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- PDB-1l0d: X-ray Crystal Structure of AmpC S64D Mutant beta-Lactamase -

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Basic information

Entry
Database: PDB / ID: 1l0d
TitleX-ray Crystal Structure of AmpC S64D Mutant beta-Lactamase
Componentsbeta-lactamase
KeywordsHYDROLASE / amide hydrolase / beta-lactamase / mutant enzyme
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 / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsBeadle, B.M. / Shoichet, B.K.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Structural bases of stability-function tradeoffs in enzymes.
Authors: Beadle, B.M. / Shoichet, B.K.
History
DepositionFeb 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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)79,3273
Polymers79,2322
Non-polymers951
Water10,845602
1
A: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7112
Polymers39,6161
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: beta-lactamase


Theoretical massNumber of molelcules
Total (without water)39,6161
Polymers39,6161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.672, 76.504, 97.722
Angle α, β, γ (deg.)90.00, 115.65, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein beta-lactamase / Cephalosporinase


Mass: 39615.934 Da / Num. of mol.: 2 / Mutation: S64D
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 602 / 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: 51.26 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 1.7 M potassium phosphate, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Details: used to seeding, Usher, K.C., (1998) Biochemistry, 37, 16082.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.7 Msodium potassium phosphate1reservoirpH8.7
210 mg/mlprotein1drop

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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: May 16, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.53→20 Å / Num. obs: 118322 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 25.4
Reflection shellResolution: 1.53→1.57 Å / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 2.7 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 427291
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1C3B

1c3b


Resolution: 1.53→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.204 11856 Random
Rwork0.186 --
all-118322 -
obs-118322 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.978 Å20 Å2-1.486 Å2
2--0.157 Å20 Å2
3---1.821 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.098 Å0.068 Å
Refinement stepCycle: LAST / Resolution: 1.53→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5473 0 5 602 6080
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_mcbond_it0.9011.5
X-RAY DIFFRACTIONc_scbond_it1.6512
X-RAY DIFFRACTIONc_mcangle_it1.4182
X-RAY DIFFRACTIONc_scangle_it2.462.5
LS refinement shellResolution: 1.53→1.58 Å
RfactorNum. reflection
Rfree0.274 1175
Rwork0.238 -
obs-10570
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water.param
X-RAY DIFFRACTION3ion.param
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.78
X-RAY DIFFRACTIONc_mcbond_it0.901

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