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- PDB-6ol8: Crystal structure of NDM-12 metallo-beta-lactamase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6ol8
TitleCrystal structure of NDM-12 metallo-beta-lactamase in complex with hydrolyzed ampicillin
ComponentsMetallo-beta-lactamase NDM-12
Keywordshydrolase/antibiotic / metallo-beta-lactamase / NDM / HYDROLASE / hydrolase-antibiotic complex
Function / homology
Function and homology information


beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / metal ion binding
Similarity search - Function
: / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-ZZ7 / beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRaczynska, J.E. / Imiolczyk, B. / Jaskolski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre Poland
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Flexible loops of New Delhi metallo-beta-lactamase modulate its activity towards different substrates.
Authors: Raczynska, J.E. / Imiolczyk, B. / Komorowska, M. / Sliwiak, J. / Czyrko-Horczak, J. / Brzezinski, K. / Jaskolski, M.
History
DepositionApr 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 20, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 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 / 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_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.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.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_conn.ptnr2_symmetry / _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: Metallo-beta-lactamase NDM-12
B: Metallo-beta-lactamase NDM-12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,67715
Polymers51,4582
Non-polymers1,22013
Water4,161231
1
A: Metallo-beta-lactamase NDM-12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3929
Polymers25,7291
Non-polymers6638
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Metallo-beta-lactamase NDM-12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2866
Polymers25,7291
Non-polymers5575
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.469, 76.449, 130.906
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 31 - 270 / Label seq-ID: 4 - 243

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

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Metallo-beta-lactamase NDM-12


Mass: 25728.873 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaNDM-12 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A024FRL9

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Non-polymers , 5 types, 244 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-ZZ7 / (2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / AMPICILLIN (open form)


Mass: 367.420 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H21N3O5S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 1.87 Å3/Da / Density % sol: 34.24 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.15M KBr, 30% PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 29, 2017
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.1→66.02 Å / Num. obs: 22766 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.149 / Rrim(I) all: 0.169 / Net I/σ(I): 7
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.8 / Num. unique obs: 3544 / CC1/2: 0.62 / Rrim(I) all: 0.92 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3q6x

3q6x
PDB Unreleased entry


Resolution: 2.1→21.65 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.935 / SU B: 13.35 / SU ML: 0.183 / Cross valid method: FREE R-VALUE / ESU R: 0.299 / ESU R Free: 0.208 / Details: HYDROGENS WERE ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22726 1160 5.1 %RANDOM
Rwork0.17214 ---
obs0.17499 21606 97.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.59 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å2-0 Å2-0 Å2
2--0.44 Å2-0 Å2
3---1.13 Å2
Refinement stepCycle: 1 / Resolution: 2.1→21.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3566 0 61 231 3858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0133763
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173366
X-RAY DIFFRACTIONr_angle_refined_deg1.6141.645130
X-RAY DIFFRACTIONr_angle_other_deg1.3981.597789
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3935487
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.17623.258178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02615547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6081517
X-RAY DIFFRACTIONr_chiral_restr0.0670.2505
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024402
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02769
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_it2.4031.9571939
X-RAY DIFFRACTIONr_mcbond_other2.4011.9561938
X-RAY DIFFRACTIONr_mcangle_it3.342.932426
X-RAY DIFFRACTIONr_mcangle_other3.3412.9322427
X-RAY DIFFRACTIONr_scbond_it3.5552.3021824
X-RAY DIFFRACTIONr_scbond_other3.5542.3031825
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8673.3212704
X-RAY DIFFRACTIONr_long_range_B_refined6.57338.08616981
X-RAY DIFFRACTIONr_long_range_B_other6.57137.91416861
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 7870 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.101→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 80 -
Rwork0.31 1545 -
obs--95.59 %
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)
10.56260.6855-0.5673.5438-2.06817.1315-0.07190.1266-0.2372-0.203-0.0938-0.56530.75380.47710.16570.18150.03640.03880.4349-0.07190.141523.17413.2544.637
20.91570.0351-0.06460.8786-0.33490.8509-0.00720.0368-0.0334-0.0798-0.0154-0.06250.03980.01820.02250.1407-0.00980.00730.25230.00130.005519.42829.17951.14
32.5799-0.03341.13451.17860.27723.02150.2329-0.0439-0.31590.1867-0.07120.05760.36720.097-0.16170.1780.0218-0.0460.1888-0.01880.047629.65742.53281.583
41.557-0.05840.25181.3080.24881.0320.00160.0413-0.03940.0395-0.04060.03010.0058-0.05910.03890.14510.0076-0.01620.2545-0.00170.005327.61259.54682.805
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 52
2X-RAY DIFFRACTION2A53 - 270
3X-RAY DIFFRACTION3B31 - 114
4X-RAY DIFFRACTION4B115 - 270

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