0710.21678
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213996
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022532
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0382.3796308
X-RAY DIFFRACTIONr_mcbond_other1.0382.3796307
X-RAY DIFFRACTIONr_mcangle_it1.813.5677872
X-RAY DIFFRACTIONr_mcangle_other1.813.5677873
X-RAY DIFFRACTIONr_scbond_it0.9732.4836181
X-RAY DIFFRACTIONr_scbond_other0.9732.4836181
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6873.6839039
X-RAY DIFFRACTIONr_long_range_B_refined4.5327.9613552
X-RAY DIFFRACTIONr_long_range_B_other4.39527.67313426
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A83480.06
12B83480.06
21A83620.06
22C83620.06
31A83790.05
32D83790.05
41A84030.04
42E84030.04
51A83810.05
52F83810.05
61B83920.05
62C83920.05
71B83680.06
72D83680.06
81B83540.05
82E83540.05
91B83820.05
92F83820.05
101C83650.06
102D83650.06
111C83770.05
112E83770.05
121C84180.04
122F84180.04
131D83750.05
132E83750.05
141D83910.05
142F83910.05
151E83910.05
152F83910.05
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 235 -
Rwork0.351 4680 -
obs--99.92 %
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)
12.94010.21681.46830.30330.42293.72660.14040.25710.0119-0.0207-0.1116-0.0864-0.06150.1927-0.02890.0179-0.00390.00890.2980.04230.0283-5.6911-17.485561.5709
24.22830.53492.40350.34310.15733.7270.2964-0.1967-0.04940.1818-0.0852-0.1374-0.0563-0.0181-0.21120.33390.09380.040.66940.1250.1533-18.2626.965761.0769
31.97771.3298-0.97431.3025-1.23583.48550.04070.05780.00010.1387-0.03170.08970.001-0.0685-0.0090.0605-0.07560.04430.1689-0.05530.033-24.3304-20.7025102.9276
42.68511.28181.75711.18320.75894.05220.07070.1625-0.02160.0504-0.01510.07290.08010.1965-0.05560.1373-0.10720.01620.19420.01170.03419.465610.3064105.6894
52.99580.17732.00710.6558-0.39543.81350.2136-0.084-0.2030.0065-0.06260.19240.2648-0.526-0.1510.1551-0.15220.01810.43-0.01780.1121.8162-36.2391104.5587
63.70111.576-2.51530.7684-1.12074.46570.5362-0.44680.1780.4145-0.1982-0.0108-0.97550.3799-0.3380.7622-0.12990.13051.13120.02270.4405-37.153625.0994102.4922
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 501
2X-RAY DIFFRACTION2B26 - 288
3X-RAY DIFFRACTION3C26 - 499
4X-RAY DIFFRACTION4D26 - 499
5X-RAY DIFFRACTION5E26 - 499
6X-RAY DIFFRACTION6F26 - 288

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