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- PDB-1li9: Crystal structure of TEM-34 beta-Lactamase at 1.5 Angstrom -

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Basic information

Entry
Database: PDB / ID: 1li9
TitleCrystal structure of TEM-34 beta-Lactamase at 1.5 Angstrom
ComponentsClass A beta-Lactamase- TEM-34
KeywordsHYDROLASE / beta-Lactamase / antibiotic resistance / TEM-34
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: 1.52 Å
AuthorsWang, X. / Minasov, G. / Shoichet, B.K.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: The structural bases of antibiotic resistance in the clinically derived mutant beta-lactamases TEM-30, TEM-32, and TEM-34.
Authors: Wang, X. / Minasov, G. / Shoichet, B.K.
History
DepositionApr 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: Class A beta-Lactamase- TEM-34
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1394
Polymers28,9101
Non-polymers2293
Water7,134396
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.371, 59.604, 88.291
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 Class A beta-Lactamase- TEM-34


Mass: 28909.932 Da / Num. of mol.: 1 / Mutation: M69V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla / Plasmid: pAlter 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.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 1.88 Å3/Da / Density % sol: 34.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: sodium-potassium buffer, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Crystal grow
*PLUS
Details: used seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
20.65 Msodium potassium Pi buffer1droppH8.0
31.4 Msodium potassium Pi buffer1reservoirpH8.0

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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: Dec 19, 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: 1.52→17 Å / Num. all: 34443 / Num. obs: 34443 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 29.5
Reflection shellResolution: 1.52→1.57 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 4.7 / Num. unique all: 3401 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 17 Å / Num. measured all: 208926
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

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

1jwp


Resolution: 1.52→17 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Crystallographic conjugate gradient minimization refinement using maximum likelihood target for amplitudes
RfactorNum. reflection% reflectionSelection details
Rfree0.189 2773 -Random
Rwork0.177 ---
all-32945 --
obs-32945 96 %-
Displacement parametersBiso mean: 19.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.652 Å20 Å20 Å2
2---3.108 Å20 Å2
3---2.456 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.52→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2090 0 11 419 2520
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.06
X-RAY DIFFRACTIONc_improper_angle_d1.04
LS refinement shellResolution: 1.52→1.57 Å
RfactorNum. reflection% reflection
Rfree0.319 183 -
Rwork0.275 --
obs-2875 90.9 %
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.06
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.04

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