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- PDB-5kmt: CTX-M9 mutant L48A -

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Basic information

Entry
Database: PDB / ID: 5kmt
TitleCTX-M9 mutant L48A
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta lactamase / ESBL
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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
: / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsLatallo, M.J. / Faham, S. / Kasson, P.M.
Funding support United States, 1items
OrganizationGrant numberCountry
The Hartwell FoundationIndividual Biomedical Research Award United States
CitationJournal: Chem Sci / Year: 2017
Title: Predicting allosteric mutants that increase activity of a major antibiotic resistance enzyme.
Authors: Latallo, M.J. / Cortina, G.A. / Faham, S. / Nakamoto, R.K. / Kasson, P.M.
History
DepositionJun 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Refinement description / Category: citation / software
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _software.classification
Revision 1.2Mar 6, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)62,21210
Polymers61,6762
Non-polymers5368
Water8,071448
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1456
Polymers30,8381
Non-polymers3075
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0674
Polymers30,8381
Non-polymers2293
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.788, 41.788, 232.401
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 1 / Auth seq-ID: 27 - 287 / Label seq-ID: 29 - 289

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.499885, -0.866092, 0.00023), (-0.866092, 0.499885, 1.1E-5), (-0.000124, -0.000194, -1)62.67332, 36.19553, 49.40359

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Components

#1: Protein Beta-lactamase


Mass: 30838.061 Da / Num. of mol.: 2 / Mutation: L48A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaCTX-M-9a, blaCTX-M-9, blaCTX-M-9b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9L5C8, beta-lactamase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 1.9 Å3/Da / Density % sol: 35.25 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: 1.2 M potassium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→77.47 Å / Num. obs: 47330 / % possible obs: 94.6 % / Redundancy: 8.1 % / Net I/σ(I): 26.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data scaling
Cootmodel building
PHASERphasing
RefinementResolution: 1.7→36.22 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.689 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.118 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21607 2278 4.8 %RANDOM
Rwork0.19437 ---
obs0.19543 45006 94.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.912 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20.41 Å2-0 Å2
2--0.41 Å20 Å2
3----1.32 Å2
Refinement stepCycle: LAST / Resolution: 1.7→36.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3875 0 24 448 4347
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193966
X-RAY DIFFRACTIONr_bond_other_d0.0060.023820
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.9685406
X-RAY DIFFRACTIONr_angle_other_deg1.08838765
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8695526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.73924.534161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89815645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3981530
X-RAY DIFFRACTIONr_chiral_restr0.0990.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214584
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02858
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCSNumber: 3799 / Type: tight thermal / Rms dev position: 1.54 Å / Weight position: 0.5
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 110 -
Rwork0.222 2361 -
obs--65.98 %
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)
10.74980.00080.84220.2752-0.09843.7968-0.07610.09680.0288-0.03970.0549-0.0035-0.49610.21630.02120.0862-0.04550.00650.0376-0.00390.156119.25641.9825.504
20.45220.30180.58430.59120.77234.46790.0278-0.12350.00370.0038-0.05370.0181-0.087-0.63530.02590.00580.00770.0020.11730.00590.161216.73340.60443.953
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 287
2X-RAY DIFFRACTION1A301 - 305
3X-RAY DIFFRACTION1A401 - 624
4X-RAY DIFFRACTION2B27 - 287
5X-RAY DIFFRACTION2B301 - 303
6X-RAY DIFFRACTION2B401 - 624

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