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- PDB-5kdv: IMPa metallopeptidase from Pseudomonas aeruginosa -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5kdv
TitleIMPa metallopeptidase from Pseudomonas aeruginosa
ComponentsMetallopeptidase
KeywordsHYDROLASE / O-glycopeptidase / PF13402/M60-like
Function / homology
Function and homology information


negative regulation of leukocyte tethering or rolling / protein transport by the Sec complex / protein secretion by the type II secretion system / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / protein catabolic process / metallopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Immunomodulating metalloprotease N-terminal domain / Immunomodulating metalloprotease helical domain / Immunomodulating metalloprotease helical domain / Immunomodulating metalloprotease N-terminal domain / Peptidase family M60 domain / Peptidase M60, enhancin-like domain 3 / Peptidase M60, enhancin and enhancin-like / Peptidase family M60 domain profile. / Peptidase M60-like family / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Immunomodulating metalloprotease
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsNoach, I. / Boraston, A.B.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Recognition of protein-linked glycans as a determinant of peptidase activity.
Authors: Noach, I. / Ficko-Blean, E. / Pluvinage, B. / Stuart, C. / Jenkins, M.L. / Brochu, D. / Buenbrazo, N. / Wakarchuk, W. / Burke, J.E. / Gilbert, M. / Boraston, A.B.
History
DepositionJun 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Feb 8, 2017Group: Database references
Revision 1.3Oct 30, 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

Downloads & links

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Assembly

Deposited unit
A: Metallopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,96829
Polymers97,1591
Non-polymers1,80928
Water13,403744
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.280, 96.410, 100.920
Angle α, β, γ (deg.)90.00, 124.66, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Metallopeptidase


Mass: 97159.109 Da / Num. of mol.: 1 / Fragment: UNP residues 42-923 / Mutation: Y766N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria)
Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA0572
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9I5W4
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 744 / 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: 3.2 Å3/Da / Density % sol: 61.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: PEG 3350, (NH4)2SO4, Bicine pH 9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.93→48.72 Å / Num. obs: 90627 / % possible obs: 98.8 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 15
Reflection shellResolution: 1.93→2.03 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 4.2 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→48.72 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.017 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.121 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2043 4538 5 %RANDOM
Rwork0.17151 ---
obs0.17314 86006 98.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.704 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å2-0.02 Å2
2---0.01 Å20 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.93→48.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6851 0 111 744 7706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0197129
X-RAY DIFFRACTIONr_bond_other_d0.0010.026665
X-RAY DIFFRACTIONr_angle_refined_deg1.531.9459659
X-RAY DIFFRACTIONr_angle_other_deg0.825315250
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1545898
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.1824.206340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.841151096
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8021552
X-RAY DIFFRACTIONr_chiral_restr0.0930.21040
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218300
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021714
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_it1.4432.0063583
X-RAY DIFFRACTIONr_mcbond_other1.4432.0063582
X-RAY DIFFRACTIONr_mcangle_it2.0513.0024484
X-RAY DIFFRACTIONr_mcangle_other2.0513.0034485
X-RAY DIFFRACTIONr_scbond_it2.0822.2233546
X-RAY DIFFRACTIONr_scbond_other2.0822.2233546
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.223.2365176
X-RAY DIFFRACTIONr_long_range_B_refined4.68617.048943
X-RAY DIFFRACTIONr_long_range_B_other4.49716.6688601
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 329 -
Rwork0.243 6321 -
obs--97.54 %

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