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- PDB-1jwz: Crystal structure of TEM-64 beta-lactamase in complex with a boro... -

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Basic information

Entry
Database: PDB / ID: 1jwz
TitleCrystal structure of TEM-64 beta-lactamase in complex with a boronic acid inhibitor (105)
ComponentsBeta-lactamase TEM
KeywordsHYDROLASE / tem-64 / beta-lactamase / serine hydrolase / evolution / antibiotic resistance
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-105 / Beta-lactamase TEM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 5, 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_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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 9, 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)29,1362
Polymers28,8421
Non-polymers2941
Water5,963331
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.002, 34.546, 105.489
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: 28841.854 Da / Num. of mol.: 1 / Fragment: TEM-64 / Mutation: E104K/M182T/R164S
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-105 / N-[5-METHYL-3-O-TOLYL-ISOXAZOLE-4-CARBOXYLIC ACID AMIDE] BORONIC ACID / CLOXACILLIN DERIVATIVE


Mass: 294.499 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H12BClN2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 1.95 Å3/Da / Density % sol: 36.32 %
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
IDConc.Common nameCrystal-IDSol-IDDetails
11.5 Msodium phosphate11pH8.0
22.5 mMtransition-state analogs11

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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: Jul 5, 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: 1.8→20 Å / Num. all: 25091 / Num. obs: 25031 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 42.16
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.9 / Num. unique all: 2445 / % possible all: 99.9
Reflection shell
*PLUS
% possible obs: 99.9 % / Num. unique obs: 2445 / Rmerge(I) obs: 0.28

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Processing

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

1btl


Resolution: 1.8→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
Rfree0.189 2028 10 %random
Rwork0.168 ---
all-25164 --
obs-24312 96.6 %-
Displacement parametersBiso mean: 19.1 Å2
Baniso -1Baniso -2Baniso -3
1--5.414 Å20 Å20 Å2
2--1.81 Å20 Å2
3---3.604 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2045 0 20 342 2407
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.55
X-RAY DIFFRACTIONc_dihedral_angle_d21.74
X-RAY DIFFRACTIONc_improper_angle_d0.95
LS refinement shellResolution: 1.8→1.86 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.275 103 10 %
Rwork0.237 1986 -
obs-1986 85.5 %
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor obs: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.56
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.74
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95
LS refinement shell
*PLUS
Rfactor obs: 0.237

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