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- PDB-6l3s: Crystal structure of metallo-beta-lactamase IMP-27 from Morganell... -

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Basic information

Entry
Database: PDB / ID: 6l3s
TitleCrystal structure of metallo-beta-lactamase IMP-27 from Morganella morganii
ComponentsIMP-27 metallo-beta-lactamase
KeywordsHYDROLASE / metallo-beta-lactamase
Function / homology
Function and homology information


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-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
Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesMorganella morganii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsKato, Y. / Shimizu-Ibuka, A.
CitationJournal: To Be Published
Title: Crystal structure of the metallo-beta-lactamase IMP-27
Authors: Kato, Y. / Shimizu-Ibuka, A.
History
DepositionOct 15, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: IMP-27 metallo-beta-lactamase
B: IMP-27 metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1396
Polymers50,8782
Non-polymers2624
Water5,711317
1
A: IMP-27 metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5703
Polymers25,4391
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-79 kcal/mol
Surface area10000 Å2
MethodPISA
2
B: IMP-27 metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5703
Polymers25,4391
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-81 kcal/mol
Surface area10040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.590, 71.250, 136.210
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 IMP-27 metallo-beta-lactamase / Metallo-beta-lactamase IMP-27


Mass: 25438.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Morganella morganii (bacteria) / Gene: blaIMP-27 / Plasmid: pLysS / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A286S0G7
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.38 Å3/Da / Density % sol: 48.33 % / Description: Plate
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: PEG 4000,Tris-HCl,magnesium chloride / PH range: 8.0-9.0

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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: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→68.11 Å / Num. all: 51881 / Num. obs: 51881 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.037 / Rrim(I) all: 0.098 / Rsym value: 0.091 / Net I/σ(I): 13.4 / Num. measured all: 365524
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.7-1.797.20.4985332774380.9270.0220.0570.0523.7100
5.38-68.116.60.0521210018230.9980.0210.0550.05125.899.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.506
Highest resolutionLowest resolution
Rotation68.11 Å1.84 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALA3.3.22data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UBQ

4ubq


Resolution: 1.7→39.57 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.1958 / WRfactor Rwork: 0.172 / FOM work R set: 0.8512 / SU B: 1.945 / SU ML: 0.064 / SU R Cruickshank DPI: 0.1024 / SU Rfree: 0.0959 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2002 2658 5.1 %RANDOM
Rwork0.1783 ---
obs0.1795 49146 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.89 Å2 / Biso mean: 17.914 Å2 / Biso min: 7.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.7→39.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3428 0 4 317 3749
Biso mean--15.08 23.84 -
Num. residues----436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133526
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173277
X-RAY DIFFRACTIONr_angle_refined_deg1.6961.6334778
X-RAY DIFFRACTIONr_angle_other_deg1.4491.5837640
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2285436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.41824.545154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47815614
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.69156
X-RAY DIFFRACTIONr_chiral_restr0.0870.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023894
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02700
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 177 -
Rwork0.225 3559 -
all-3736 -
obs--100 %

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