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- PDB-1kvm: X-ray Crystal Structure of AmpC WT beta-Lactamase in Complex with... -

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Basic information

Entry
Database: PDB / ID: 1kvm
TitleX-ray Crystal Structure of AmpC WT beta-Lactamase in Complex with Covalently Bound Cephalothin
Componentsbeta-lactamase
KeywordsHYDROLASE / amide hydrolase / beta-lactamase / cephalothin / acyl-enzyme 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-CEO / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsBeadle, B.M. / Trehan, I. / Focia, P.J. / Shoichet, B.K.
CitationJournal: Structure / Year: 2002
Title: Structural milestones in the reaction pathway of an amide hydrolase: substrate, acyl, and product complexes of cephalothin with AmpC beta-lactamase.
Authors: Beadle, B.M. / Trehan, I. / Focia, P.J. / Shoichet, B.K.
History
DepositionJan 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 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 9, 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)79,6094
Polymers79,1762
Non-polymers4332
Water6,107339
1
A: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6832
Polymers39,5881
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9262
Polymers39,5881
Non-polymers3381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.69, 77.20, 97.59
Angle α, β, γ (deg.)90.0, 116.13, 90.0
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-CEO / 5-METHYLENE-2-[2-OXO-1-(2-THIOPHEN-2-YL-ACETYLAMINO)-ETHYL]-5,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID / HYDROLYZED CEPHALOTHIN


Mass: 338.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14N2O4S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.51 Å3/Da / Density % sol: 51.06 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 1.7 M potassium phosphate, then crystal soaked with saturated cephalothin solution in crystallizing buffer for 2x 15 minutes, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Temperature: 23 ℃
Components of the solutions
*PLUS
Conc.: 1.7 M / Common name: potassium phosphate / Details: pH8.7

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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: Jul 5, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.06→20 Å / Num. obs: 46729 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 23.2
Reflection shellResolution: 2.06→2.11 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.93 / % possible all: 83.4
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 168893
Reflection shell
*PLUS
% possible obs: 83.4 % / Rmerge(I) obs: 0.32

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FSY

1fsy


Resolution: 2.06→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.219 2071 Random
Rwork0.176 --
all-46729 -
obs-41731 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.888 Å20 Å2-6.252 Å2
2--0.242 Å20 Å2
3---1.646 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.06→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5541 0 27 339 5907
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_mcbond_it1.2391.5
X-RAY DIFFRACTIONc_scbond_it2.0192
X-RAY DIFFRACTIONc_mcangle_it1.8872
X-RAY DIFFRACTIONc_scangle_it2.9362.5
LS refinement shellResolution: 2.06→2.13 Å
RfactorNum. reflection
Rfree0.311 138
Rwork0.221 -
obs-2916
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2cephalothin.parcephalothin.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Lowest resolution: 2.11 Å

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