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- PDB-1jwp: Structure of M182T mutant of TEM-1 beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 1jwp
TitleStructure of M182T mutant of TEM-1 beta-lactamase
ComponentsBETA-LACTAMASE TEM
KeywordsHYDROLASE / Protein stability / TEM-1 / beta-lactamase / antibiotic resistance / evolution
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: 1.75 Å
AuthorsWang, X. / Minasov, G. / Shoichet, B.K.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs.
Authors: Wang, X. / Minasov, G. / Shoichet, B.K.
History
DepositionSep 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-LACTAMASE TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0072
Polymers28,9121
Non-polymers951
Water4,936274
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.465, 61.691, 89.205
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BETA-LACTAMASE TEM


Mass: 28911.904 Da / Num. of mol.: 1 / Fragment: TEM-1 / Mutation: M182T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla / Plasmid: pAiter EX II / Production host: Escherichia coli (E. coli) / Strain (production host): SF120 / References: UniProt: P62593, beta-lactamase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 1.75 Å3/Da / Density % sol: 29.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: sodium-potassium phosphate buffer, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
Conc.: 1.5 M / Common name: sodium phosphate / Details: pH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2001 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. all: 22408 / Num. obs: 22408 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 30.23
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 6.4 / Num. unique all: 2202 / % possible all: 93.3
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 93.3 % / Num. unique obs: 2202

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BTL

1btl


Resolution: 1.75→19 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Crystallographic conjugate gradient minimization refinement using maximum likelihood target for amplitudes
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2163 10 %random
Rwork0.186 ---
obs-21771 91.7 %-
Displacement parametersBiso mean: 21.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.93 Å20 Å20 Å2
2---5.139 Å20 Å2
3---1.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.75→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2026 0 5 291 2322
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.46
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d1
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.75-1.810.2838207100.23422202220293.3
1.81-1.890.24622080.2016220893.8
1.89-1.970.23391960.1909219893.3
1.97-2.070.24462230.1859218192.2
2.07-2.20.22892270.1835218592.4
2.2-2.370.20792220.1659221093.6
2.37-2.610.21722210.1815228495.7
2.61-2.990.23892190.1898233296
2.99-3.760.1922210.1788230394.7
3.76-190.20922290.1876230589.9
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.186 / Rfactor Rfree: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1
LS refinement shell
*PLUS
Rfactor obs: 0.2342

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