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- PDB-5u53: CTX-M-14 E166A with acylated ceftazidime molecule -

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Basic information

Entry
Database: PDB / ID: 5u53
TitleCTX-M-14 E166A with acylated ceftazidime molecule
ComponentsBeta-lactamase
KeywordsHYDROLASE/ANTIBIOTIC / CTX-M beta-lactamase / ceftazidime acyl-enzyme complex / HYDROLASE-ANTIBIOTIC complex
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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACYLATED CEFTAZIDIME / NITRATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsPatel, M. / Stojanoski, V. / Sankaran, B. / Prasad, B.V.V. / Palzkill, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI32956 United States
CitationJournal: Biochemistry / Year: 2017
Title: The Drug-Resistant Variant P167S Expands the Substrate Profile of CTX-M beta-Lactamases for Oxyimino-Cephalosporin Antibiotics by Enlarging the Active Site upon Acylation.
Authors: Patel, M.P. / Hu, L. / Stojanoski, V. / Sankaran, B. / Prasad, B.V.V. / Palzkill, T.
History
DepositionDec 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5804
Polymers27,9871
Non-polymers5943
Water5,909328
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.030, 42.030, 262.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-547-

HOH

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Components

#1: Protein Beta-lactamase


Mass: 27986.562 Da / Num. of mol.: 1 / Fragment: UNP residues 24-284
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CTX-M-14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: H6UQI0, beta-lactamase
#2: Chemical ChemComp-CAZ / ACYLATED CEFTAZIDIME


Mass: 469.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19N5O7S2
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.1 Å3/Da / Density % sol: 41.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M ammonium nitrate, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.4→30.32 Å / Num. obs: 47304 / % possible obs: 98.4 % / Redundancy: 12.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.042 / Rrim(I) all: 0.158 / Net I/σ(I): 10 / Num. measured all: 611303 / Scaling rejects: 473
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.4-1.42150.983492023240.6390.3111.2682.598.3
7.54-30.3214.30.04960014190.9990.0130.05126.498.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Aimless0.5.1data scaling
PDB_EXTRACT3.22data extraction
MOLREPphasing
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YLT

1ylt


Resolution: 1.4→30.33 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0.86 / Phase error: 17.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1953 4360 5.06 %RANDOM
Rwork0.1688 ---
obs0.1702 86191 97.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→30.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1947 0 39 328 2314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092048
X-RAY DIFFRACTIONf_angle_d1.0632795
X-RAY DIFFRACTIONf_dihedral_angle_d8.6761184
X-RAY DIFFRACTIONf_chiral_restr0.086330
X-RAY DIFFRACTIONf_plane_restr0.007369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.41590.30261650.2922694X-RAY DIFFRACTION97
1.4159-1.43260.29191280.26722697X-RAY DIFFRACTION97
1.4326-1.45010.30771390.25952819X-RAY DIFFRACTION97
1.4501-1.46840.24791410.24162621X-RAY DIFFRACTION97
1.4684-1.48770.29281530.23422769X-RAY DIFFRACTION98
1.4877-1.50810.27211670.2322688X-RAY DIFFRACTION97
1.5081-1.52970.25951340.22722737X-RAY DIFFRACTION98
1.5297-1.55250.26021180.21952800X-RAY DIFFRACTION98
1.5525-1.57670.24721800.2162684X-RAY DIFFRACTION98
1.5767-1.60260.24641570.20182775X-RAY DIFFRACTION98
1.6026-1.63020.19611570.19942724X-RAY DIFFRACTION99
1.6302-1.65990.20681510.18222773X-RAY DIFFRACTION99
1.6599-1.69180.22371680.18792765X-RAY DIFFRACTION99
1.6918-1.72630.20531380.18372770X-RAY DIFFRACTION99
1.7263-1.76390.21711380.18122813X-RAY DIFFRACTION99
1.7639-1.80490.20721330.17592805X-RAY DIFFRACTION99
1.8049-1.850.19681600.17262756X-RAY DIFFRACTION99
1.85-1.90.18471410.16372794X-RAY DIFFRACTION99
1.9-1.95590.22881570.16552729X-RAY DIFFRACTION99
1.9559-2.0190.24031250.16722787X-RAY DIFFRACTION98
2.019-2.09120.19981420.16562828X-RAY DIFFRACTION99
2.0912-2.17490.18111400.15772714X-RAY DIFFRACTION98
2.1749-2.27380.1951190.15712752X-RAY DIFFRACTION97
2.2738-2.39370.20611720.15692648X-RAY DIFFRACTION95
2.3937-2.54360.16561240.15062611X-RAY DIFFRACTION93
2.5436-2.73990.18751470.15332500X-RAY DIFFRACTION90
2.7399-3.01540.19161340.1532570X-RAY DIFFRACTION91
3.0154-3.45120.16321480.13892696X-RAY DIFFRACTION97
3.4512-4.3460.12241430.1312688X-RAY DIFFRACTION96
4.346-30.33670.15811410.15612824X-RAY DIFFRACTION100
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)
10.4406-0.0025-0.07230.35720.16620.4807-0.01430.0463-0.0142-0.02370.0060.04440.0055-0.04990.0040.11410.00480.02880.077-0.00640.0836-6.69447.849115.4673
21.6578-0.0136-0.31371.5170.75943.4854-0.0170.0520.239-0.2302-0.0227-0.1812-0.20590.3052-0.00690.2339-0.03030.05980.16760.00930.264915.779929.113217.8731
30.40340.1138-0.11560.60640.02210.3550.0056-0.01050.00470.030.0008-0.0261-0.02230.0074-0.00190.11030.00950.02460.0657-0.00660.08632.026414.576619.2107
41.2527-0.3082-0.59624.28212.48853.45840.02390.0431-0.072-0.0062-0.0388-0.07920.19770.0471-0.01850.12650.00360.04060.0471-0.00190.0987-4.8572-2.459722.705
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 86 )
2X-RAY DIFFRACTION2chain 'A' and (resid 87 through 101 )
3X-RAY DIFFRACTION3chain 'A' and (resid 102 through 275 )
4X-RAY DIFFRACTION4chain 'A' and (resid 276 through 290 )

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