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- PDB-6mz2: CTX-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9 -

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Basic information

Entry
Database: PDB / ID: 6mz2
TitleCTX-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9
ComponentsBeta-lactamase
KeywordsHYDROLASE/INHIBITOR / beta-lactamase / complex / ultrahigh / avibactam / HYDROLASE / HYDROLASE-INHIBITOR 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
: / Chem-NXL / PHOSPHATE ION / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 0.83 Å
AuthorsPemberton, O.A. / Chen, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI103158-04 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Mechanism of proton transfer in class A beta-lactamase catalysis and inhibition by avibactam.
Authors: Pemberton, O.A. / Noor, R.E. / Kumar M V, V. / Sanishvili, R. / Kemp, M.T. / Kearns, F.L. / Woodcock, H.L. / Gelis, I. / Chen, Y.
History
DepositionNov 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 2.0Dec 18, 2019Group: Author supporting evidence / Polymer sequence / Category: entity_poly / pdbx_audit_support
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_audit_support.funding_organization
Revision 2.1Dec 25, 2019Group: Database references / Category: struct_ref_seq_dif
Revision 2.2Mar 11, 2020Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 2.3Mar 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.4Apr 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.5Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,29223
Polymers55,9672
Non-polymers1,32521
Water17,529973
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,68813
Polymers27,9841
Non-polymers70512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,60310
Polymers27,9841
Non-polymers6209
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.161, 106.842, 47.913
Angle α, β, γ (deg.)90.000, 101.820, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-lactamase /


Mass: 27983.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaCTX-M-14 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A2S1PK93, UniProt: Q9L5C7*PLUS, beta-lactamase

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Non-polymers , 5 types, 994 molecules

#2: Chemical ChemComp-NXL / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide / avibactam, bound form / NXL104, bound form / Avibactam


Mass: 267.260 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H13N3O6S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic, inhibitor*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 973 / 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: 2.02 Å3/Da / Density % sol: 39.16 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 1.0 M Potassium Phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.7 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 0.83→50 Å / Num. obs: 413177 / % possible obs: 99 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.032 / Rrim(I) all: 0.084 / Χ2: 1.052 / Net I/σ(I): 5.4 / Num. measured all: 2512561
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
0.83-0.842.50.624176920.6040.4170.7560.86585
0.84-0.863.50.621200830.6870.3550.720.86996.4
0.86-0.884.40.586205930.7540.3010.6620.87499
0.88-0.895.20.571207580.8040.270.6330.87399.7
0.89-0.915.70.519208070.850.2340.570.87899.7
0.91-0.936.20.444208040.8930.1920.4850.88399.9
0.93-0.966.60.378208890.9250.1580.4110.90199.9
0.96-0.986.70.331208230.9420.1380.3590.917100
0.98-1.016.50.273207910.9580.1150.2970.934100
1.01-1.056.20.224209070.9670.0970.2440.961100
1.05-1.086.50.183208410.9770.0780.1990.992100
1.08-1.136.70.151208470.9840.0630.1641.021100
1.13-1.186.80.133208310.9870.0550.1441.041100
1.18-1.246.70.121208860.9890.050.1311.069100
1.24-1.326.50.11208710.990.0470.121.117100
1.32-1.426.70.101209080.9910.0420.111.148100
1.42-1.5670.085208970.9940.0350.0921.157100
1.56-1.796.60.073209060.9950.0310.0791.214100
1.79-2.256.90.058209560.9970.0240.0621.326100
2.25-506.80.05210870.9970.0210.0541.542100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.38 Å34.17 Å
Translation4.38 Å34.17 Å

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASER2.8.1phasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UA6

4ua6


Resolution: 0.83→34.171 Å / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 11.5
RfactorNum. reflection% reflection
Rfree0.1265 20325 4.92 %
Rwork0.1161 --
obs0.1166 413046 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 56.1 Å2 / Biso mean: 10.2557 Å2 / Biso min: 2.68 Å2
Refinement stepCycle: final / Resolution: 0.83→34.171 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3894 0 129 973 4996
Biso mean--15.19 24 -
Num. residues----521
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.8293-0.83880.26535440.2706105021104679
0.8388-0.84860.25746760.2454121461282292
0.8486-0.8590.23256920.2245128301352297
0.859-0.86990.22336740.2064131061378099
0.8699-0.88130.20026520.1943131011375399
0.8813-0.89340.21116330.18941320213835100
0.8934-0.90610.18646910.181322513916100
0.9061-0.91970.16646740.15971325313927100
0.9197-0.9340.15337070.14731309413801100
0.934-0.94940.14197140.13431320213916100
0.9494-0.96570.1356510.1251323313884100
0.9657-0.98330.13676710.1231330113972100
0.9833-1.00220.11856530.11331325413907100
1.0022-1.02270.11647250.10761312413849100
1.0227-1.04490.11227020.10271325113953100
1.0449-1.06920.10667230.09621318613909100
1.0692-1.0960.1036730.09411325113924100
1.096-1.12560.10157030.08951318713890100
1.1256-1.15870.09816820.08931324713929100
1.1587-1.19610.09896650.09141327313938100
1.1961-1.23890.10366790.09431317413853100
1.2389-1.28850.09997020.09631330914011100
1.2885-1.34710.10787060.1011316613872100
1.3471-1.41810.10866820.10081328113963100
1.4181-1.5070.10867570.10041321313970100
1.507-1.62330.11566050.10281329513900100
1.6233-1.78670.12696410.11271331313954100
1.7867-2.04520.11916810.11341327413955100
2.0452-2.57660.12626540.11431336014014100
2.5766-34.20020.14097130.12471336814081100

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