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- PDB-1ny0: Crystal Structure of the complex between M182T mutant of TEM-1 an... -

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Basic information

Entry
Database: PDB / ID: 1ny0
TitleCrystal Structure of the complex between M182T mutant of TEM-1 and a boronic acid inhibitor (NBF)
ComponentsBeta-lactamase TEM
KeywordsHYDROLASE / Antibiotic resistance / beta-lactamase / acylation 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
: / [(2-ETHOXY-1-NAPHTHOYL)AMINO]METHYLBORONIC ACID / 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. / 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 / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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_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 1.5Nov 20, 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)29,3194
Polymers28,9121
Non-polymers4073
Water6,612367
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.289, 58.967, 88.630
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / 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: Chemical ChemComp-NBF / [(2-ETHOXY-1-NAPHTHOYL)AMINO]METHYLBORONIC ACID


Mass: 273.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16BNO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 1.48 Å3/Da / Density % sol: 16.42 %
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: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 27, 2002 / 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→19 Å / Num. all: 22129 / Num. obs: 22129 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 27.5
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 3.5 / Num. unique all: 2162 / % possible all: 97.7
Reflection
*PLUS
Num. measured all: 125153
Reflection shell
*PLUS
% possible obs: 97.7 % / Num. unique obs: 2162 / Rmerge(I) obs: 0.413

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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: 1.75→19 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
Rfree0.198 2061 -Random
Rwork0.171 ---
all-22481 --
obs-21232 94.4 %-
Displacement parametersBiso mean: 20.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.831 Å20 Å20 Å2
2---8.443 Å20 Å2
3---5.612 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.75→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2116 0 46 436 2598
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d20.9
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it1.6651.5
X-RAY DIFFRACTIONc_scbond_it2.6252
X-RAY DIFFRACTIONc_mcangle_it2.1262
X-RAY DIFFRACTIONc_scangle_it3.6122.5
LS refinement shellResolution: 1.75→1.81 Å
RfactorNum. reflection% reflection
Rfree0.2996 181 -
Rwork0.2915 --
obs-1885 85.14 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4naftb.param
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.44
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89

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