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- PDB-7dtm: Crystal structure of metallo-beta-lactamase IMP-1 in complex with... -

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Basic information

Entry
Database: PDB / ID: 7dtm
TitleCrystal structure of metallo-beta-lactamase IMP-1 in complex with citrate.
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE / metallo-beta-lactamase / zinc(II) ion / citrate
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / 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 / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / 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 / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Metallo-beta-lactamase IMP-1
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYamaguchi, Y. / Kurosaki, H.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: J.Med.Chem. / Year: 2021
Title: Crystal Structures of Metallo-beta-Lactamase (IMP-1) and Its D120E Mutant in Complexes with Citrate and the Inhibitory Effect of the Benzyl Group in Citrate Monobenzyl Ester.
Authors: Yamaguchi, Y. / Kato, K. / Ichimaru, Y. / Jin, W. / Sakai, M. / Abe, M. / Wachino, J.I. / Arakawa, Y. / Miyagi, Y. / Imai, M. / Fukuishi, N. / Yamagata, Y. / Otsuka, M. / Fujita, M. / Kurosaki, H.
History
DepositionJan 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)101,86616
Polymers100,5874
Non-polymers1,28012
Water9,872548
1
A: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4674
Polymers25,1471
Non-polymers3203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-78 kcal/mol
Surface area9970 Å2
MethodPISA
2
B: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4674
Polymers25,1471
Non-polymers3203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-78 kcal/mol
Surface area10100 Å2
MethodPISA
3
C: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4674
Polymers25,1471
Non-polymers3203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-78 kcal/mol
Surface area10080 Å2
MethodPISA
4
D: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4674
Polymers25,1471
Non-polymers3203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-78 kcal/mol
Surface area10040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.944, 75.675, 82.264
Angle α, β, γ (deg.)83.530, 75.440, 74.130
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 25146.676 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Plasmid: pET9a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 548 / 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: 2.87 Å3/Da / Density % sol: 57.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M citric acid-sodium citrate buffer, 0.2M sodium acetate, PEG4000 30w/v%

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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: Oct 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→79.53 Å / Num. obs: 73344 / % possible obs: 97.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 33.4
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 7.8 / Num. unique obs: 3554

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.27data extraction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DD6

1dd6


Resolution: 2→79.53 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.756 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2482 3681 5 %RANDOM
Rwork0.2122 ---
obs0.2141 69486 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.8 Å2 / Biso mean: 35.129 Å2 / Biso min: 15.85 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20.01 Å2-0.01 Å2
2---0.01 Å2-0.01 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 2→79.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6812 0 60 548 7420
Biso mean--36.09 37.43 -
Num. residues----872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0197036
X-RAY DIFFRACTIONr_bond_other_d0.0020.026744
X-RAY DIFFRACTIONr_angle_refined_deg1.2981.9699556
X-RAY DIFFRACTIONr_angle_other_deg0.892315624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2355868
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.38125.072276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.755151200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0711512
X-RAY DIFFRACTIONr_chiral_restr0.0770.21060
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217804
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021504
LS refinement shellResolution: 2.002→2.054 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 232 -
Rwork0.365 4703 -
all-4935 -
obs--88.95 %

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