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- PDB-3jyi: Structural and biochemical evidence that a TEM-1 {beta}-lactamase... -

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Basic information

Entry
Database: PDB / ID: 3jyi
TitleStructural and biochemical evidence that a TEM-1 {beta}-lactamase Asn170Gly active site mutant acts via substrate-assisted catalysis
ComponentsBeta-lactamase TEM
KeywordsHYDROLASE / Beta-lactamase / Enzyme / antibiotic resistance / Disulfide bond / Plasmid / Transposable element
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
PHOSPHATE ION / Beta-lactamase TEM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.703 Å
AuthorsBrown, N.G. / Palzkill, T.G. / Prasad, B.V.V. / Shanker, S.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural and biochemical evidence that a TEM-1 beta-lactamase N170G active site mutant acts via substrate-assisted catalysis
Authors: Brown, N.G. / Shanker, S. / Prasad, B.V. / Palzkill, T.
History
DepositionSep 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: 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
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)175,11916
Polymers173,3106
Non-polymers1,81010
Water3,135174
1
A: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2183
Polymers28,8851
Non-polymers3332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2183
Polymers28,8851
Non-polymers3332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2183
Polymers28,8851
Non-polymers3332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1232
Polymers28,8851
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2183
Polymers28,8851
Non-polymers3332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1232
Polymers28,8851
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.099, 88.099, 500.352
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-ID
11
21
31
41
51
61

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 26:288 )
211chain B and (resseq 26:288 )
311chain C and (resseq 26:288 )
411chain D and (resseq 26:288 )
511chain E and (resseq 26:288 )
611chain F and (resseq 26:288 )

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Components

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


Mass: 28884.943 Da / Num. of mol.: 6 / Mutation: N170G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: bla, blaT-3, blaT-4, blaT-5, blaT-6, TEM-1 / Plasmid: pET-24a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62593, beta-lactamase
#2: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O

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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: 2.8 Å3/Da / Density % sol: 56.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG6000, 0.2 M LiCl, 0.1 M Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 29, 2008
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 55684 / Num. obs: 55684 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 16.1
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2 / Num. unique all: 2694 / % possible all: 99.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.4_95)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BTL

1btl


Resolution: 2.703→39.277 Å / SU ML: 0.38 / σ(F): 0.1 / Phase error: 28.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2602 2624 5.05 %Random
Rwork0.2296 ---
obs0.2312 51923 93.31 %-
all-51923 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.856 Å2 / ksol: 0.324 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.0022 Å20 Å2-0 Å2
2--9.0022 Å2-0 Å2
3----18.0044 Å2
Refinement stepCycle: LAST / Resolution: 2.703→39.277 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12132 0 110 174 12416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812448
X-RAY DIFFRACTIONf_angle_d1.09116848
X-RAY DIFFRACTIONf_dihedral_angle_d18.9284680
X-RAY DIFFRACTIONf_chiral_restr0.071920
X-RAY DIFFRACTIONf_plane_restr0.0042172
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2022X-RAY DIFFRACTIONPOSITIONAL
12B2022X-RAY DIFFRACTIONPOSITIONAL0.04
13C2022X-RAY DIFFRACTIONPOSITIONAL0.043
14D2022X-RAY DIFFRACTIONPOSITIONAL0.044
15E2022X-RAY DIFFRACTIONPOSITIONAL0.044
16F2022X-RAY DIFFRACTIONPOSITIONAL0.047
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7028-2.75190.34731330.31012190X-RAY DIFFRACTION81
2.7519-2.80480.34351220.29512221X-RAY DIFFRACTION83
2.8048-2.86210.33981070.28712379X-RAY DIFFRACTION86
2.8621-2.92430.40371230.27462379X-RAY DIFFRACTION88
2.9243-2.99230.28581390.26742383X-RAY DIFFRACTION88
2.9923-3.06710.31821370.27382481X-RAY DIFFRACTION91
3.0671-3.150.35151310.28562536X-RAY DIFFRACTION92
3.15-3.24260.33881510.26562518X-RAY DIFFRACTION93
3.2426-3.34730.32941410.25742589X-RAY DIFFRACTION94
3.3473-3.46680.28561310.24722644X-RAY DIFFRACTION96
3.4668-3.60550.26131380.22942654X-RAY DIFFRACTION97
3.6055-3.76950.25361460.22272700X-RAY DIFFRACTION97
3.7695-3.96810.26961340.21882709X-RAY DIFFRACTION97
3.9681-4.21640.21261280.2052723X-RAY DIFFRACTION97
4.2164-4.54150.24561410.19132726X-RAY DIFFRACTION98
4.5415-4.99770.21551530.18642770X-RAY DIFFRACTION99
4.9977-5.7190.24731650.2082782X-RAY DIFFRACTION98
5.719-7.19810.21021370.21042847X-RAY DIFFRACTION98
7.1981-39.28160.18481670.2013068X-RAY DIFFRACTION99

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