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

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Basic information

Entry
Database: PDB / ID: 8rlj
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 / MOLECULAR REPLACEMENT / Resolution: 2.45 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

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)261,4196
Polymers261,4196
Non-polymers00
Water4,540252
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
5
E: 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
6
F: 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)77.760, 100.821, 269.665
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 31 through 85 or resid 88 through 414))
d_2ens_1(chain "B" and (resid 31 through 85 or resid 88 through 322 or resid 363 through 414))
d_3ens_1(chain "C" and (resid 31 through 85 or resid 88 through 322 or resid 363 through 414))
d_4ens_1(chain "D" and (resid 31 through 85 or resid 88 through 322 or resid 363 through 414))
d_5ens_1(chain "E" and (resid 31 through 322 or resid 363 through 414))
d_6ens_1(chain "F" and (resid 31 through 85 or resid 88 through 322 or resid 363 through 414))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ASNASNILEILEAA31 - 858 - 62
d_12GLUGLUARGARGAA88 - 41465 - 391
d_21ASNASNILEILEBB31 - 858 - 62
d_22GLUGLUVALVALBB88 - 32265 - 299
d_23ALAALAARGARGBB363 - 414340 - 391
d_31ASNASNILEILECC31 - 858 - 62
d_32GLUGLUVALVALCC88 - 32265 - 299
d_33ALAALAARGARGCC363 - 414340 - 391
d_41ASNASNILEILEDD31 - 858 - 62
d_42GLUGLUVALVALDD88 - 32265 - 299
d_43ALAALAARGARGDD363 - 414340 - 391
d_51ASNASNVALVALEE31 - 3228 - 299
d_52ALAALAARGARGEE363 - 414340 - 391
d_61ASNASNILEILEFF31 - 858 - 62
d_62GLUGLUVALVALFF88 - 32265 - 299
d_63ALAALAARGARGFF363 - 414340 - 391

NCS oper:
IDCodeMatrixVector
1given(-0.355152401251, 0.775599484302, -0.521835426007), (-0.832544422453, -0.516300561705, -0.200757352606), (-0.425131222716, 0.363151717514, 0.82908640897)-24.8530330112, -5.52400314541, -7.89539464526
2given(-0.349043632111, -0.859234354573, -0.374011853828), (0.784982271075, -0.486074415959, 0.384102195057), (-0.511831395071, -0.159524249163, 0.844144914661)-18.5805996832, 18.5217589477, -7.15770130077
3given(0.999937453448, -0.0111829793307, 0.000173683025203), (-0.00469755408727, -0.434028259289, -0.900887009077), (0.0101499841429, 0.900829845815, -0.434053644968)-0.981034795579, 50.0444509584, 135.992334736
4given(0.362389165968, -0.78336107249, 0.504994576699), (0.729116659906, -0.0992346378763, -0.677156837737), (0.580571260602, 0.61359426069, 0.535200051019)-50.9243087617, 9.7756742165, 1.35158718737
5given(0.35921894422, 0.851270171892, 0.382492934), (-0.119449062563, -0.364539813286, 0.923494800192), (0.925577480045, -0.377425249521, -0.0292661828341)-19.2519575624, -48.2272487572, 21.1185144309

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.02 Å3/Da / Density % sol: 39.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M TRIS-HCl buffer at pH 8.6 containing 17.5% PEG 4000 and 0.2 M CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.040248 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: 1.040248 Å / Relative weight: 1
ReflectionResolution: 2.45→49.55 Å / Num. obs: 78813 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 46.54 Å2 / CC1/2: 0.987 / Net I/σ(I): 5.82
Reflection shellResolution: 2.45→2.6 Å / Redundancy: 6.89 % / Mean I/σ(I) obs: 0.86 / Num. unique obs: 12543 / CC1/2: 0.994 / % possible all: 35.6

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Processing

Software
NameVersionClassification
PHENIXdev_4746refinement
PHENIXdev_4746refinement
autoPROCdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→49.55 Å / SU ML: 0.4563 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.5962
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2705 2000 2.54 %
Rwork0.2215 76798 -
obs0.2227 78798 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.96 Å2
Refinement stepCycle: LAST / Resolution: 2.45→49.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17834 0 0 253 18087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008418269
X-RAY DIFFRACTIONf_angle_d1.112124765
X-RAY DIFFRACTIONf_chiral_restr0.06352578
X-RAY DIFFRACTIONf_plane_restr0.02763257
X-RAY DIFFRACTIONf_dihedral_angle_d13.84216780
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.959958602793
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.05301919816
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS1.0536690049
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS0.918749553616
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS0.924273917431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.510.4481400.3965365X-RAY DIFFRACTION98.71
2.51-2.580.4121400.3575388X-RAY DIFFRACTION99.95
2.58-2.650.36971410.32375428X-RAY DIFFRACTION99.89
2.65-2.740.34481410.30475392X-RAY DIFFRACTION99.87
2.74-2.840.30811420.28155457X-RAY DIFFRACTION99.8
2.84-2.950.34821420.27185454X-RAY DIFFRACTION99.91
2.95-3.090.31811420.27475458X-RAY DIFFRACTION99.95
3.09-3.250.28621420.24825468X-RAY DIFFRACTION99.95
3.25-3.450.25751420.22195442X-RAY DIFFRACTION99.98
3.45-3.720.22741440.20065518X-RAY DIFFRACTION99.81
3.72-4.090.24471430.18285502X-RAY DIFFRACTION99.88
4.09-4.680.22181440.16135514X-RAY DIFFRACTION99.79
4.68-5.90.2381450.18935597X-RAY DIFFRACTION99.88
5.9-49.550.24261520.19325815X-RAY DIFFRACTION99.53

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