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- PDB-6jka: Crystal structure of metallo-beta-lactamse, IMP-1, in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6jka
TitleCrystal structure of metallo-beta-lactamse, IMP-1, in complex with a thiazole-bearing inhibitor
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / antibiotic catabolic process / beta-lactamase / beta-lactamase activity / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
Beta-lactamases class B signature 2. / Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / : / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like ...Beta-lactamases class B signature 2. / Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / : / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-BQU / Chem-BS0 / Metallo-beta-lactamase IMP-1
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.006 Å
AuthorsKamo, T. / Kuroda, K. / Kondo, S. / Hayashi, U. / Fudo, S. / Nukaga, M. / Hoshino, T.
CitationJournal: Chem Pharm Bull (Tokyo) / Year: 2021
Title: Identification of the Inhibitory Compounds for Metallo-beta-lactamases and Structural Analysis of the Binding Modes.
Authors: Kamo, T. / Kuroda, K. / Kondo, S. / Hayashi, U. / Fudo, S. / Yoneda, T. / Takaya, A. / Nukaga, M. / Hoshino, T.
History
DepositionFeb 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_conn
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)101,61315
Polymers100,0624
Non-polymers1,55111
Water6,539363
1
A: Metallo-beta-lactamase type 2
C: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9658
Polymers50,0312
Non-polymers9346
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo-beta-lactamase type 2
D: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6477
Polymers50,0312
Non-polymers6165
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.477, 77.764, 261.527
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Metallo-beta-lactamase type 2 / B2 metallo-beta-lactamase / BLA-IMP / IMP-1 / Beta-lactamase type II / Metallo-beta-lactamase type II


Mass: 25015.523 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Plasmid: pET48b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLys / References: UniProt: P52699, beta-lactamase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-BS0 / 6-[2-(phenoxymethyl)-1,3-thiazol-4-yl]-3,4-dihydro-1H-quinolin-2-one


Mass: 336.408 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H16N2O2S
#4: Chemical ChemComp-BQU / 3-[2-azanyl-5-[2-(phenoxymethyl)-1,3-thiazol-4-yl]phenyl]propanoic acid


Mass: 354.423 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H18N2O3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.46 Å3/Da / Density % sol: 50.07 % / Mosaicity: 0.293 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.1M Sodium Citrate, 0.2M Sodium Acetate, 28%(v/v) PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 27, 2014 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 59827 / % possible obs: 88.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 29.68 Å2 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.057 / Rrim(I) all: 0.147 / Χ2: 1.051 / Net I/σ(I): 6.9 / Num. measured all: 388681
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2-2.0350.95119390.6210.4390.9758.8
2.03-2.075.10.79521650.670.3621.002660.879
2.07-2.115.30.7524020.7420.3331.04171.70.825
2.11-2.155.40.62327210.8040.2751.07882.60.685
2.15-2.260.51329100.8830.2211.07887.30.561
2.2-2.256.60.46829840.9230.1921.08690.20.507
2.25-2.316.90.40329880.9510.1621.07489.30.436
2.31-2.376.90.37630040.9420.1511.07190.90.406
2.37-2.446.90.32329940.9620.131.07289.40.348
2.44-2.526.90.28830350.9650.1161.05890.50.311
2.52-2.616.90.25930190.9670.1041.06290.20.279
2.61-2.716.90.22930340.970.0921.06991.20.248
2.71-2.846.80.18931170.980.0771.064920.205
2.84-2.996.80.16431170.9830.0671.06992.80.177
2.99-3.176.70.13832170.9870.0561.04795.30.149
3.17-3.426.60.11833100.9860.0491.03797.40.128
3.42-3.766.70.10933540.9890.0451.02198.70.118
3.76-4.316.80.134080.990.0410.98199.20.109
4.31-5.436.90.09334790.9920.0381.02999.70.101
5.43-506.70.08936300.9920.0371.06198.70.097

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WXC

3wxc


Resolution: 2.006→33.676 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2498 2919 4.89 %
Rwork0.1932 56821 -
obs0.196 59740 88.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.41 Å2 / Biso mean: 35.5173 Å2 / Biso min: 1.41 Å2
Refinement stepCycle: final / Resolution: 2.006→33.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6975 0 81 363 7419
Biso mean--51.64 36.13 -
Num. residues----895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0227237
X-RAY DIFFRACTIONf_angle_d2.4359820
X-RAY DIFFRACTIONf_chiral_restr0.0941075
X-RAY DIFFRACTIONf_plane_restr0.0121230
X-RAY DIFFRACTIONf_dihedral_angle_d4.5934241
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.006-2.03890.3659880.28441673176155
2.0389-2.07410.3485940.25521938203265
2.0741-2.11180.26561120.24382129224170
2.1118-2.15240.27511180.23612396251481
2.1524-2.19630.29341250.23112670279587
2.1963-2.2440.29471330.21952651278489
2.244-2.29620.28481380.21552771290990
2.2962-2.35360.26871440.20282679282389
2.3536-2.41730.26041430.20592749289291
2.4173-2.48840.28281390.20282706284590
2.4884-2.56870.30221470.2062725287290
2.5687-2.66040.30231310.20592797292891
2.6604-2.76690.23691480.20082757290591
2.7669-2.89280.27871310.20452831296293
2.8928-3.04520.28131460.20132856300293
3.0452-3.23580.25961580.18592932309096
3.2358-3.48540.23241460.18213011315798
3.4854-3.83580.21781720.17593035320799
3.8358-4.38980.23061550.16913109326499
4.3898-5.52670.21911890.172231103299100
5.5267-33.68070.23041620.19563296345899

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