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- PDB-8di7: CMY-2 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8di7
TitleCMY-2
ComponentsBeta-lactamase
KeywordsHYDROLASE / antibiotic / b-lactamase / CMY-2 / class C / apo crystal 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/transpeptidase-like
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsAhmadvand, P. / Call, D.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NA United States
CitationJournal: To Be Published
Title: Structural characterization of CMY-2 and its interactions with ampicillin and the cephalosporins - ceftiofur, DFC, DFC-dimer, DFC-cysteine, and nitrocefin
Authors: Ahmadvand, P. / Call, D.R.
History
DepositionJun 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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
D: Beta-lactamase
A: Beta-lactamase
B: Beta-lactamase
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,69011
Polymers159,0174
Non-polymers6727
Water28,9861609
1
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9463
Polymers39,7541
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9463
Polymers39,7541
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8502
Polymers39,7541
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9463
Polymers39,7541
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.939, 75.374, 97.552
Angle α, β, γ (deg.)81.190, 87.840, 69.510
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Beta-lactamase


Mass: 39754.336 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaCMY-61 / Production host: Escherichia coli (E. coli) / References: UniProt: G3F7G9, beta-lactamase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1609 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.39 Å3/Da / Density % sol: 48.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 300 mM Ammonium sulfate, 20% PEG 4000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→61.04 Å / Num. obs: 113721 / % possible obs: 96.26 % / Redundancy: 20 % / CC1/2: 1 / Net I/σ(I): 1
Reflection shellResolution: 1.89→1.958 Å / Rmerge(I) obs: 0.2667 / Num. unique obs: 11281 / CC1/2: 0.96 / CC star: 0.99 / Rpim(I) all: 0.202 / Rrim(I) all: 0.3372 / % possible all: 94.56

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZC2

1zc2


Resolution: 1.89→61.04 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 27.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2391 1274 1.12 %
Rwork0.2 112447 -
obs0.2004 113721 96.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.81 Å2 / Biso mean: 24.1485 Å2 / Biso min: 7.4 Å2
Refinement stepCycle: final / Resolution: 1.89→61.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11156 0 35 1632 12823
Biso mean--32.42 30.79 -
Num. residues----1436
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.89-1.970.34181300.29981227894
1.97-2.060.28851410.27921218994
2.06-2.160.26991440.25461219794
2.16-2.30.26521330.21951246296
2.3-2.480.28691490.22161260797
2.48-2.730.2821420.21861251597
2.73-3.120.23381480.20031255797
3.12-3.930.1811430.1621279899
3.93-100.20931440.15611284499

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