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- PDB-8ddz: TEM-1 beta-lactamase A237Y -

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Basic information

Entry
Database: PDB / ID: 8ddz
TitleTEM-1 beta-lactamase A237Y
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 / 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: 1.45 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
DepositionJun 19, 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 / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase TEM
B: Beta-lactamase TEM
C: Beta-lactamase TEM
D: Beta-lactamase TEM


Theoretical massNumber of molelcules
Total (without water)116,2444
Polymers116,2444
Non-polymers00
Water12,863714
1
A: Beta-lactamase TEM


Theoretical massNumber of molelcules
Total (without water)29,0611
Polymers29,0611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase TEM


Theoretical massNumber of molelcules
Total (without water)29,0611
Polymers29,0611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase TEM


Theoretical massNumber of molelcules
Total (without water)29,0611
Polymers29,0611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase TEM


Theoretical massNumber of molelcules
Total (without water)29,0611
Polymers29,0611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.610, 83.770, 95.660
Angle α, β, γ (deg.)90.000, 90.230, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 29061.053 Da / Num. of mol.: 4 / Mutation: M182T, A237Y
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 / Production host: Escherichia coli (E. coli) / References: UniProt: P62593, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 714 / Source method: isolated from a natural source / Formula: H2O
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: 2.09 Å3/Da / Density % sol: 41.12 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, 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: Mar 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.45→38.37 Å / Num. obs: 164606 / % possible obs: 97.6 % / Redundancy: 13.812 % / Biso Wilson estimate: 15.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.167 / Rrim(I) all: 0.174 / Χ2: 0.818 / Net I/σ(I): 9.51
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
1.46-1.514.0672.0021.5616468812239117070.7292.07695.7
1.5-1.5414.0011.6691.9915917311832113690.7881.73196.1
1.54-1.5813.4461.3962.3515047411602111910.8441.45196.5
1.58-1.6313.9061.1672.915100311242108590.8851.21196.6
1.63-1.6913.8260.9783.4114600010906105600.9131.01596.8
1.69-1.7514.2370.8294.0714592810552102500.9390.8697.1
1.75-1.8114.0150.6684.931382151013198620.9610.69397.3
1.81-1.8813.3120.5185.95127625982195870.9690.53997.6
1.88-1.9713.6290.3777.79125001937991720.9820.39297.8
1.97-2.0614.2290.2969.67125571899888250.9880.30798.1
2.06-2.1814.1760.23211.79119362858084200.9920.24198.1
2.18-2.3113.9220.19313.1111099810079800.9940.298.5
2.31-2.4713.230.1614.4899251760975020.9960.16698.6
2.47-2.6713.9460.13217.1597653707970020.9970.13798.9
2.67-2.9214.2060.11619.2591958653164730.9970.12199.1
2.92-3.2613.7150.09921.8880590591858760.9980.10399.3
3.26-3.7712.5810.08124.7565474523552040.9980.08499.4
3.77-4.6214.0760.07429.6762117442744130.9980.07699.7
4.62-6.5313.1980.07227.8645349345034360.9990.07599.6
6.53-38.3713.2940.06230.0425246193618990.9990.06498.1

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Processing

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

1erm


Resolution: 1.45→38.37 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2121 8086 4.91 %
Rwork0.1769 156520 -
obs0.1786 164606 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.05 Å2 / Biso mean: 19.185 Å2 / Biso min: 9.33 Å2
Refinement stepCycle: final / Resolution: 1.45→38.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8092 0 0 717 8809
Biso mean---27.12 -
Num. residues----1048
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.470.22822060.18583699390570
1.47-1.490.20792420.18085214545698
1.49-1.510.21452850.17335170545598
1.51-1.530.20052800.16525194547499
1.53-1.550.16722500.15545251550198
1.55-1.570.20122950.15355206550199
1.57-1.590.20542620.15755207546999
1.59-1.610.17622890.15175216550599
1.61-1.640.22812590.16195281554099
1.64-1.660.19852630.1615194545799
1.66-1.690.20022640.15555274553899
1.69-1.720.16892520.15515237548999
1.72-1.760.21372730.1645246551999
1.76-1.790.19552870.15295258554599
1.79-1.830.20922540.16135267552199
1.83-1.870.20682830.16655226550999
1.87-1.920.19822800.1575248552899
1.92-1.970.22052510.173952945545100
1.97-2.030.21212540.16375323557799
2.03-2.10.22712790.175752785557100
2.1-2.170.21572900.174552935583100
2.17-2.260.21112650.170952795544100
2.26-2.360.20892620.174452895551100
2.36-2.490.22762990.178952735572100
2.49-2.640.22652730.172753695642100
2.64-2.850.21912620.185852985560100
2.85-3.130.22632910.195553355626100
3.13-3.590.24062760.194353405616100
3.59-4.520.18692700.175553555625100
4.52-38.370.20942900.19555406569699

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