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- PDB-8rlk: Structure of the apo form of PIB-1 in an Orthorombic space group -

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Basic information

Entry
Database: PDB / ID: 8rlk
TitleStructure of the apo form of PIB-1 in an Orthorombic space group
ComponentsClass C beta-lactamase-related serine hydrolase
KeywordsHYDROLASE / Beta-lactamase / AmpC / PIB-1
Function / homology: / Beta-lactamase-related / Beta-lactamase / Beta-lactamase/transpeptidase-like / hydrolase activity / Chem-MER / Serine hydrolase
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMedrano, F.J. / Romero, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2020-113521RB-I00 Spain
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: A new type of Class C beta-lactamases defined by PIB-1. A metal-dependent carbapenem-hydrolyzing beta-lactamase, from Pseudomonas aeruginosa: Structural and functional analysis.
Authors: Medrano, F.J. / Hernando-Amado, S. / Martinez, J.L. / Romero, A.
History
DepositionJan 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Class C beta-lactamase-related serine hydrolase
B: Class C beta-lactamase-related serine hydrolase
C: Class C beta-lactamase-related serine hydrolase
D: Class C beta-lactamase-related serine hydrolase
E: Class C beta-lactamase-related serine hydrolase
F: Class C beta-lactamase-related serine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)263,49220
Polymers261,4196
Non-polymers2,07314
Water12,755708
1
A: Class C beta-lactamase-related serine hydrolase
B: Class C beta-lactamase-related serine hydrolase
C: Class C beta-lactamase-related serine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,20113
Polymers130,7103
Non-polymers1,49110
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-165 kcal/mol
Surface area41150 Å2
MethodPISA
2
D: Class C beta-lactamase-related serine hydrolase
hetero molecules

F: Class C beta-lactamase-related serine hydrolase
hetero molecules

E: Class C beta-lactamase-related serine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,2917
Polymers130,7103
Non-polymers5824
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1/2,-y,z+1/21
crystal symmetry operation3_455-x-1,y+1/2,-z+1/21
Buried area4890 Å2
ΔGint-133 kcal/mol
Surface area41930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.890, 101.452, 267.758
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Class C beta-lactamase-related serine hydrolase / Serine hydrolase


Mass: 43569.887 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: CAZ10_27720, DT376_01770, GUL26_24405 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1J0J3U4
#2: Chemical
ChemComp-MER / (4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-d ihydro-1H-pyrrole-2-carboxylic acid / Meropenem, bound form


Mass: 385.478 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H27N3O5S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 708 / 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: 2.05 Å3/Da / Density % sol: 39.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium cacodylate buffer at pH 6.5 containing 20% PEG 1000 and 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.28368 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28368 Å / Relative weight: 1
ReflectionResolution: 2→47.44 Å / Num. obs: 145980 / % possible obs: 99.6 % / Redundancy: 10.64 % / Biso Wilson estimate: 36.16 Å2 / CC1/2: 0.997 / Net I/σ(I): 11.08
Reflection shellResolution: 2→2.12 Å / Mean I/σ(I) obs: 10.7 / Num. unique obs: 23145 / CC1/2: 0.683 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIXdev_4746refinement
PHENIXdev_4746refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→47.44 Å / SU ML: 0.2813 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.6761
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2353 2000 1.37 %
Rwork0.1913 143972 -
obs0.1919 145972 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.42 Å2
Refinement stepCycle: LAST / Resolution: 2→47.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18246 0 114 709 19069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007918810
X-RAY DIFFRACTIONf_angle_d1.017725518
X-RAY DIFFRACTIONf_chiral_restr0.05532652
X-RAY DIFFRACTIONf_plane_restr0.01023350
X-RAY DIFFRACTIONf_dihedral_angle_d6.99422638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.35481380.28999933X-RAY DIFFRACTION97.62
2.05-2.10.32531420.257210217X-RAY DIFFRACTION100
2.1-2.160.2751410.238710206X-RAY DIFFRACTION100
2.16-2.230.35731410.301110107X-RAY DIFFRACTION98.85
2.23-2.310.33111400.262310091X-RAY DIFFRACTION98.61
2.31-2.410.29081430.220110249X-RAY DIFFRACTION100
2.41-2.520.25941420.21410241X-RAY DIFFRACTION99.99
2.52-2.650.26461430.201510279X-RAY DIFFRACTION99.98
2.65-2.810.25171430.193110304X-RAY DIFFRACTION100
2.81-3.030.24851430.196710291X-RAY DIFFRACTION99.98
3.03-3.340.22991430.189910330X-RAY DIFFRACTION99.98
3.34-3.820.22191440.166510398X-RAY DIFFRACTION100
3.82-4.810.17861470.153310485X-RAY DIFFRACTION100
4.81-47.440.20781500.177310841X-RAY DIFFRACTION99.9

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