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- PDB-2qmi: Structure of the octameric penicillin-binding protein homologue f... -

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Basic information

Entry
Database: PDB / ID: 2qmi
TitleStructure of the octameric penicillin-binding protein homologue from Pyrococcus abyssi
ComponentsPbp related beta-lactamase
KeywordsHYDROLASE / PAB87 / OCTAMER / LU-HPDO3A / PBP / ARCHAEA
Function / homology
Function and homology information


Pab87 octamerisation domain / Pab87 octamerisation domain / Pab87 octamerisation domain superfamily / Pab87 octamerisation domain / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Lipocalin / Beta-lactamase/transpeptidase-like ...Pab87 octamerisation domain / Pab87 octamerisation domain / Pab87 octamerisation domain superfamily / Pab87 octamerisation domain / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Lipocalin / Beta-lactamase/transpeptidase-like / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-DO3 / : / Beta-lactamase-like protein
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsDelfosse, V. / Girard, E. / Moulinier, L. / Schultz, P. / Mayer, C.
CitationJournal: Plos One / Year: 2009
Title: Structure of the archaeal pab87 peptidase reveals a novel self-compartmentalizing protease family
Authors: Delfosse, V. / Girard, E. / Birck, C. / Delmarcelle, M. / Delarue, M. / Poch, O. / Schultz, P. / Mayer, C.
History
DepositionJul 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pbp related beta-lactamase
B: Pbp related beta-lactamase
C: Pbp related beta-lactamase
D: Pbp related beta-lactamase
E: Pbp related beta-lactamase
F: Pbp related beta-lactamase
G: Pbp related beta-lactamase
H: Pbp related beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)408,61929
Polymers404,0278
Non-polymers4,59221
Water42,6602368
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.940, 105.630, 112.920
Angle α, β, γ (deg.)72.170, 66.510, 81.390
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Pbp related beta-lactamase / Penicillin-binding protein


Mass: 50503.371 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Strain: GE5 / Gene: pbp / Plasmid: pET29a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: Q9V2D6, beta-lactamase
#2: Chemical
ChemComp-LU / LUTETIUM (III) ION / LU / Lutetium


Mass: 174.967 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Lu
#3: Chemical
ChemComp-DO3 / 10-((2R)-2-HYDROXYPROPYL)-1,4,7,10-TETRAAZACYCLODODECANE 1,4,7-TRIACETIC ACID


Mass: 404.459 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H32N4O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2368 / 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: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.02M calcium chloride dihydrate, 0.1M sodium acetate trihydrate, 30% MPD, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.34029 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 22, 2007
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34029 Å / Relative weight: 1
ReflectionAv σ(I) over netI: 17.36 / Number: 1542549 / Rmerge(I) obs: 0.081 / D res high: 2.2 Å / Num. obs: 198621 / % possible obs: 95.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obs
2.22.3294.410.291
2.322.4894.910.226
2.482.6795.410.175
2.672.9295.910.123
2.923.2796.410.085
3.273.7696.910.058
3.764.5997.310.046
ReflectionResolution: 2.2→30 Å / Num. all: 198053 / Num. obs: 198053 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 26.2 Å2 / Rsym value: 0.08 / Net I/σ(I): 17.4
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 7.2 / Num. unique all: 28540 / Rsym value: 0.289 / % possible all: 93.8

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
XDSdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→30 Å / Isotropic thermal model: Restrained / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 9931 4.8 %Random
Rwork0.196 ---
obs0.196 198053 96.2 %-
all-198621 --
Solvent computationBsol: 37.475 Å2
Displacement parametersBiso mean: 24.451 Å2
Baniso -1Baniso -2Baniso -3
1--2.581 Å22.616 Å20.055 Å2
2--2.853 Å23.112 Å2
3----0.272 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28385 0 129 2368 30882
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it0.9851.5
X-RAY DIFFRACTIONc_scbond_it1.5292
X-RAY DIFFRACTIONc_mcangle_it1.4322
X-RAY DIFFRACTIONc_scangle_it2.1552.5
LS refinement shellResolution: 2.2→2.28 Å
RfactorNum. reflection% reflection
Rfree0.335 972 -
Rwork0.277 --
obs-18488 94.4 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3LU_3.param
X-RAY DIFFRACTION4DO3_eric.param

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