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

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Basic information

Entry
Database: PDB / ID: 6kxo
TitleCrystal Structure Of VIM-2 Metallo-beta-lactamase In Complex With Inhibitor NO9
ComponentsBeta-lactamase class B VIM-2
KeywordsHYDROLASE
Function / homology
Function and homology information


antibiotic catabolic process / 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
FORMIC ACID / 2,5-dimethyl-4-sulfamoyl-furan-3-carboxylic acid / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 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 12, 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.pdbx_leaving_atom_flag / _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

Downloads & links

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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)52,41019
Polymers51,0792
Non-polymers1,33117
Water11,476637
1
A: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,31510
Polymers25,5391
Non-polymers7759
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
ΔGint-36 kcal/mol
Surface area9740 Å2
MethodPISA
2
B: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0959
Polymers25,5391
Non-polymers5568
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-28 kcal/mol
Surface area9650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.501, 79.210, 67.660
Angle α, β, γ (deg.)90.000, 130.130, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 654 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NO9 / 2,5-dimethyl-4-sulfamoyl-furan-3-carboxylic acid


Mass: 219.215 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H9NO5S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 637 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 39.58 %
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: AichiSR / Beamline: BL2S1 / Wavelength: 1.12 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 1.49→55.43 Å / Num. obs: 66587 / % possible obs: 99.3 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 15.3
Reflection shellResolution: 1.49→1.57 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.319 / Num. unique obs: 9647 / % possible all: 99.5

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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: 1.49→51.487 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.172 / WRfactor Rwork: 0.148 / SU B: 1.048 / SU ML: 0.04 / Average fsc free: 0.9586 / Average fsc work: 0.9643 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.067
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1691 3468 5.208 %
Rwork0.1456 63117 -
all0.147 --
obs-66585 99.73 %
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: 12.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.416 Å20 Å20.025 Å2
2---0.476 Å20 Å2
3---0.007 Å2
Refinement stepCycle: LAST / Resolution: 1.49→51.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3492 0 64 637 4193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133765
X-RAY DIFFRACTIONr_bond_other_d00.0173373
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.6595157
X-RAY DIFFRACTIONr_angle_other_deg1.4281.5777808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4235493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.66821.895190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26415546
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg2.073152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8981525
X-RAY DIFFRACTIONr_chiral_restr0.0680.2494
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024315
X-RAY DIFFRACTIONr_gen_planes_other00.02783
X-RAY DIFFRACTIONr_nbd_refined0.2020.2750
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.23200
X-RAY DIFFRACTIONr_nbtor_refined0.1650.21761
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21541
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2433
X-RAY DIFFRACTIONr_metal_ion_refined0.1140.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2140.217
X-RAY DIFFRACTIONr_nbd_other0.260.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1780.241
X-RAY DIFFRACTIONr_mcbond_it1.2581.061884
X-RAY DIFFRACTIONr_mcbond_other1.2571.061885
X-RAY DIFFRACTIONr_mcangle_it1.8491.5892360
X-RAY DIFFRACTIONr_mcangle_other1.8481.5912361
X-RAY DIFFRACTIONr_scbond_it2.2731.2911879
X-RAY DIFFRACTIONr_scbond_other2.2721.291880
X-RAY DIFFRACTIONr_scangle_it3.2971.8512780
X-RAY DIFFRACTIONr_scangle_other3.2971.8512781
X-RAY DIFFRACTIONr_lrange_it4.94514.8774394
X-RAY DIFFRACTIONr_lrange_other4.82714.4014306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.5290.242650.2114598X-RAY DIFFRACTION99.1639
1.529-1.5710.2032120.1794564X-RAY DIFFRACTION99.7285
1.571-1.6160.1832430.1624417X-RAY DIFFRACTION99.8714
1.616-1.6660.1642720.1524247X-RAY DIFFRACTION99.9337
1.666-1.720.1651940.1434197X-RAY DIFFRACTION99.9317
1.72-1.7810.1652220.1374038X-RAY DIFFRACTION99.9062
1.781-1.8480.1462160.1423866X-RAY DIFFRACTION99.8288
1.848-1.9230.2081910.1473747X-RAY DIFFRACTION99.7973
1.923-2.0090.1882540.1513547X-RAY DIFFRACTION99.8424
2.009-2.1060.1511940.1443409X-RAY DIFFRACTION99.7508
2.106-2.220.1681890.1433266X-RAY DIFFRACTION99.7978
2.22-2.3550.1571640.1363078X-RAY DIFFRACTION99.6618
2.355-2.5170.1581850.1362874X-RAY DIFFRACTION99.6417
2.517-2.7180.1441310.1362718X-RAY DIFFRACTION99.5458
2.718-2.9770.1741150.1442515X-RAY DIFFRACTION99.5458
2.977-3.3270.1791000.1452264X-RAY DIFFRACTION99.8311
3.327-3.8390.1661030.1342016X-RAY DIFFRACTION99.3436
3.839-4.6970.149860.1281693X-RAY DIFFRACTION100
4.697-6.6180.167620.1531343X-RAY DIFFRACTION100
6.618-100.173700.168720X-RAY DIFFRACTION99.1217

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