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- PDB-7wzu: Crystal structure of metallo-beta-lactamase IMP-6. -

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Basic information

Entry
Database: PDB / ID: 7wzu
TitleCrystal structure of metallo-beta-lactamase IMP-6.
ComponentsBeta-lactamase
KeywordsHYDROLASE / metallo-beta-lactamase / zinc(II) ion
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
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 / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.954 Å
AuthorsYamaguchi, Y. / Kurosaki, H.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17K08376 Japan
Japan Society for the Promotion of Science (JSPS)17K08240 Japan
CitationJournal: Acs Infect Dis. / Year: 2023
Title: Difference in the Inhibitory Effect of Thiol Compounds and Demetallation Rates from the Zn(II) Active Site of Metallo-beta-lactamases (IMP-1 and IMP-6) Associated with a Single Amino Acid Substitution.
Authors: Yamaguchi, Y. / Kato, K. / Ichimaru, Y. / Uenosono, Y. / Tawara, S. / Ito, R. / Matsuse, N. / Wachino, J.I. / Toma-Fukai, S. / Jin, W. / Arakawa, Y. / Otsuka, M. / Fujita, M. / Fukuishi, N. ...Authors: Yamaguchi, Y. / Kato, K. / Ichimaru, Y. / Uenosono, Y. / Tawara, S. / Ito, R. / Matsuse, N. / Wachino, J.I. / Toma-Fukai, S. / Jin, W. / Arakawa, Y. / Otsuka, M. / Fujita, M. / Fukuishi, N. / Sugiura, K. / Imai, M. / Kurosaki, H.
History
DepositionFeb 19, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 4, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 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

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,99012
Polymers100,4674
Non-polymers5238
Water5,188288
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2473
Polymers25,1171
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-80 kcal/mol
Surface area10160 Å2
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2473
Polymers25,1171
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-79 kcal/mol
Surface area10130 Å2
MethodPISA
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2473
Polymers25,1171
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-78 kcal/mol
Surface area10150 Å2
MethodPISA
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2473
Polymers25,1171
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-79 kcal/mol
Surface area10130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.799, 76.098, 82.114
Angle α, β, γ (deg.)83.446, 75.317, 74.063
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Beta-lactamase / metallo-beta-lactamase IMP-6


Mass: 25116.648 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaIMP-6 / Plasmid: pET29a(+) / Production host: Escherichia coli (E. coli) / References: UniProt: K4PWX3, beta-lactamase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.88 Å3/Da / Density % sol: 57.26 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: Hepes, sodium acetate, sodium citrate, PEG 4000

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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: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.954→50 Å / Num. obs: 75127 / % possible obs: 92.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 20
Reflection shellResolution: 1.96→1.99 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.172 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2694 / % possible all: 66.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
AMoREphasing
REFMAC5.8.0267refinement
PHENIX1.20.1-4487refinement
Coot0.9.6model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DD6

1dd6


Resolution: 1.954→35.415 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.193 / SU ML: 0.114 / Cross valid method: FREE R-VALUE / ESU R: 0.157 / ESU R Free: 0.145
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2263 3754 5 %
Rwork0.1899 71326 -
all0.192 --
obs-75080 92.517 %
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: 31.882 Å2
Baniso -1Baniso -2Baniso -3
1-0.001 Å2-0 Å20.001 Å2
2--0 Å2-0 Å2
3----0.001 Å2
Refinement stepCycle: LAST / Resolution: 1.954→35.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6780 0 8 288 7076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0136956
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166660
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.6329444
X-RAY DIFFRACTIONr_angle_other_deg1.1911.58215436
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0535864
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.13824.444288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.841151192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2481512
X-RAY DIFFRACTIONr_chiral_restr0.0620.2868
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027728
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021464
X-RAY DIFFRACTIONr_nbd_refined0.1960.21249
X-RAY DIFFRACTIONr_symmetry_nbd_other0.170.25917
X-RAY DIFFRACTIONr_nbtor_refined0.1580.23382
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.23088
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2289
X-RAY DIFFRACTIONr_metal_ion_refined0.0510.213
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1720.218
X-RAY DIFFRACTIONr_nbd_other0.1930.2121
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1130.228
X-RAY DIFFRACTIONr_mcbond_it2.053.1653468
X-RAY DIFFRACTIONr_mcbond_other2.0473.1643467
X-RAY DIFFRACTIONr_mcangle_it3.3944.7374328
X-RAY DIFFRACTIONr_mcangle_other3.3954.7384329
X-RAY DIFFRACTIONr_scbond_it2.3173.5583488
X-RAY DIFFRACTIONr_scbond_other2.3153.5563486
X-RAY DIFFRACTIONr_scangle_it3.875.1865116
X-RAY DIFFRACTIONr_scangle_other3.875.1865116
X-RAY DIFFRACTIONr_lrange_it6.00636.9867670
X-RAY DIFFRACTIONr_lrange_other6.00836.9717633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.954-2.0050.3071940.2833871X-RAY DIFFRACTION67.3571
2.005-2.060.2952310.2714871X-RAY DIFFRACTION87.4379
2.06-2.1190.2912820.2574792X-RAY DIFFRACTION89.1583
2.119-2.1850.2622610.2424744X-RAY DIFFRACTION90.9008
2.185-2.2560.252470.2294713X-RAY DIFFRACTION92.3822
2.256-2.3350.2452500.2094547X-RAY DIFFRACTION93.1095
2.335-2.4230.2372470.1934429X-RAY DIFFRACTION93.5574
2.423-2.5220.2442050.1874346X-RAY DIFFRACTION94.7928
2.522-2.6340.2452410.1884224X-RAY DIFFRACTION95.8772
2.634-2.7630.2032120.1924016X-RAY DIFFRACTION96.0036
2.763-2.9120.251880.2143889X-RAY DIFFRACTION96.5885
2.912-3.0880.2572040.1973614X-RAY DIFFRACTION97.2491
3.088-3.3010.2611830.1933484X-RAY DIFFRACTION97.8911
3.301-3.5650.21670.1773245X-RAY DIFFRACTION98.3002
3.565-3.9050.1881700.1582969X-RAY DIFFRACTION98.6177
3.905-4.3640.1921400.1552682X-RAY DIFFRACTION98.6024
4.364-5.0370.1611080.142432X-RAY DIFFRACTION99.1026
5.037-6.1630.1881080.1632023X-RAY DIFFRACTION98.7031
6.163-8.6890.221660.1691575X-RAY DIFFRACTION99.5752

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