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- PDB-3mh7: HtrA proteases are activated by a conserved mechanism that can be... -

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Basic information

Entry
Database: PDB / ID: 3mh7
TitleHtrA proteases are activated by a conserved mechanism that can be triggered by distinct molecular cues
Components
  • 5-mer peptide
  • Protease do
KeywordsHYDROLASE / DegP / HtrA / protease / outer membrane protein
Function / homology
Function and homology information


peptidase Do / response to temperature stimulus / protein quality control for misfolded or incompletely synthesized proteins / : / serine-type peptidase activity / protein folding / peptidase activity / outer membrane-bounded periplasmic space / response to heat / response to oxidative stress ...peptidase Do / response to temperature stimulus / protein quality control for misfolded or incompletely synthesized proteins / : / serine-type peptidase activity / protein folding / peptidase activity / outer membrane-bounded periplasmic space / response to heat / response to oxidative stress / periplasmic space / serine-type endopeptidase activity / proteolysis / identical protein binding / plasma membrane
Similarity search - Function
Peptidase S1C, Do / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily ...Peptidase S1C, Do / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Trypsin-like serine proteases / Thrombin, subunit H / Roll / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Periplasmic serine endoprotease DegP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.961 Å
AuthorsKrojer, T. / Sawa, J. / Huber, R. / Clausen, T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: HtrA proteases have a conserved activation mechanism that can be triggered by distinct molecular cues
Authors: Krojer, T. / Sawa, J. / Huber, R. / Clausen, T.
History
DepositionApr 7, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease do
B: 5-mer peptide
C: 5-mer peptide


Theoretical massNumber of molelcules
Total (without water)49,4703
Polymers49,4703
Non-polymers00
Water00
1
A: Protease do
B: 5-mer peptide
C: 5-mer peptide
x 24


Theoretical massNumber of molelcules
Total (without water)1,187,27272
Polymers1,187,27272
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_555-z,-y,-x1
Buried area105750 Å2
ΔGint-647 kcal/mol
Surface area377900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)253.929, 253.929, 253.929
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432

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Components

#1: Protein Protease do / DegP / HtrA


Mass: 48582.594 Da / Num. of mol.: 1 / Mutation: S210A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: DegP / Plasmid: pQE60 / Production host: Escherichia coli (E. coli)
References: UniProt: P0C0V0, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein/peptide 5-mer peptide


Mass: 443.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: this peptide apparently picked up during protein purification.
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: DegP / Plasmid: pQE60 / Production host: Escherichia coli (E. coli)
Has protein modificationY
Sequence detailsTHE DEPOSITORS COULD NOT DETERMINE THE SEQUENCE FOR CHAIN B, C AND COULD NOT PROVE WHETHER CHIAN B ...THE DEPOSITORS COULD NOT DETERMINE THE SEQUENCE FOR CHAIN B, C AND COULD NOT PROVE WHETHER CHIAN B AND C ARE SAME OR DIFFERENT.

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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: 3.45 Å3/Da / Density % sol: 64.32 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 8.5
Details: PEG 550 MME, NaCl, pH 8.5, VAPOR DIFFUSION, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.961→30 Å / Num. obs: 15145 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 60.3 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 13
Reflection shellResolution: 2.961→3.19 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.579 / % possible all: 99.9

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Processing

Software
NameVersionClassification
DNAdata collection
SHARPphasing
PHENIX(phenix.refine: 1.6_289)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.961→29.321 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.828 / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.249 762 5.03 %RANDOM
Rwork0.1986 ---
all0.2011 15144 --
obs0.2011 15144 99.86 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.861 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso max: 176.98 Å2 / Biso mean: 75.679 Å2 / Biso min: 33.13 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.961→29.321 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2919 0 0 0 2919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012942
X-RAY DIFFRACTIONf_angle_d1.283972
X-RAY DIFFRACTIONf_dihedral_angle_d19.0471087
X-RAY DIFFRACTIONf_chiral_restr0.081477
X-RAY DIFFRACTIONf_plane_restr0.004525
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.9609-3.18920.3191460.2862815
3.1892-3.50970.26711560.22172802
3.5097-4.01650.23911380.17692838
4.0165-5.05610.19731510.15532881
5.0561-29.32260.26071710.20683046

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