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

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Basic information

Entry
Database: PDB / ID: 1nym
TitleCrystal Structure of the complex between M182T mutant of TEM-1 and a boronic acid inhibitor (CXB)
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
Chem-CXB / : / PHOSPHATE ION / Beta-lactamase TEM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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. / Caselli, E. / Prati, F. / Shoichet, B.K.
History
DepositionFeb 12, 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
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)29,4777
Polymers28,9121
Non-polymers5656
Water7,855436
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.344, 61.659, 89.129
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.: 3 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CXB / [(2-AMINO-ALPHA-METHOXYIMINO-4-THIAZOLYLACETYL)AMINO]METHYLBORONIC ACID


Mass: 258.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11BN4O4S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 1.96 Å3/Da / Density % sol: 37.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: sodium-potassium buffer, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K
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 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 6, 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: 1.2→15 Å / Num. all: 71168 / Num. obs: 71168 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 30.3
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 4.1 / Num. unique all: 6965 / % possible all: 98
Reflection
*PLUS
Num. measured all: 421106 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 98 % / Num. unique obs: 6965

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXmodel building
SHELXL-97refinement
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JWP

1jwp


Resolution: 1.2→15 Å / Num. parameters: 26888 / Num. restraintsaints: 46021 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Konnert-Hendrickson Conjugate-Gradient Algorithm used in Refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.148 3556 -RANDOM
Rwork0.1062 ---
all-67554 --
obs-67554 93.9 %-
Displacement parametersBiso mean: 16.7 Å2
Refine analyzeNum. disordered residues: 170 / Occupancy sum hydrogen: 2034 / Occupancy sum non hydrogen: 2419.54
Refinement stepCycle: LAST / Resolution: 1.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2434 0 30 488 2952
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.017
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.014
X-RAY DIFFRACTIONs_zero_chiral_vol0.083
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.087
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.046
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.01
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.039
X-RAY DIFFRACTIONs_approx_iso_adps0.082
LS refinement shellResolution: 1.2→1.24 Å
RfactorNum. reflection% reflection
Rfree0.197 304 -
Rwork0.172 --
obs-6075 91.64 %
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rwork: 0.106
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.46

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