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

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Basic information

Entry
Database: PDB / ID: 8rll
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 / Serine hydrolase
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.72 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


Theoretical massNumber of molelcules
Total (without water)174,2804
Polymers174,2804
Non-polymers00
Water70339
1
A: Class C beta-lactamase-related serine hydrolase


Theoretical massNumber of molelcules
Total (without water)43,5701
Polymers43,5701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Class C beta-lactamase-related serine hydrolase


Theoretical massNumber of molelcules
Total (without water)43,5701
Polymers43,5701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Class C beta-lactamase-related serine hydrolase


Theoretical massNumber of molelcules
Total (without water)43,5701
Polymers43,5701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Class C beta-lactamase-related serine hydrolase


Theoretical massNumber of molelcules
Total (without water)43,5701
Polymers43,5701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.491, 149.491, 247.014
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

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


Mass: 43569.887 Da / Num. of mol.: 4
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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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: 3.05 Å3/Da / Density % sol: 59.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate buffer at pH 4.6 containing 8% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.978815 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978815 Å / Relative weight: 1
ReflectionResolution: 2.72→48 Å / Num. obs: 55462 / % possible obs: 99.8 % / Redundancy: 5.24 % / Biso Wilson estimate: 63.96 Å2 / CC1/2: 0.996 / Net I/σ(I): 9.67
Reflection shellResolution: 2.72→2.88 Å / Mean I/σ(I) obs: 1.46 / Num. unique obs: 17754 / CC1/2: 0.717 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIXdev_4746refinement
PHENIXdev_4746refinement
XDSdata reduction
XDSdata scaling
CRANKphasing
RefinementMethod to determine structure: SAD / Resolution: 2.72→48 Å / SU ML: 0.3334 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.7894
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2265 2006 3.62 %
Rwork0.1828 53372 -
obs0.1844 55378 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.52 Å2
Refinement stepCycle: LAST / Resolution: 2.72→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12164 0 0 39 12203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007912468
X-RAY DIFFRACTIONf_angle_d1.007516908
X-RAY DIFFRACTIONf_chiral_restr0.05391752
X-RAY DIFFRACTIONf_plane_restr0.0092228
X-RAY DIFFRACTIONf_dihedral_angle_d6.17111748
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.72-2.780.34661410.30913721X-RAY DIFFRACTION97.75
2.78-2.860.31241400.28123810X-RAY DIFFRACTION99.67
2.86-2.940.33921450.28183820X-RAY DIFFRACTION99.7
2.94-3.040.31281460.27173830X-RAY DIFFRACTION99.65
3.04-3.150.31771400.24593793X-RAY DIFFRACTION99.75
3.15-3.270.27681420.22813790X-RAY DIFFRACTION99.67
3.27-3.420.28721470.22583867X-RAY DIFFRACTION99.88
3.42-3.60.23171430.20133792X-RAY DIFFRACTION99.95
3.6-3.830.26041450.19053853X-RAY DIFFRACTION99.85
3.83-4.120.2271450.16593820X-RAY DIFFRACTION99.92
4.12-4.540.1961410.15093810X-RAY DIFFRACTION99.87
4.54-5.190.19951440.14973818X-RAY DIFFRACTION99.95
5.19-6.540.21761460.17273826X-RAY DIFFRACTION99.97
6.54-480.151410.13323822X-RAY DIFFRACTION99.87

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