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- PDB-1pzp: TEM-1 Beta-Lactamase in Complex with a Novel, Core-Disrupting, Al... -

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Basic information

Entry
Database: PDB / ID: 1pzp
TitleTEM-1 Beta-Lactamase in Complex with a Novel, Core-Disrupting, Allosteric Inhibitor
ComponentsBeta-lactamase TEM
KeywordsHYDROLASE / beta-lactamase / novel allosteric inhibitor / core-disruption
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-FTA / Beta-lactamase TEM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsHorn, J.R. / Shoichet, B.K.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Allosteric inhibition through core disruption.
Authors: Horn, J.R. / Shoichet, B.K.
History
DepositionJul 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2004Provider: 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

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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)29,5923
Polymers28,9851
Non-polymers6072
Water4,089227
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.553, 60.673, 89.092
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase TEM / E.C.3.5.2.6 / 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 / TEM beta-lactamase / ampicillin resistance protein


Mass: 28985.088 Da / Num. of mol.: 1 / Mutation: R100N
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-FTA / 3-(4-PHENYLAMINO-PHENYLAMINO)-2-(1H-TETRAZOL-5-YL)-ACRYLONITRILE


Mass: 303.321 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H13N7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 1.74 Å3/Da / Density % sol: 28.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: potassium phosphate buffer, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
pH: 8 / Method: other / Details: Wang, X., (2002) J.Mol.Biol., 320, 85.
Components of the solutions
*PLUS
Conc.: 1.5 M / Common name: sodium phosphate / Details: pH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.97014 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 4, 2003 / Details: Mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97014 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. all: 40724 / Num. obs: 40562 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 5.77
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 1.6 / Num. unique all: 20643 / % possible all: 99.8
Reflection
*PLUS
Highest resolution: 1.47 Å / Lowest resolution: 20 Å / Num. obs: 38464 / % possible obs: 99.51 % / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
Highest resolution: 1.47 Å / Lowest resolution: 1.58 Å / % possible obs: 99.8 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 1.449 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.083 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24487 2025 5 %RANDOM
Rwork0.20091 ---
obs0.20313 38464 99.46 %-
all-40562 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.786 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å20 Å2
2--0.85 Å20 Å2
3----0.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.089 Å0.083 Å
Refinement stepCycle: LAST / Resolution: 1.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 46 227 2303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0212113
X-RAY DIFFRACTIONr_angle_refined_deg1.8641.9932854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9385260
X-RAY DIFFRACTIONr_chiral_restr0.1270.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021568
X-RAY DIFFRACTIONr_nbd_refined0.3250.21084
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3880.285
X-RAY DIFFRACTIONr_mcbond_it1.1261.51304
X-RAY DIFFRACTIONr_mcangle_it1.88522092
X-RAY DIFFRACTIONr_scbond_it2.8813809
X-RAY DIFFRACTIONr_scangle_it4.5124.5762
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.31 146
Rwork0.265 2801
obs-5834
Refinement
*PLUS
Highest resolution: 1.47 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.234 / Rfactor Rwork: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.019
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.89

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