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- PDB-1zc2: Crystal Structure of plasmid-encoded class C beta-lactamase CMY-2... -

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Basic information

Entry
Database: PDB / ID: 1zc2
TitleCrystal Structure of plasmid-encoded class C beta-lactamase CMY-2 complexed with citrate molecule
Componentsbeta-lactamase class C
KeywordsHYDROLASE / beta-lactamase cephalosporinase / AMPC-type / serine hydrolase / citrate
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
CITRIC ACID / Beta-lactamase CMY-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsBauvois, C. / Jacquamet, L. / Fieulaine, S. / Frere, J.-M. / Galleni, M. / Ferrer, J.-L.
CitationJournal: To be Published
Title: Crystallographic structure of plasmid-encoded CMY-2 beta-lactamase revealed citrate molecule in the active site.
Authors: Bauvois, C. / Jacquamet, L. / Fieulaine, S. / Frere, J.-M. / Galleni, M. / Ferrer, J.-L.
History
DepositionApr 10, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: beta-lactamase class C
B: beta-lactamase class C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1774
Polymers79,7932
Non-polymers3842
Water8,017445
1
A: beta-lactamase class C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0892
Polymers39,8961
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: beta-lactamase class C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0892
Polymers39,8961
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.710, 97.100, 103.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein beta-lactamase class C / CMY-2 beta-lactamase


Mass: 39896.492 Da / Num. of mol.: 2 / Fragment: residues 1-361
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla CMY-2 / Plasmid: pET26b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q48434, beta-lactamase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: citric acid 0.1M, PEG 6000 30 % w/v, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979565 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 4, 2004 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979565 Å / Relative weight: 1
ReflectionResolution: 2.09→43.85 Å / Num. all: 44320 / Num. obs: 43482 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.09→2.21 Å / % possible all: 90.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→43.85 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.901 / SU B: 7.538 / SU ML: 0.198 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.284 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29893 2170 5 %RANDOM
Rwork0.22464 ---
obs0.2284 43482 100 %-
all-44320 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.796 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å20 Å2
2--2.39 Å20 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 2.09→43.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5562 0 26 445 6033
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0360.0225740
X-RAY DIFFRACTIONr_angle_refined_deg2.7521.9487832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.715712
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.68224.486243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.64815912
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.4511525
X-RAY DIFFRACTIONr_chiral_restr0.1880.2843
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.024407
X-RAY DIFFRACTIONr_nbd_refined0.2840.23111
X-RAY DIFFRACTIONr_nbtor_refined0.3220.23782
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2290.2455
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2620.214
X-RAY DIFFRACTIONr_mcbond_it1.9271.53729
X-RAY DIFFRACTIONr_mcangle_it2.30525715
X-RAY DIFFRACTIONr_scbond_it4.21432504
X-RAY DIFFRACTIONr_scangle_it5.6234.52117
LS refinement shellResolution: 2.09→2.144 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 142 -
Rwork0.29 2699 -
obs--100 %

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