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

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Basic information

Entry
Database: PDB / ID: 5kdw
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
PHOSPHATE ION / Immunomodulating metalloprotease
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metallopeptidase
B: Metallopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,16153
Polymers192,7592
Non-polymers3,40251
Water37,1112060
1
A: Metallopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,12827
Polymers96,3791
Non-polymers1,74926
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Metallopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,03326
Polymers96,3791
Non-polymers1,65425
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.920, 132.730, 103.070
Angle α, β, γ (deg.)90.00, 103.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Metallopeptidase


Mass: 96379.289 Da / Num. of mol.: 2 / Fragment: UNP residues 42-923
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 42 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2060 / 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: 3.41 Å3/Da / Density % sol: 63.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: PEG 3350, NaH2PO4, Bicine pH 9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.85→100.09 Å / Num. obs: 219649 / % possible obs: 100 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 9.5
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KDV

5kdv


Resolution: 1.85→100.09 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.564 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18638 10928 5 %RANDOM
Rwork0.15315 ---
obs0.15481 208686 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.172 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å22.05 Å2
2---1.33 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.85→100.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13549 0 205 2060 15814
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01914150
X-RAY DIFFRACTIONr_bond_other_d0.0010.0213193
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.94919191
X-RAY DIFFRACTIONr_angle_other_deg0.841330207
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.88751796
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10924.238663
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.597152177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.17915103
X-RAY DIFFRACTIONr_chiral_restr0.0980.22069
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02116499
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023376
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_it1.5521.957145
X-RAY DIFFRACTIONr_mcbond_other1.5471.9497144
X-RAY DIFFRACTIONr_mcangle_it2.2332.9188954
X-RAY DIFFRACTIONr_mcangle_other2.2332.9188955
X-RAY DIFFRACTIONr_scbond_it2.7522.2487005
X-RAY DIFFRACTIONr_scbond_other2.7422.2466992
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2013.2410220
X-RAY DIFFRACTIONr_long_range_B_refined6.26217.74318226
X-RAY DIFFRACTIONr_long_range_B_other6.08617.29417648
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 809 -
Rwork0.257 15429 -
obs--99.99 %

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