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- PDB-7u6q: TEM-1 beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 7u6q
TitleTEM-1 beta-lactamase
ComponentsBeta-lactamase
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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJi, Z. / Boxer, S.G. / Mathews, I.I.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118044 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM133894 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Protein Electric Fields Enable Faster and Longer-Lasting Covalent Inhibition of beta-Lactamases.
Authors: Ji, Z. / Kozuch, J. / Mathews, I.I. / Diercks, C.S. / Shamsudin, Y. / Schulz, M.A. / Boxer, S.G.
History
DepositionMar 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: 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 1.3Oct 30, 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

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4839
Polymers86,9073
Non-polymers5766
Water14,502805
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1613
Polymers28,9691
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1613
Polymers28,9691
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1613
Polymers28,9691
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.730, 96.330, 154.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 27 through 42 or resid 44...
21(chain B and (resid 27 through 42 or resid 44...
31(chain C and (resid 27 through 42 or resid 44...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROALAALA(chain A and (resid 27 through 42 or resid 44...AA27 - 423 - 18
12VALVALLEULEU(chain A and (resid 27 through 42 or resid 44...AA44 - 8120 - 57
13ARGARGGLUGLU(chain A and (resid 27 through 42 or resid 44...AA83 - 8959 - 65
14LEULEUGLYGLY(chain A and (resid 27 through 42 or resid 44...AA91 - 24167 - 217
15ARGARGALAALA(chain A and (resid 27 through 42 or resid 44...AA243 - 282219 - 258
16LEULEULEULEU(chain A and (resid 27 through 42 or resid 44...AA284260
17LYSLYSTRPTRP(chain A and (resid 27 through 42 or resid 44...AA286 - 288262 - 264
21PROPROALAALA(chain B and (resid 27 through 42 or resid 44...BB27 - 423 - 18
22VALVALLEULEU(chain B and (resid 27 through 42 or resid 44...BB44 - 8120 - 57
23ARGARGGLUGLU(chain B and (resid 27 through 42 or resid 44...BB83 - 8959 - 65
24LEULEUGLYGLY(chain B and (resid 27 through 42 or resid 44...BB91 - 24167 - 217
25ARGARGALAALA(chain B and (resid 27 through 42 or resid 44...BB243 - 282219 - 258
26LEULEULEULEU(chain B and (resid 27 through 42 or resid 44...BB284260
27LYSLYSTRPTRP(chain B and (resid 27 through 42 or resid 44...BB286 - 288262 - 264
31PROPROALAALA(chain C and (resid 27 through 42 or resid 44...CC27 - 423 - 18
32VALVALLEULEU(chain C and (resid 27 through 42 or resid 44...CC44 - 8120 - 57
33ARGARGGLUGLU(chain C and (resid 27 through 42 or resid 44...CC83 - 8959 - 65
34LEULEUGLYGLY(chain C and (resid 27 through 42 or resid 44...CC91 - 24167 - 217
35ARGARGALAALA(chain C and (resid 27 through 42 or resid 44...CC243 - 282219 - 258
36LEULEULEULEU(chain C and (resid 27 through 42 or resid 44...CC284260
37LYSLYSTRPTRP(chain C and (resid 27 through 42 or resid 44...CC286 - 288262 - 264

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Components

#1: Protein Beta-lactamase / TEM-1 beta-lactamase


Mass: 28968.955 Da / Num. of mol.: 3 / Mutation: M182T
Source method: isolated from a genetically manipulated source
Details: An extra glycine at the N-terminus / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaTEM-1, peH4H_0137 / Production host: Escherichia coli (E. coli) / References: UniProt: C4NV37, beta-lactamase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 805 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.59 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ammonium sulfate, potassium phosphate, 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.9→39.23 Å / Num. obs: 71785 / % possible obs: 99.6 % / Redundancy: 13.21 % / Biso Wilson estimate: 22.01 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.288 / Rrim(I) all: 0.3 / Χ2: 0.763 / Net I/σ(I): 8.23 / Num. measured all: 948292 / Scaling rejects: 140
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.9513.532.5121.570787523852320.642.6199.9
1.95-213.2732.0221.8468103514451310.7252.10299.7
2-2.0612.411.6622.1961357498249440.7911.73499.2
2.06-2.1213.7271.3762.7366272485048280.8511.42999.5
2.12-2.1913.7381.0513.5564692471547090.9021.09199.9
2.19-2.2713.7420.8854.0862693456845620.9340.91999.9
2.27-2.3613.4080.8314.2758807439643860.940.86399.8
2.36-2.4513.0960.7124.8355424424942320.9480.74199.6
2.45-2.5612.7670.575.651464406840310.9630.59499.1
2.56-2.6913.8510.4736.8454046390339020.9780.491100
2.69-2.8313.7130.4057.5751011372737200.9860.4299.8
2.83-313.510.3199.0447434352235110.9880.33299.7
3-3.2112.6220.23810.9741942333933230.9920.24899.5
3.21-3.4713.0310.15215.3140082308830760.9960.15999.6
3.47-3.813.2740.11319.5138336288928880.9970.118100
3.8-4.2512.8440.0922.7933227259125870.9980.09499.8
4.25-4.9111.7110.0823.4926829232922910.9980.08398.4
4.91-6.0113.1910.08722.5826131198719810.9980.0999.7
6.01-8.512.3990.07624.5919318156215580.9990.0899.7
8.5-39.2311.5760.04934.1103379268930.9990.05296.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ERM

1erm


Resolution: 1.9→39.23 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2385 3588 5 %
Rwork0.1911 68168 -
obs0.1935 71756 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.82 Å2 / Biso mean: 24.4209 Å2 / Biso min: 10.38 Å2
Refinement stepCycle: final / Resolution: 1.9→39.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6076 0 30 814 6920
Biso mean--38.83 33.09 -
Num. residues----790
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3622X-RAY DIFFRACTION10.991TORSIONAL
12B3622X-RAY DIFFRACTION10.991TORSIONAL
13C3622X-RAY DIFFRACTION10.991TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.920.33951340.307725652699100
1.92-1.950.3481370.296625972734100
1.95-1.980.33541360.276425852721100
1.98-2.010.29631360.271425832719100
2.01-2.040.30241380.251626202758100
2.04-2.070.28541340.2542532266699
2.07-2.110.27841380.235526212759100
2.11-2.150.30571360.224825822718100
2.15-2.190.23911370.212826072744100
2.19-2.230.27311380.21326232761100
2.23-2.280.2481360.199425892725100
2.28-2.340.2411380.198526172755100
2.34-2.390.27971370.206825982735100
2.39-2.460.2741370.19782605274299
2.46-2.530.24411360.20112603273999
2.53-2.610.25321360.186925762712100
2.61-2.710.2211390.178626442783100
2.71-2.810.22211380.179126212759100
2.81-2.940.23451370.186126132750100
2.94-3.10.25871400.186626512791100
3.1-3.290.2361370.18652614275199
3.29-3.540.21591410.169626642805100
3.55-3.90.18431400.152626692809100
3.9-4.460.18871410.144726772818100
4.47-5.620.19241420.16492688283099
5.62-39.230.24391490.1892824297399

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