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- PDB-6c6i: Crystal structure of a chimeric NDM-1 metallo-beta-lactamase harb... -

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Basic information

Entry
Database: PDB / ID: 6c6i
TitleCrystal structure of a chimeric NDM-1 metallo-beta-lactamase harboring the IMP-1 L3 loop
ComponentsMetallo-beta-lactamase type 2 chimera
KeywordsHYDROLASE / Chimeric protein / NDM-1 / Zn-contaning protein
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsOtero, L. / Giannini, E. / Klinke, S. / Palacios, A. / Mojica, M. / Bonomo, R. / Llarrull, L. / Vila, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI100560/AI/NIAID NIH HHS/United States United States
CitationJournal: Antimicrob. Agents Chemother. / Year: 2019
Title: The Reaction Mechanism of Metallo-beta-Lactamases Is Tuned by the Conformation of an Active-Site Mobile Loop.
Authors: Palacios, A.R. / Mojica, M.F. / Giannini, E. / Taracila, M.A. / Bethel, C.R. / Alzari, P.M. / Otero, L.H. / Klinke, S. / Llarrull, L.I. / Bonomo, R.A. / Vila, A.J.
History
DepositionJan 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2019Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metallo-beta-lactamase type 2 chimera
B: Metallo-beta-lactamase type 2 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9376
Polymers49,6762
Non-polymers2624
Water4,846269
1
A: Metallo-beta-lactamase type 2 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9693
Polymers24,8381
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo-beta-lactamase type 2 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9693
Polymers24,8381
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.289, 39.250, 73.873
Angle α, β, γ (deg.)90.89, 93.10, 90.02
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Metallo-beta-lactamase type 2 chimera / B2 metallo-beta-lactamase / Beta-lactamase type II / Metallo-beta-lactamase NDM-1 / Metallo-beta- ...B2 metallo-beta-lactamase / Beta-lactamase type II / Metallo-beta-lactamase NDM-1 / Metallo-beta-lactamase type II / New Delhi metallo-beta-lactamase-1 / NDM-1


Mass: 24837.850 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Plasmid: Modified PET28+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: C7C422, beta-lactamase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.23 Å3/Da / Density % sol: 45 % / Description: bars
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.55
Details: 1.35 M ammonium sulfate. 0.1 M HEPES pH 7.55, 0.1 M sodium chloride, microseeding

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2016 / Details: TOROIDAL FOCUSING MIRROR
RadiationMonochromator: SI(111) CHANNEL CUT MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.65→34.72 Å / Num. obs: 49940 / % possible obs: 96.6 % / Redundancy: 2 % / Biso Wilson estimate: 18.19 Å2 / CC1/2: 0.992 / Rpim(I) all: 0.1 / Rrim(I) all: 0.141 / Net I/σ(I): 5.3
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4798 / CC1/2: 0.787 / Rpim(I) all: 0.365 / Rrim(I) all: 0.516 / % possible all: 94.8

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4hl2

4hl2


Resolution: 1.65→24.16 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.109 / SU Rfree Blow DPI: 0.103 / SU Rfree Cruickshank DPI: 0.103
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2345 4.7 %RANDOM
Rwork0.203 ---
obs0.204 49915 96.6 %-
Displacement parametersBiso mean: 19.73 Å2
Baniso -1Baniso -2Baniso -3
1-2.8104 Å2-0.1691 Å20.0048 Å2
2---4.4802 Å22.0452 Å2
3---1.6698 Å2
Refine analyzeLuzzati coordinate error obs: 0 Å
Refinement stepCycle: 1 / Resolution: 1.65→24.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3396 0 4 269 3669
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013478HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.024742HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1540SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes86HARMONIC2
X-RAY DIFFRACTIONt_gen_planes520HARMONIC5
X-RAY DIFFRACTIONt_it3478HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.04
X-RAY DIFFRACTIONt_other_torsion2.64
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion462SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4161SEMIHARMONIC4
LS refinement shellResolution: 1.65→1.69 Å
RfactorNum. reflection% reflection
Rfree0.303 162 4.48 %
Rwork0.239 3453 -
obs--94.97 %

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