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- PDB-1nxy: Crystal Structure of the complex between M182T mutant of TEM-1 an... -

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Basic information

Entry
Database: PDB / ID: 1nxy
TitleCrystal Structure of the complex between M182T mutant of TEM-1 and a boronic acid inhibitor (SM2)
ComponentsBeta-lactamase TEM
KeywordsHYDROLASE / Antibiotic resistance / beta-lactamase / deacylation transition-state analog
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
: / Chem-SM2 / Beta-lactamase TEM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWang, X. / Minasov, G. / Blazquez, J. / Caselli, E. / Prati, F. / Shoichet, B.K.
CitationJournal: Biochemistry / Year: 2003
Title: Recognition and Resistance in TEM beta-lactamase
Authors: Wang, X. / Minasov, G. / Blazquez, J. / Caselli, E. / Prati, F. / Shoichet, B.K.
History
DepositionFeb 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5894
Polymers28,9121
Non-polymers6773
Water8,053447
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.625, 34.560, 105.360
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 / 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: 28911.904 Da / Num. of mol.: 1 / Mutation: M182T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla / Plasmid: pAlter EX II-TEM-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62593, beta-lactamase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-SM2 / (1R)-1-(2-THIENYLACETYLAMINO)-1-(3-CARBOXYPHENYL)METHYLBORONIC ACID


Mass: 319.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H14BNO5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 447 / 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: 2.32 Å3/Da / Density % sol: 46.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: sodium-potassium buffer, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
13-5 mg/mlenzyme1drop
22.5-3.0 mMboronic acid inhibitor1drop
30.65-0.70 Msodium potassium phosphate1droppH8.3
41.4 Mpotassium phosphate1reservoirpH8.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.98012 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 4, 2001 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98012 Å / Relative weight: 1
ReflectionResolution: 1.6→15 Å / Num. all: 36330 / Num. obs: 36330 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 29.8
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 7.2 / Num. unique all: 3568 / % possible all: 99.5
Reflection
*PLUS
Num. measured all: 220946
Reflection shell
*PLUS
% possible obs: 99.5 % / Num. unique obs: 3568

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Processing

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

1jwp


Resolution: 1.6→15 Å
Isotropic thermal model: Isotropic, individual B values refined
Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Maximum likelihood target for amplitudes was used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.196 3580 -Random
Rwork0.172 ---
all-36317 --
obs-35945 99 %-
Displacement parametersBiso mean: 15.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.116 Å20 Å20 Å2
2--2.725 Å20 Å2
3----2.609 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2365 0 45 510 2920
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.51
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_mcbond_it1.5511.5
X-RAY DIFFRACTIONc_mcangle_it1.9922
X-RAY DIFFRACTIONc_scbond_it2.6632
X-RAY DIFFRACTIONc_scangle_it3.5362.5
LS refinement shellResolution: 1.6→1.66 Å
RfactorNum. reflection% reflection
Rfree0.2772 337 -
Rwork0.2485 --
obs-3120 96.35 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3sme_sem.param
X-RAY DIFFRACTION4ion.param
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.198 / Rfactor Rwork: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.52
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.98

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