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- PDB-5twd: CTX-M-14 P167S apoenzyme -

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Basic information

Entry
Database: PDB / ID: 5twd
TitleCTX-M-14 P167S apoenzyme
ComponentsBeta-lactamase
KeywordsHYDROLASE / CTX-M beta-lactamase apoenzyme / HYDROLASE/ANTIBIOTIC
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding
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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 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)R01 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
DepositionNov 12, 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


Theoretical massNumber of molelcules
Total (without water)27,9911
Polymers27,9911
Non-polymers00
Water4,792266
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.600, 41.600, 231.932
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-564-

HOH

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Components

#1: Protein Beta-lactamase


Mass: 27990.510 Da / Num. of mol.: 1 / Fragment: UNP residues 29-291 / Mutation: P167S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: blaCTX-M-14, beta-lactamase CTX-M-14, bla-CTX-M-14a, blaCTX-M-14a, blaCTX-M-14b, blaCTX-M-14c, blaCTX-M-27b, blatoho-3, blaUOE-2, CTX-M-14, AN206_26770, APT94_14605, BJJ90_27545, BK334_27290, ...Gene: blaCTX-M-14, beta-lactamase CTX-M-14, bla-CTX-M-14a, blaCTX-M-14a, blaCTX-M-14b, blaCTX-M-14c, blaCTX-M-27b, blatoho-3, blaUOE-2, CTX-M-14, AN206_26770, APT94_14605, BJJ90_27545, BK334_27290, ETN48_p0088, pCT_085, pHK01_011
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9L5C7, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.07 Å3/Da / Density % sol: 40.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M magnesium chloride, 0.1M TRIS pH 8.0, 20% (w/v) PEG 6000

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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: Aug 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.7→30.601 Å / Num. obs: 66171 / % possible obs: 99.8 % / Redundancy: 10.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.021 / Rrim(I) all: 0.068 / Net I/σ(I): 18.2 / Num. measured all: 692102 / Scaling rejects: 526
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.651 / Mean I/σ(I) obs: 16.5 / Num. measured all: 16338 / Num. unique all: 3086 / CC1/2: 0.796 / Rpim(I) all: 0.303 / Rrim(I) all: 0.724 / Net I/σ(I) obs: 2.3 / % possible all: 100

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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_EXTRACT3.2data extraction
MOLREPphasing
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YLT

1ylt


Resolution: 1.7→30.601 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0.12 / Phase error: 24.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2366 2450 4.96 %RANDOM
Rwork0.2079 ---
obs0.2094 49409 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→30.601 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1939 0 0 266 2205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061988
X-RAY DIFFRACTIONf_angle_d0.7862708
X-RAY DIFFRACTIONf_dihedral_angle_d6.8741650
X-RAY DIFFRACTIONf_chiral_restr0.048320
X-RAY DIFFRACTIONf_plane_restr0.006357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.73270.34471720.29462648X-RAY DIFFRACTION100
1.7327-1.76810.33951320.28522535X-RAY DIFFRACTION100
1.7681-1.80650.30951450.27272715X-RAY DIFFRACTION100
1.8065-1.84860.30711140.26322519X-RAY DIFFRACTION100
1.8486-1.89480.2891640.26512678X-RAY DIFFRACTION100
1.8948-1.9460.3278960.25112602X-RAY DIFFRACTION100
1.946-2.00330.29881140.24922635X-RAY DIFFRACTION100
2.0033-2.06790.25751920.2262556X-RAY DIFFRACTION100
2.0679-2.14180.24711320.22882570X-RAY DIFFRACTION100
2.1418-2.22750.27231380.22222600X-RAY DIFFRACTION100
2.2275-2.32890.27261200.21512652X-RAY DIFFRACTION100
2.3289-2.45160.25131120.21852650X-RAY DIFFRACTION100
2.4516-2.60510.26171330.21142601X-RAY DIFFRACTION100
2.6051-2.80610.22561440.20272561X-RAY DIFFRACTION100
2.8061-3.08830.22651660.20262539X-RAY DIFFRACTION100
3.0883-3.53460.18731200.17642655X-RAY DIFFRACTION100
3.5346-4.45110.17791200.15352636X-RAY DIFFRACTION100
4.4511-30.60570.15291360.16462607X-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)
10.7858-0.2224-0.77110.7069-0.10152.73380.00220.0343-0.1815-0.1762-0.03750.05640.9438-0.58320.06930.1957-0.0855-0.06310.2189-0.00470.1206-1.3162-12.9465-22.6005
20.0478-0.0360.00240.04620.04330.05740.0704-0.10090.148-0.0037-0.1469-0.0187-0.2845-0.3054-0.21020.39060.4242-0.01010.50040.26580.0049-9.247211.0711-11.077
30.2025-0.0624-0.22640.36430.31031.4880.14750.2805-0.01880.19350.0330.02850.2966-1.01630.2983-0.0887-0.0837-0.02990.43440.01430.1313-5.146-5.6447-18.1451
44.39710.25911.20051.6851-0.09622.76440.00680.18560.2392-0.13180.171-0.1080.1010.064-0.19490.1103-0.01970.02280.2262-0.03680.11274.4983-6.2257-31.9483
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 85 )
2X-RAY DIFFRACTION2chain 'A' and (resid 86 through 129 )
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 265 )
4X-RAY DIFFRACTION4chain 'A' and (resid 266 through 288 )

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