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- PDB-1pi4: Structure of N289A mutant of AmpC in complex with SM3, a phenylgl... -

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Basic information

Entry
Database: PDB / ID: 1pi4
TitleStructure of N289A mutant of AmpC in complex with SM3, a phenylglyclboronic acid bearing the cephalothin R1 side chain
ComponentsBeta-lactamase
KeywordsHYDROLASE / Enzyme Inhibitor Complex / Beta-Lactamase
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / Chem-SM3 / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsRoth, T.A. / Minasov, G. / Focia, P.J. / Shoichet, B.K.
CitationJournal: Biochemistry / Year: 2003
Title: Thermodynamic cycle analysis and inhibitor design against beta-lactamase.
Authors: Roth, T.A. / Minasov, G. / Morandi, S. / Prati, F. / Shoichet, B.K.
History
DepositionMay 29, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 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 / 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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 1.5Oct 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
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,8137
Polymers79,0902
Non-polymers7235
Water18,8621047
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9544
Polymers39,5451
Non-polymers4093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8593
Polymers39,5451
Non-polymers3142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.628, 76.104, 97.836
Angle α, β, γ (deg.)90.00, 115.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-lactamase / Cephalosporinase


Mass: 39544.898 Da / Num. of mol.: 2 / Fragment: AmpC / Mutation: N289A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: AMPC OR AMPA OR B4150 / Plasmid: POGO295 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, 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.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-SM3 / (1R)-1-(2-THIENYLACETYLAMINO)-1-PHENYLMETHYLBORONIC ACID


Mass: 275.131 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H14BNO3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1047 / 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: 1.99 Å3/Da / Density % sol: 37.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: Potassium Phosphate Buffer, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 23 ℃ / Method: vapor diffusion, hanging drop / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.7 Mpotassium phosphate1reservoirpH8.7
23.8 mg/mlprotein1drop
31.2 %DMSO1drop
41 Mpotassium phosphate1droppH8.7

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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 1, 2002 / Details: Mirrors
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.39→20 Å / Num. all: 156947 / Num. obs: 156947 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 29
Reflection shellResolution: 1.39→1.44 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.134 / Mean I/σ(I) obs: 10.4 / Num. unique all: 15495 / % possible all: 98.3
Reflection
*PLUS
Num. measured all: 903131
Reflection shell
*PLUS
Lowest resolution: 1.45 Å / % possible obs: 98.3 % / Num. unique obs: 15495

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Processing

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

1mxo


Resolution: 1.39→20 Å
Isotropic thermal model: Isotropic with refined individual B-factors
Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Maximum Likelihood in the refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.173 6345 4 %Random
Rwork0.159 ---
all0.159 157400 --
obs-155164 98.6 %-
Solvent computationBsol: 250 Å2 / ksol: 0.732 e/Å3
Displacement parametersBiso mean: 17 Å2
Baniso -1Baniso -2Baniso -3
1-0.065 Å20 Å2-1.324 Å2
2--0.704 Å20 Å2
3----0.768 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.14 Å0.13 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.39→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5986 0 60 1111 7157
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.2
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it1.862
X-RAY DIFFRACTIONc_scbond_it2.642
X-RAY DIFFRACTIONc_scangle_it3.712.5
LS refinement shellResolution: 1.39→1.44 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.23 809 5.14 %
Rwork0.209 14231 -
obs--95.64 %
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.71
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.2

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