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- PDB-1kdw: X-ray crystal structure of AmpC beta-lactamase from E. coli in co... -

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Basic information

Entry
Database: PDB / ID: 1kdw
TitleX-ray crystal structure of AmpC beta-lactamase from E. coli in complex with the inhibitor 4-carboxyphenylboronic acid
Componentsbeta-lactamase
KeywordsHYDROLASE / cephalosporinase / beta-lactamase / serine hydrolase / phenylboronic acid inhibitor
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
4-CARBOXYPHENYLBORONIC ACID / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsPowers, R.A. / Shoichet, B.K.
CitationJournal: J.Med.Chem. / Year: 2002
Title: Structure-based approach for binding site identification on AmpC beta-lactamase.
Authors: Powers, R.A. / Shoichet, B.K.
History
DepositionNov 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)79,6035
Polymers79,1762
Non-polymers4273
Water4,738263
1
A: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8493
Polymers39,5881
Non-polymers2612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7542
Polymers39,5881
Non-polymers1661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.550, 77.380, 97.330
Angle α, β, γ (deg.)90.00, 115.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein beta-lactamase / Cephalosporinase


Mass: 39587.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: K12 / 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-4CB / 4-CARBOXYPHENYLBORONIC ACID


Mass: 165.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7BO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.55 Å3/Da / Density % sol: 51.71 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 1.7 M potassium phosphate, 485 uM 4-carboxyphenylboronic acid, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Temperature: 23 ℃ / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.7 Mpotassium phosphate1reservoirpH8.7
20.485 mMprotein1drop
31.7 Mpotassium phosphate1droppH8.7

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.28→20 Å / Num. all: 36794 / Num. obs: 33450 / % possible obs: 91 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Biso Wilson estimate: 25.46 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 16.2
Reflection shellResolution: 2.28→2.37 Å / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.5 / % possible all: 62.6
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 90630 / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
% possible obs: 62.6 % / Rmerge(I) obs: 0.19

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Processing

Software
NameVersionClassification
X-PLORmodel building
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1C3B

1c3b


Resolution: 2.28→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 3282 10 %random
Rwork0.186 ---
all-33450 --
obs-33018 --
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.28→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5553 0 29 263 5845
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
LS refinement shellResolution: 2.28→2.37 Å
RfactorNum. reflection% reflection
Rfree0.345 263 10 %
Rwork0.252 --
obs-2632 -
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.234 / Rfactor Rwork: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.345 / Rfactor Rwork: 0.252

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