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- PDB-3o3v: Crystal structure of ClbP peptidase domain -

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Basic information

Entry
Database: PDB / ID: 3o3v
TitleCrystal structure of ClbP peptidase domain
Componentsbeta-lactamase
KeywordsHYDROLASE / alpha/beta / disulfide bridge
Function / homologyBeta-lactamase / DD-peptidase/beta-lactamase superfamily / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDubois, D. / Cougnoux, A. / Delmas, J. / Bonnet, R.
CitationJournal: To be Published
Title: ClbP x-ray structure, the prototype of a peptidase family associated to NRP production
Authors: Dubois, D. / Baron, O. / Cougnoux, A. / Delmas, J. / Pradel, N. / Nougayrede, J.P. / Robin, F. / Oswald, E. / Bonnet, R.
History
DepositionJul 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: beta-lactamase
B: beta-lactamase
C: beta-lactamase


Theoretical massNumber of molelcules
Total (without water)110,4003
Polymers110,4003
Non-polymers00
Water4,486249
1
A: beta-lactamase


Theoretical massNumber of molelcules
Total (without water)36,8001
Polymers36,8001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: beta-lactamase


Theoretical massNumber of molelcules
Total (without water)36,8001
Polymers36,8001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: beta-lactamase


Theoretical massNumber of molelcules
Total (without water)36,8001
Polymers36,8001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.940, 149.930, 87.330
Angle α, β, γ (deg.)90.00, 123.90, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
DetailsBIOLOGICAL ASSEMBLY IS UNKNOWN AS PER AUTHORS

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Components

#1: Protein beta-lactamase / ClbP protein


Mass: 36800.004 Da / Num. of mol.: 3 / Fragment: UNP residues 38-372
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: IHE3034 / Gene: clbp, ECOK1_2171 / Plasmid: pET9a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D5D5I9, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: potassium phosphate 1.2M, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2008
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.4→19.94 Å / Num. obs: 39793 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Redundancy: 3 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 11.5
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.7 / % possible all: 94.3

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.94 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.885 / Cross valid method: THROUGHOUT / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24125 1993 5 %RANDOM
Rwork0.2042 ---
obs0.20604 37796 92.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.384 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.2894 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7713 0 0 249 7962
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0227885
X-RAY DIFFRACTIONr_angle_refined_deg0.9191.95810730
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.34451004
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.88924.176340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4151286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4361548
X-RAY DIFFRACTIONr_chiral_restr0.0650.21222
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215984
X-RAY DIFFRACTIONr_mcbond_it1.0951.55004
X-RAY DIFFRACTIONr_mcangle_it1.77328040
X-RAY DIFFRACTIONr_scbond_it0.63932881
X-RAY DIFFRACTIONr_scangle_it1.0444.52689
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2565 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.060.5
Bmedium positional0.050.5
Cmedium positional0.050.5
Amedium thermal0.022
Bmedium thermal0.022
Cmedium thermal0.022
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 129 -
Rwork0.237 2834 -
obs--94.15 %

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