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- PDB-1o07: Crystal Structure of the complex between Q120L/Y150E mutant of Am... -

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Basic information

Entry
Database: PDB / ID: 1o07
TitleCrystal Structure of the complex between Q120L/Y150E mutant of AmpC and a beta-lactam inhibitor (MXG)
ComponentsBeta-lactamase
KeywordsHYDROLASE / Enzyme Inhibitor Complex / Beta-Lactamase beta-lactam complex
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
: / Chem-MXG / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsMeroueh, S.O. / Minasov, G. / Lee, W. / Shoichet, B.K. / Mobashery, S.
CitationJournal: J.Am.Chem.Soc. / Year: 2003
Title: Structural Aspects for Evolution of beta-Lactamases from Penicillin-Binding Proteins
Authors: Meroueh, S.O. / Minasov, G. / Lee, W. / Shoichet, B.K. / Mobashery, S.
History
DepositionFeb 20, 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: Atomic model / 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 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3256
Polymers79,0782
Non-polymers1,2474
Water14,520806
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1633
Polymers39,5391
Non-polymers6242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1633
Polymers39,5391
Non-polymers6242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.808, 76.298, 98.127
Angle α, β, γ (deg.)90.00, 116.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-lactamase / / Cephalosporinase


Mass: 39538.891 Da / Num. of mol.: 2 / Mutation: Q120L, Y150E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: POGO295 / Production host: Escherichia coli (E. coli) / References: UniProt: P00811, beta-lactamase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-MXG / 2-(1-{2-[4-(2-ACETYLAMINO-PROPIONYLAMINO)-4-CARBOXY-BUTYRYLAMINO]-6-AMINO-HEXANOYLAMINO}-2-OXO-ETHYL)-5-METHYLENE-5,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID


Mass: 584.642 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H36N6O9S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 806 / 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: 2.52 Å3/Da / Density % sol: 51.25 %
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
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
13.9 mg/mlprotein1drop
21.0 Mpotassium phosphate1droppH8.7
31.7 Mpotassium phosphate1reservoirpH8.7

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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: Aug 20, 2000 / Details: Mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.71→25 Å / Num. all: 83273 / Num. obs: 83273 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 32.7
Reflection shellResolution: 1.71→1.77 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.122 / Mean I/σ(I) obs: 10.7 / Num. unique all: 8238 / % possible all: 97
Reflection
*PLUS
Num. measured all: 440555
Reflection shell
*PLUS
% possible obs: 97 %

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Isotropic with individual B factors refined

Resolution: 1.71→24.77 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.106 / ESU R Free: 0.103 / Stereochemistry target values: Engh & Huber / Details: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19105 4052 5 %RANDOM
Rwork0.15366 ---
obs0.15552 76559 98.1 %-
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: 12.264 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å20 Å20.87 Å2
2---0.61 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.71→24.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5572 0 82 806 6460
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0216737
X-RAY DIFFRACTIONr_bond_other_d00.025941
X-RAY DIFFRACTIONr_angle_refined_deg2.091.9619308
X-RAY DIFFRACTIONr_angle_other_deg4.079313994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1125888
X-RAY DIFFRACTIONr_chiral_restr0.1270.2981
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.027932
X-RAY DIFFRACTIONr_gen_planes_other0.0130.021295
X-RAY DIFFRACTIONr_nbd_refined0.1610.21281
X-RAY DIFFRACTIONr_nbd_other0.2230.26250
X-RAY DIFFRACTIONr_nbtor_other0.1130.23164
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.298
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.236
X-RAY DIFFRACTIONr_mcbond_it1.1681.54120
X-RAY DIFFRACTIONr_mcangle_it1.91126775
X-RAY DIFFRACTIONr_scbond_it3.07932614
X-RAY DIFFRACTIONr_scangle_it4.7854.52532
LS refinement shellResolution: 1.71→1.755 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 284 -
Rwork0.181 5519 -
obs-5519 97 %
Refinement
*PLUS
Lowest resolution: 25 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.191 / Rfactor Rwork: 0.154
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.017
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2

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