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- PDB-2zc7: Crystal Structure of Class C beta-Lactamase ACT-1 -

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Basic information

Entry
Database: PDB / ID: 2zc7
TitleCrystal Structure of Class C beta-Lactamase ACT-1
ComponentsBeta-lactamase ACT-1
KeywordsHYDROLASE / two-domain structure
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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsShimizu-Ibuka, A. / Sakai, H. / Galleni, M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Structure of the plasmid-mediated class C beta-lactamase ACT-1
Authors: Shimizu-Ibuka, A. / Bauvois, C. / Sakai, H. / Galleni, M.
History
DepositionNov 2, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase ACT-1
B: Beta-lactamase ACT-1
C: Beta-lactamase ACT-1
D: Beta-lactamase ACT-1


Theoretical massNumber of molelcules
Total (without water)157,2884
Polymers157,2884
Non-polymers00
Water6,413356
1
A: Beta-lactamase ACT-1


Theoretical massNumber of molelcules
Total (without water)39,3221
Polymers39,3221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase ACT-1


Theoretical massNumber of molelcules
Total (without water)39,3221
Polymers39,3221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase ACT-1


Theoretical massNumber of molelcules
Total (without water)39,3221
Polymers39,3221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase ACT-1


Theoretical massNumber of molelcules
Total (without water)39,3221
Polymers39,3221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.047, 80.521, 86.881
Angle α, β, γ (deg.)76.23, 68.88, 63.46
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Beta-lactamase ACT-1


Mass: 39321.953 Da / Num. of mol.: 4 / Fragment: residues in database 23-381
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q48428, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.81 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG4000, 0.1M Tris-HCl, 0.2M sodium acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 28, 2003
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 86460 / Num. obs: 86460 / % possible obs: 89.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 2 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 14.7
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 30.2 / Num. unique all: 8455 / % possible all: 84.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1XX2

1xx2


Resolution: 2.4→20 Å / Isotropic thermal model: anisotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 6747 -random
Rwork0.24 ---
obs0.24 67758 98.5 %-
all-67762 --
Refine analyzeLuzzati coordinate error obs: 0.51 Å / Luzzati d res low obs: 20 Å / Luzzati sigma a obs: -0.89 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11088 0 0 356 11444
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.021
X-RAY DIFFRACTIONc_angle_deg2.54
LS refinement shellResolution: 2.4→2.51 Å

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