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- PDB-4nnz: Subunit PA0372 of heterodimeric zinc protease PA0371-PA0372 -

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Basic information

Entry
Database: PDB / ID: 4nnz
TitleSubunit PA0372 of heterodimeric zinc protease PA0371-PA0372
ComponentsProbable zinc protease
KeywordsHYDROLASE / Zinc Finger / Protease / Outer Membrane
Function / homology
Function and homology information


pyrroloquinoline quinone biosynthetic process / outer membrane / metallopeptidase activity / metal ion binding
Similarity search - Function
Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Probable zinc protease
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.478 Å
AuthorsMamelli, L. / Goemaere, E. / Spinelli, S. / Vuillard, L.
CitationJournal: To be Published
Title: Structure of PA0372, subunit of the heterodimeric zinc protease PA0371-PA0372
Authors: Mamelli, L. / Goemaere, E. / Vuillard, L. / Spinelli, S.
History
DepositionNov 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Probable zinc protease
B: Probable zinc protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9884
Polymers98,7752
Non-polymers2122
Water1,47782
1
A: Probable zinc protease
hetero molecules

B: Probable zinc protease


Theoretical massNumber of molelcules
Total (without water)98,9884
Polymers98,7752
Non-polymers2122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area3190 Å2
ΔGint-2 kcal/mol
Surface area32680 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-0 kcal/mol
Surface area33410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.880, 106.510, 112.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Probable zinc protease


Mass: 49387.719 Da / Num. of mol.: 2 / Fragment: delta leader peptide
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA0372 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9I6C2
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.25
Details: 15% PEG 4000, 0.1M Imidazole Malonate, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2012 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.478→77.4 Å / Num. all: 34856 / Num. obs: 34553 / % possible obs: 99.11 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3
Reflection shellResolution: 2.478→50 Å / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
CNSrefinement
HKL-2000data collection
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.478→77.4 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.934 / Cross valid method: THROUGHOUT / ESU R: 0.473 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22704 1521 4.4 %RANDOM
Rwork0.20177 ---
obs0.2029 33030 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.539 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2---1.39 Å2-0 Å2
3---1.62 Å2
Refinement stepCycle: LAST / Resolution: 2.478→77.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6293 0 14 82 6389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0196459
X-RAY DIFFRACTIONr_bond_other_d00.026167
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.9698772
X-RAY DIFFRACTIONr_angle_other_deg3.595314168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6635795
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1923.616307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.185151085
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3141557
X-RAY DIFFRACTIONr_chiral_restr0.1570.2971
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217302
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021471
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3534.8853180
X-RAY DIFFRACTIONr_mcbond_other3.3534.8843179
X-RAY DIFFRACTIONr_mcangle_it4.9827.3243969
X-RAY DIFFRACTIONr_mcangle_other4.9827.3313985
X-RAY DIFFRACTIONr_scbond_it4.2335.3953279
X-RAY DIFFRACTIONr_scbond_other4.0825.4133275
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4487.914797
X-RAY DIFFRACTIONr_long_range_B_refined9.1739.777501
X-RAY DIFFRACTIONr_long_range_B_other9.1739.7747502
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.478→2.542 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 95 -
Rwork0.341 2439 -
obs--99.65 %

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