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- PDB-8doe: Crystal Structure of CTX-M-14 N106A -

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Basic information

Entry
Database: PDB / ID: 8doe
TitleCrystal Structure of CTX-M-14 N106A
ComponentsBeta-lactamase
KeywordsHYDROLASE / Beta-lactamase / b-lactam antibiotic resistance / mutation
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLu, S. / Palzkill, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Mutagenesis and structural analysis reveal the CTX-M beta-lactamase active site is optimized for cephalosporin catalysis and drug resistance.
Authors: Lu, S. / Montoya, M. / Hu, L. / Neetu, N. / Sankaran, B. / Prasad, B.V.V. / Palzkill, T.
History
DepositionJul 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 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

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Assembly

Deposited unit
A: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)27,8291
Polymers27,8291
Non-polymers00
Water7,837435
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.840, 37.910, 65.460
Angle α, β, γ (deg.)90.000, 103.440, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Beta-lactamase


Mass: 27829.391 Da / Num. of mol.: 1 / Mutation: N106A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CTX-M-14
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: H6UQI0, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 2.16 Å3/Da / Density % sol: 43.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium chloride ,0.1 M Tris pH 8 20% (w/v), PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.11 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 23, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 1.5→48.48 Å / Num. obs: 37847 / % possible obs: 98.46 % / Redundancy: 2 % / Biso Wilson estimate: 8.41 Å2 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.077 / Net I/σ(I): 9.12
Reflection shellResolution: 1.5→1.554 Å / Rmerge(I) obs: 0.2716 / Num. unique obs: 3704 / Rrim(I) all: 0.3842 / % possible all: 97.22

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YLT

1ylt


Resolution: 1.5→48.48 Å / SU ML: 0.105 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.5409
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1652 1900 5.02 %
Rwork0.1446 35947 -
obs0.1456 37847 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.94 Å2
Refinement stepCycle: LAST / Resolution: 1.5→48.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1953 0 0 435 2388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01011982
X-RAY DIFFRACTIONf_angle_d1.22632699
X-RAY DIFFRACTIONf_chiral_restr0.073322
X-RAY DIFFRACTIONf_plane_restr0.0117355
X-RAY DIFFRACTIONf_dihedral_angle_d5.7364282
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.19481320.1652505X-RAY DIFFRACTION96.95
1.54-1.580.19171340.15472538X-RAY DIFFRACTION97.7
1.58-1.630.15571210.14332505X-RAY DIFFRACTION97.77
1.63-1.680.16411370.14412560X-RAY DIFFRACTION98.36
1.68-1.740.19971610.14062529X-RAY DIFFRACTION98.32
1.74-1.810.16151270.13722575X-RAY DIFFRACTION98.76
1.81-1.890.16841320.1392575X-RAY DIFFRACTION98.83
1.89-1.990.16141450.13082549X-RAY DIFFRACTION98.79
1.99-2.110.16131200.12952583X-RAY DIFFRACTION99.01
2.11-2.280.14021550.13332565X-RAY DIFFRACTION99.09
2.28-2.510.15071450.13752599X-RAY DIFFRACTION99.24
2.51-2.870.16011330.14692573X-RAY DIFFRACTION99.01
2.87-3.610.17431250.15012642X-RAY DIFFRACTION99.18
3.62-48.480.16941330.162649X-RAY DIFFRACTION97.51
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.727382721760.6786193916620.2747746173851.04601038224-0.2998464232431.333274075880.01609052819610.1789906540450.00250545791572-0.162528349551-0.0774801921073-0.114777752462-0.05944900540160.1705888065610.02738929620530.05936190130930.01744283063960.02690069521250.0534014094951-0.001020111728880.050661151891923.44553684326.963099354011.70071616044
20.7448774336330.0283282550032-0.3746763719570.314003343885-0.02371793754940.4414112112950.01651728632140.0770837982964-0.0757605769511-0.00673544298949-0.0292158667235-0.005647583805370.0822493769843-0.0487984554710.00413167196270.04376118252040.00184730117598-0.00115045711720.0553696130249-0.006498477881960.0456418248149.877515940350.19416664532212.1225900472
33.999125148343.160629199232.292060310422.623730113162.112930191372.03015741660.134943221751-0.207107731796-0.01961589415430.197992575129-0.1676494262560.08968779042570.191247128656-0.2135168813610.04646038963060.0746343748927-0.01457065489540.01492114732690.0815675350909-0.0178819772920.0680046008237-3.139983887373.4739060738633.1626162985
40.7954029030690.0640725531912-0.02173232776870.750125151564-0.009497087450742.24546071740.0214405560095-0.0268232682950.08758895043660.0429060341005-0.003832288165650.0306581477826-0.131983919930.029495051641-0.01996319459970.05068801530850.001157242987760.007395638503640.0300837378087-0.0171226925160.05535302579023.7993093918412.045906990130.6651717019
50.810397296884-0.156020486766-0.2032968389940.450934628421-0.2784583093130.436581034049-0.0343458073302-0.0248612661534-0.0464044973827-0.0496601459630.01359406008170.01816120345810.0533320042510.05584974566040.01525968930350.06158423728930.00647140818563-0.0007335535666750.0471886091086-0.0004195675093960.047002523905912.402292993-1.876131217323.7778682274
65.11693424561-2.144175476740.7469963404251.00645143428-0.2885671250870.1686529844920.05580786216990.029748392378-0.155935525576-0.0286672011967-0.03813015614290.08447829546230.0304840544526-0.0250459828098-0.02459544644250.05040512805330.0006083318137420.003058111032180.01903998173690.00260044581750.03890823250369.0422230016-1.153849570789.04647443894
71.509813543480.54530261146-0.3326345436593.853680637540.980053590251.43094910310.005133852079040.02319827648990.0423083218268-0.0539439167664-0.02544998799990.211593528285-0.00268146906173-0.2203521152020.03922193387330.0325548786549-0.0012804117193-0.008246693651140.0529352426851-0.003179389284440.0347234318907-3.501019369834.5296203733313.2459655559
81.09045801616-0.0674106628503-0.05622457536690.564955543772-0.05802931130660.222517430909-0.0504120478046-0.02132615905930.190571330820.02691185007890.0003764371578760.00775177178828-0.1538429313190.004123007701980.03817690687780.06232646835520.00192892731238-0.00301002410220.03907138070450.001507795774270.055034676477611.667640674313.308625131311.3951654846
93.82204180204-0.2399523997632.370513751220.915139168073-0.5513439264082.46706889313-0.0413102987965-0.1014681997490.09797440101250.00297457490725-0.0416691355795-0.0500831808423-0.1186409341120.0363809543670.02629128523250.03152306073160.006670533172890.01977264591510.033345767314-0.01503950305180.016625370221817.951545086410.107240713110.1518532155
104.05585534455-0.3958569245360.3387226192973.97238300947-0.9474612677236.68820504048-0.1310504646470.2682302046250.137664452603-0.2364176825960.04563363371880.1015816079710.00636614618851-0.1425361696220.1074550579830.0565296481279-0.02675408653680.02092494936680.04390945592750.02431482806010.065942353540417.777988234214.50304113582.92048835652
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 26 through 50 )26 - 501 - 25
22chain 'A' and (resid 51 through 86 )51 - 8626 - 60
33chain 'A' and (resid 87 through 101 )87 - 10161 - 75
44chain 'A' and (resid 102 through 129 )102 - 12976 - 103
55chain 'A' and (resid 130 through 179 )130 - 179104 - 153
66chain 'A' and (resid 180 through 195 )180 - 195154 - 169
77chain 'A' and (resid 196 through 212 )196 - 212170 - 186
88chain 'A' and (resid 213 through 251 )213 - 251187 - 224
99chain 'A' and (resid 252 through 275 )252 - 275225 - 247
1010chain 'A' and (resid 276 through 290 )276 - 290248 - 262

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