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

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Basic information

Entry
Database: PDB / ID: 7xhx
TitleCrystal structure of metallo-beta-lactamase IMP-6
ComponentsBeta-lactamase
KeywordsHYDROLASE / Metallo-beta-lactamase / Carbapenemase / Zinc protein / Antimicrobial protein
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 / 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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsYamamoto, K. / Tanaka, H. / Kurisu, G. / Nakano, R. / Yano, H. / Sakai, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21K07010 Japan
CitationJournal: J.Biochem. / Year: 2022
Title: Structural insights into the substrate specificity of IMP-6 and IMP-1 metallo-beta-lactamases.
Authors: Yamamoto, K. / Tanaka, H. / Kurisu, G. / Nakano, R. / Yano, H. / Sakai, H.
History
DepositionApr 11, 2022Deposition site: PDBJ / Processing site: PDBJ
SupersessionFeb 15, 2023ID: 6LVJ
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 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)109,02412
Polymers108,5004
Non-polymers5238
Water6,792377
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2563
Polymers27,1251
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2563
Polymers27,1251
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2563
Polymers27,1251
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2563
Polymers27,1251
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.156, 78.340, 260.225
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 27125.119 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaIMP-6 / 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.31 Å3/Da / Density % sol: 46.73 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium acetate, 0.2 M ammonium acetate, 17% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 112203 / % possible obs: 100 % / Redundancy: 6.76 % / CC1/2: 0.997 / Net I/σ(I): 13.73
Reflection shellResolution: 1.7→1.79 Å / Num. unique obs: 17827 / CC1/2: 0.941

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DDK

1ddk


Resolution: 1.7→48.3 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.534 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23782 5610 5 %RANDOM
Rwork0.20449 ---
obs0.20616 106591 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.136 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.7→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6756 0 8 377 7141
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0136932
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166644
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.6329412
X-RAY DIFFRACTIONr_angle_other_deg1.3621.58215396
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0615860
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55424.444288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.613151188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7551512
X-RAY DIFFRACTIONr_chiral_restr0.0870.2864
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027700
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021460
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_it3.2733.7283452
X-RAY DIFFRACTIONr_mcbond_other3.2733.7283451
X-RAY DIFFRACTIONr_mcangle_it4.285.5844308
X-RAY DIFFRACTIONr_mcangle_other4.285.5844309
X-RAY DIFFRACTIONr_scbond_it4.364.233480
X-RAY DIFFRACTIONr_scbond_other4.3574.233478
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3636.1365104
X-RAY DIFFRACTIONr_long_range_B_refined7.69943.6027671
X-RAY DIFFRACTIONr_long_range_B_other7.69343.4767611
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.741 Å
RfactorNum. reflection% reflection
Rfree0.334 406 -
Rwork0.293 7727 -
obs--99.73 %

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