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- PDB-7ct2: New Delhi metallo-beta-lactamase 1 (NDM1) mutant - H116Q -

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Basic information

Entry
Database: PDB / ID: 7ct2
TitleNew Delhi metallo-beta-lactamase 1 (NDM1) mutant - H116Q
ComponentsMetallo beta lactamase NDM-1
KeywordsHYDROLASE / Apo
Function / homology: / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / beta-lactamase activity / metal ion binding / Beta-lactamase NDM-1
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKong, W.P. / Chen, Y.W. / Wong, K.Y.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)P0011953 China
Citation
Journal: J.Struct.Biol. / Year: 2022
Title: The crystal structure of the H116Q mutant of NDM-1: An enzyme devoid of zinc ions.
Authors: Kong, W.P. / Chen, Y.W. / Wong, K.Y.
#1: Journal: Biochim Biophys Acta Proteins Proteom / Year: 2022
Title: NDM-1 Zn1-binding residue His116 plays critical roles in antibiotic hydrolysis.
Authors: Fung, Y.H. / Kong, W.P. / Leung, A.S.L. / Du, R. / So, P.K. / Wong, W.L. / Leung, Y.C. / Chen, Y.W. / Wong, K.Y.
History
DepositionAug 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 2.0Mar 2, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_sites ...atom_site / atom_sites / atom_type / chem_comp / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_audit_support / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / 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_conn / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] ..._atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_number_of_molecules / _entity_name_com.name / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_average_fsc_free / _refine.pdbx_average_fsc_work / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _software.version / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet.number_strands
Description: Model completeness
Details: Response to issues/queries 1. Model revised (ASN B176 side-chain amide flipped) 2. Sequence: verified 3. Sequence DB discrepancies: all correct 4. Ligand: confirmed 5. All checked to be ...Details: Response to issues/queries 1. Model revised (ASN B176 side-chain amide flipped) 2. Sequence: verified 3. Sequence DB discrepancies: all correct 4. Ligand: confirmed 5. All checked to be regions of poor densities 6. All checked, please keep 7. LINK Records: all good 8. All "riding hydrogens" in refinement removed
Provider: author / Type: Coordinate replacement
Revision 2.1Nov 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _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 / _citation.year
Revision 2.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metallo beta lactamase NDM-1
B: Metallo beta lactamase NDM-1
C: Metallo beta lactamase NDM-1
D: Metallo beta lactamase NDM-1


Theoretical massNumber of molelcules
Total (without water)106,1354
Polymers106,1354
Non-polymers00
Water10,845602
1
A: Metallo beta lactamase NDM-1


Theoretical massNumber of molelcules
Total (without water)26,5341
Polymers26,5341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo beta lactamase NDM-1


Theoretical massNumber of molelcules
Total (without water)26,5341
Polymers26,5341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Metallo beta lactamase NDM-1


Theoretical massNumber of molelcules
Total (without water)26,5341
Polymers26,5341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Metallo beta lactamase NDM-1


Theoretical massNumber of molelcules
Total (without water)26,5341
Polymers26,5341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.630, 68.550, 69.410
Angle α, β, γ (deg.)87.950, 88.820, 77.580
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Metallo beta lactamase NDM-1 / Metallo beta-lactamase / Metallo-beta-lactamase NDM1 / Metallobetalactamase NDM-1 / NDM1 metallo- ...Metallo beta-lactamase / Metallo-beta-lactamase NDM1 / Metallobetalactamase NDM-1 / NDM1 metallo-beta-lactamase / NDM_carbapenemase / New Delhi Metallo carbapenemase-1 / New Delhi metallo-beta-lactamase NDM-1 / New Delhi metallo-beta-lactamse 1 / Subclass B1 metallo-beta-lactamase NDM-1


Mass: 26533.773 Da / Num. of mol.: 4 / Mutation: H116Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: NDM-1, bla NDM-1, blaNDM-1, blaNDM1, D647_p47098, DBX64_28130, DDJ63_29735, EC13450_007, NCTC13443_00040, p2146_00143, pCRE380_21, pN11x00042NDM_090, pNDM-SX04_5, pNDM10469_138, SAMEA3499901_05193, TR3_031, TR4_031
Plasmid: pET28a
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: E9NWK5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 602 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.24 Å3/Da / Density % sol: 45.22 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 30% PEG 3350, 100 mM Sodium succinate,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54184 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.95→38.3 Å / Num. obs: 56672 / % possible obs: 92.7 % / Redundancy: 2 % / Biso Wilson estimate: 20.98 Å2 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.09 / Rrim(I) all: 0.128 / Rsym value: 0.09 / Net I/σ(I): 4.5
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 3 / Num. unique obs: 7888 / Rpim(I) all: 0.242 / Rrim(I) all: 0.342 / Rsym value: 0.242 / % possible all: 88.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.22data extraction
MOSFLM7.3.0data reduction
SCALA3.3.22data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZGY

5zgy


Resolution: 1.95→30.538 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.888 / WRfactor Rfree: 0.311 / WRfactor Rwork: 0.24 / SU B: 6.462 / SU ML: 0.18 / Average fsc free: 0.8295 / Average fsc work: 0.8605 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.216
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflectionSelection details
Rfree0.2856 2785 4.921 %RANDOM
Rwork0.2223 53814 --
all0.225 ---
obs-56599 92.574 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 26.251 Å2
Baniso -1Baniso -2Baniso -3
1-1.929 Å21.91 Å2-1.534 Å2
2---1.628 Å2-0.396 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.95→30.538 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6808 0 0 602 7410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0126968
X-RAY DIFFRACTIONr_angle_refined_deg1.6251.6269492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1365912
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92623.133332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.546151024
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1051532
X-RAY DIFFRACTIONr_chiral_restr0.1130.2928
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025420
X-RAY DIFFRACTIONr_nbd_refined0.2330.23217
X-RAY DIFFRACTIONr_nbtor_refined0.3090.24650
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2320.2536
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2590.2143
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2330.237
X-RAY DIFFRACTIONr_mcbond_it2.3972.4653660
X-RAY DIFFRACTIONr_mcangle_it3.6233.6844568
X-RAY DIFFRACTIONr_scbond_it2.6822.6793308
X-RAY DIFFRACTIONr_scangle_it3.9043.9024924
X-RAY DIFFRACTIONr_lrange_it7.21234.17410508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.0010.3381910.3093686X-RAY DIFFRACTION86.1364
2.001-2.0550.3472110.2733790X-RAY DIFFRACTION90.4385
2.055-2.1150.3571820.2683723X-RAY DIFFRACTION90.5822
2.115-2.180.3081800.2543566X-RAY DIFFRACTION90.9886
2.18-2.2510.2931940.2383502X-RAY DIFFRACTION91.3495
2.251-2.330.2991980.2133421X-RAY DIFFRACTION92.3686
2.33-2.4180.3361880.2223232X-RAY DIFFRACTION92.084
2.418-2.5170.311550.2143224X-RAY DIFFRACTION92.6769
2.517-2.6290.3461250.2233128X-RAY DIFFRACTION93.0758
2.629-2.7570.3081560.2182973X-RAY DIFFRACTION93.4867
2.757-2.9060.2561370.2062806X-RAY DIFFRACTION93.8457
2.906-3.0810.3071250.2042688X-RAY DIFFRACTION94.2379
3.081-3.2940.2821270.2232551X-RAY DIFFRACTION94.7629
3.294-3.5570.2781270.2192354X-RAY DIFFRACTION95.3497
3.557-3.8950.2631210.2192170X-RAY DIFFRACTION95.1017
3.895-4.3530.2481070.1991970X-RAY DIFFRACTION95.6702
4.353-5.0240.223790.1941762X-RAY DIFFRACTION96.4379
5.024-6.1450.279850.2281490X-RAY DIFFRACTION96.6851
6.145-8.6560.278670.241147X-RAY DIFFRACTION97.0424
8.656-30.5380.201300.201631X-RAY DIFFRACTION94.2939

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