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- PDB-6kzn: Crystal Structure Of VIM-2 Metallo-beta-lactamase In Complex With... -

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Basic information

Entry
Database: PDB / ID: 6kzn
TitleCrystal Structure Of VIM-2 Metallo-beta-lactamase In Complex With Inhibitor X2
ComponentsBeta-lactamase class B VIM-2
KeywordsHYDROLASE
Function / homology
Function and homology information


beta-lactamase / hydrolase activity / metal 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
Chem-E1C / FORMIC ACID / beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsWachino, J.
CitationJournal: Mbio / Year: 2020
Title: Sulfamoyl Heteroarylcarboxylic Acids as Promising Metallo-beta-Lactamase Inhibitors for Controlling Bacterial Carbapenem Resistance.
Authors: Wachino, J.I. / Jin, W. / Kimura, K. / Kurosaki, H. / Sato, A. / Arakawa, Y.
History
DepositionSep 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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
Revision 1.2Nov 22, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase class B VIM-2
B: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,17614
Polymers51,0792
Non-polymers1,09712
Water10,215567
1
A: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0887
Polymers25,5391
Non-polymers5496
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-28 kcal/mol
Surface area9770 Å2
MethodPISA
2
B: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0887
Polymers25,5391
Non-polymers5496
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-26 kcal/mol
Surface area9760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.960, 79.150, 77.740
Angle α, β, γ (deg.)90.000, 138.400, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-lactamase class B VIM-2 / BlaVIM-2 / Metallo beta-lactamase / Metallo-beta-lactamase VIM-2 / Subclass B1 metallo-beta- ...BlaVIM-2 / Metallo beta-lactamase / Metallo-beta-lactamase VIM-2 / Subclass B1 metallo-beta-lactamase VIM-2 / VIM-2 / VIM-2 class B beta-lactamase / VIM-2 class B metallo b-lactamase / VIM-2 metallo-beta-lactamase / VIM-2 type metallo-beta-lactamase


Mass: 25539.322 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: bla vim-2, bla-VIM-2, blasVIM-2, blaVIM-2, blaVIM2, VIM-2, vim-2, IPC669_36195
Production host: Escherichia coli (E. coli) / References: UniProt: Q9K2N0
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-E1C / 2,5-diethyl-1-methyl-4-sulfamoyl-pyrrole-3-carboxylic acid


Mass: 260.310 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O4S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 567 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.04 Å3/Da / Density % sol: 39.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M magnesium formate dihydrate, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→55.46 Å / Num. obs: 65271 / % possible obs: 99.6 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 13.7
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.16 / Num. unique obs: 9533 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4nq2

4nq2


Resolution: 1.5→39.606 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.193 / WRfactor Rwork: 0.163 / SU B: 1.081 / SU ML: 0.042 / Average fsc free: 0.9549 / Average fsc work: 0.9616 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.073
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1829 3385 5.186 %
Rwork0.1552 61882 -
all0.157 --
obs-65267 99.591 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 12.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.325 Å20 Å20.007 Å2
2---0.621 Å20 Å2
3---0.079 Å2
Refinement stepCycle: LAST / Resolution: 1.5→39.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3494 0 52 567 4113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133733
X-RAY DIFFRACTIONr_bond_other_d00.0173353
X-RAY DIFFRACTIONr_angle_refined_deg1.451.6545112
X-RAY DIFFRACTIONr_angle_other_deg1.4251.5827753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6025483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.55722185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33115536
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg2.297152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3781524
X-RAY DIFFRACTIONr_chiral_restr0.0680.2485
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024313
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02775
X-RAY DIFFRACTIONr_nbd_refined0.2040.2729
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.23182
X-RAY DIFFRACTIONr_nbtor_refined0.1630.21784
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21529
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2375
X-RAY DIFFRACTIONr_metal_ion_refined0.0880.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0950.213
X-RAY DIFFRACTIONr_nbd_other0.2250.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2190.234
X-RAY DIFFRACTIONr_mcbond_it1.3611.0811908
X-RAY DIFFRACTIONr_mcbond_other1.3641.0811909
X-RAY DIFFRACTIONr_mcangle_it2.0981.6182399
X-RAY DIFFRACTIONr_mcangle_other2.0991.6192400
X-RAY DIFFRACTIONr_scbond_it2.181.2811823
X-RAY DIFFRACTIONr_scbond_other2.181.2811824
X-RAY DIFFRACTIONr_scangle_it3.2221.842713
X-RAY DIFFRACTIONr_scangle_other3.2221.842714
X-RAY DIFFRACTIONr_lrange_it4.70914.394265
X-RAY DIFFRACTIONr_lrange_other4.70914.3914266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5390.1982210.1544591X-RAY DIFFRACTION100
1.539-1.5810.1982480.1544460X-RAY DIFFRACTION100
1.581-1.6270.1912180.1524362X-RAY DIFFRACTION100
1.627-1.6770.1822630.1454182X-RAY DIFFRACTION100
1.677-1.7320.1882410.1474068X-RAY DIFFRACTION100
1.732-1.7930.1941720.1494014X-RAY DIFFRACTION100
1.793-1.860.1862260.1543776X-RAY DIFFRACTION100
1.86-1.9360.1822280.1573657X-RAY DIFFRACTION99.9485
1.936-2.0220.1682030.1533501X-RAY DIFFRACTION100
2.022-2.1210.1761890.1523382X-RAY DIFFRACTION99.9161
2.121-2.2350.1911680.1523199X-RAY DIFFRACTION99.8517
2.235-2.370.1781280.153075X-RAY DIFFRACTION100
2.37-2.5340.1811620.1572852X-RAY DIFFRACTION99.8344
2.534-2.7360.1711560.1552641X-RAY DIFFRACTION99.7859
2.736-2.9970.1671410.1592428X-RAY DIFFRACTION99.0744
2.997-3.3490.1911260.1632150X-RAY DIFFRACTION97.3898
3.349-3.8650.1921190.1621902X-RAY DIFFRACTION97.1635
3.865-4.7280.182570.1471696X-RAY DIFFRACTION99.5457
4.728-6.6620.181850.1591279X-RAY DIFFRACTION99.6348
6.662-100.187340.187667X-RAY DIFFRACTION88.622

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