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- PDB-6d7i: CTX-M-14 Apoenzyme D233N Point Mutant -

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Basic information

Entry
Database: PDB / ID: 6d7i
TitleCTX-M-14 Apoenzyme D233N Point Mutant
ComponentsBeta-lactamase
KeywordsHYDROLASE / Beta-Lactamase / ESBL / Apoenzyme
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
Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsKemp, M. / Nichols, D. / Chen, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI03158-04 United States
CitationJournal: To be Published
Title: The Role of Asp-Asp Short Hydrogen Bond in Maintaining Active Site Integrity of CTX-M Beta-Lactamase
Authors: Nichols, D.A. / Kemp, M.T. / Chen, Y.
History
DepositionApr 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 6, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / database_2 / diffrn_source / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_conf / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type / _entity.formula_weight / _entity.pdbx_fragment / _entity.pdbx_number_of_molecules / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _entity_src_gen.pdbx_gene_src_gene / _pdbx_poly_seq_scheme.mon_id / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_comp_id / _pdbx_unobs_or_zero_occ_residues.label_comp_id / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_percent_reflns_R_free / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_starting_model / _refine.pdbx_stereochemistry_target_values / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_solvent / _software.version / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Description: Model completeness / Details: removed hydrogens / Provider: author / Type: Coordinate replacement
Revision 2.1Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)28,0001
Polymers28,0001
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.809, 41.809, 231.951
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-435-

HOH

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Components

#1: Protein Beta-lactamase /


Mass: 27999.561 Da / Num. of mol.: 1 / Fragment: UNP residues 29-291 / Mutation: D233N
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, bla CTX-M-14, bla-CTX-M-14a, blaCTX-M, blaCTX-M-14a, blaCTX-M-14b, blaCTX-M-14c, blaCTX-M-27b, blatoho-3, blaUOE-2, CTX-M-14, AM333_26030, AM340_ ...Gene: blaCTX-M-14, beta-lactamase CTX-M-14, bla, bla CTX-M-14, bla-CTX-M-14a, blaCTX-M, blaCTX-M-14a, blaCTX-M-14b, blaCTX-M-14c, blaCTX-M-27b, blatoho-3, blaUOE-2, CTX-M-14, AM333_26030, AM340_28340, AM465_01285, AM465_06510, AM465_23360, APT94_14605, BEN53_26220, BJJ90_27545, BK334_27290, BOH76_00730, BON63_16015, BON65_15195, BON66_01305, BON69_22545, BON72_03470, BON75_10525, BON76_14325, BON83_15455, BON86_08515, BON91_02075, BON92_04750, BON94_23850, BON95_01680, BON96_03940, BON98_23175, BXT93_06855, C5N07_28500, CDL37_21060, CR538_26855, DW236_20870, E4K51_21070, EIA08_25160, EIA21_26975, ELT23_05930, ELV24_09995, ELX61_24095, EST51_15935, EST51_18575, EST51_22260, EST51_22365, ETN48_p0088, FNJ69_13810, FTV90_03295, GE096_24920, GE096_25355, GQE36_23945, HGR36_01450, HGR36_27140, HHH24_004455, HHH24_005319, HJI79_003882, HJI79_004995, HK427_004976, HK427_005087, HL152_24835, HL152_25835, HL563_21800, HL563_23665, HLT96_25270, HLT96_28700, HLU13_27785, HLY53_18605, HLY53_26190, HLZ85_26065, HMW26_20895, HMW26_29355, HNC73_28650, HNC75_27190, HNC75_29165, HNC80_26145, HNC80_27675, HNC88_26185, HNC88_27880, HND23_26750, HND23_28285, HNV91_23425, HNV91_24920, HNV94_24095, HNV94_27845, pCT_085, pHK01_011, RCS103_P0010, RCS30_P0082, RCS56_P0085, RCS60_P0031, RCS63_P0006, RCS65_P0008, RCS66_P0053, SAMEA4362930_00013, SAMEA4363083_00099, SAMEA4370290_00046, WP4S18E07_P40650, WP7S17E01_P10270, WP7S18E09_37980
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9L5C7, UniProt: H6UQI0*PLUS, beta-lactamase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.09 Å3/Da / Density % sol: 41.15 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: 1.0 M potassium phosphate, pH 8.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 29916 / % possible obs: 99.9 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.036 / Rrim(I) all: 0.112 / Χ2: 1.065 / Net I/σ(I): 8.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.0310.10.2817980.9890.0930.2960.631100
2.03-2.0710.10.2838410.9880.0930.2980.705100
2.07-2.1110.10.2488110.9950.0810.2610.732100
2.11-2.15100.2418250.9870.080.2540.803100
2.15-2.210.30.2258570.990.0740.2370.782100
2.2-2.259.90.2118080.9870.070.2230.957100
2.25-2.3110.10.1958350.9920.0650.2060.892100
2.31-2.37100.1787990.9920.0590.1880.928100
2.37-2.44100.1648630.9960.0540.1730.925100
2.44-2.5210.10.1548140.9950.0510.1620.98100
2.52-2.619.80.1448780.9930.0480.1521.036100
2.61-2.71100.1418040.9930.0470.1491.092100
2.71-2.849.80.1178570.9960.0390.1231.078100
2.84-2.999.80.1168670.9960.0390.1221.296100
2.99-3.179.80.1068230.9960.0350.1111.395100
3.17-3.429.70.0968680.9950.0330.1021.513100
3.42-3.769.70.0858590.9980.0290.091.4999.9
3.76-4.319.60.0798670.9970.0260.0831.556100
4.31-5.439.80.0769030.9960.0250.081.45299.9
5.43-508.90.069890.9980.0220.0641.0498.2

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ua6

4ua6


Resolution: 2.001→34.562 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2329 2959 9.89 %
Rwork0.1982 26957 -
obs0.2016 29916 97.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.02 Å2 / Biso mean: 36.1865 Å2 / Biso min: 11.78 Å2
Refinement stepCycle: final / Resolution: 2.001→34.562 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1956 0 0 153 2109
Biso mean---31.81 -
Num. residues----262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042009
X-RAY DIFFRACTIONf_angle_d0.7012741
X-RAY DIFFRACTIONf_chiral_restr0.043326
X-RAY DIFFRACTIONf_plane_restr0.005362
X-RAY DIFFRACTIONf_dihedral_angle_d15.8261234
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.001-2.03340.261370.26115491
2.0334-2.06840.31091260.2437123891
2.0684-2.1060.22641230.2264121792
2.106-2.14650.31761360.2423122196
2.1465-2.19040.2571350.241127493
2.1904-2.2380.26881440.2397122996
2.238-2.290.29711310.2295128297
2.29-2.34730.29371450.2419128696
2.3473-2.41070.2881480.24531300100
2.4107-2.48160.23771440.21741314100
2.4816-2.56170.27331480.2351315100
2.5617-2.65320.24971460.23081296100
2.6532-2.75940.30551390.21061338100
2.7594-2.8850.25871370.20681300100
2.885-3.0370.2591580.20331312100
3.037-3.22710.2321440.20861328100
3.2271-3.47610.19251540.17641322100
3.4761-3.82550.21311400.15441303100
3.8255-4.37810.17081390.14571282100
4.3781-5.51230.15971440.14651326100
5.5123-34.5620.2091410.1938132099
Refinement TLS params.Method: refined / Origin x: 16.571 Å / Origin y: 31.9183 Å / Origin z: 96.8346 Å
111213212223313233
T0.1116 Å2-0.088 Å2-0.0491 Å2-0.2477 Å20.0571 Å2--0.2239 Å2
L0.662 °2-0.4217 °2-0.1197 °2-0.5779 °20.3372 °2--7.1084 °2
S0.203 Å °0.103 Å °0.0005 Å °-0.0678 Å °0.0558 Å °0.0409 Å °0.5731 Å °-0.7604 Å °-0.0036 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA26 - 290
2X-RAY DIFFRACTION1allS1 - 154

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