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- PDB-3mh6: HtrA proteases are activated by a conserved mechanism that can be... -

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Basic information

Entry
Database: PDB / ID: 3mh6
TitleHtrA proteases are activated by a conserved mechanism that can be triggered by distinct molecular cues
ComponentsProtease do
KeywordsHYDROLASE / DegP / HtrA / protease
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
DIISOPROPYL PHOSPHONATE / Periplasmic serine endoprotease DegP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 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 1.3Nov 1, 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 / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 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: Protease do
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1082
Polymers47,9421
Non-polymers1661
Water00
1
A: Protease do
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)1,154,59748
Polymers1,150,61024
Non-polymers3,98824
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 area74190 Å2
ΔGint-478 kcal/mol
Surface area388190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)261.500, 261.500, 261.500
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: 47942.070 Da / Num. of mol.: 1
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: Chemical ChemComp-DFP / DIISOPROPYL PHOSPHONATE


Mass: 166.155 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15O3P
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: 3.97 Å3/Da / Density % sol: 69.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 12% Isopropanol, 0.1M Tris, 12% PEG 2000 MME, pH 8.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.6→29.24 Å / Num. all: 9340 / Num. obs: 9340 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 77.8 Å2 / Rmerge(I) obs: 0.243 / Rsym value: 0.243 / Net I/σ(I): 9.1
Reflection shellResolution: 3.6→3.79 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.787 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1318 / Rsym value: 0.787 / % possible all: 100

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Processing

Software
NameVersionClassification
DNAdata collection
CNSrefinement
PHENIX(phenix.refine: 1.6_289)refinement
XDSdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CS0

3cs0


Resolution: 3.6→28.703 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.66 / SU ML: 0.63 / Cross valid method: THROUGHOUT / σ(F): 1.35 / σ(I): 0 / Phase error: 37.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3091 423 4.97 %RANDOM
Rwork0.2732 ---
obs0.275 8508 90.99 %-
all-8508 --
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.836 Å2 / ksol: 0.237 e/Å3
Displacement parametersBiso max: 287.98 Å2 / Biso mean: 129.65 Å2 / Biso min: 68.63 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.6→28.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2868 0 10 0 2878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052903
X-RAY DIFFRACTIONf_angle_d0.9153918
X-RAY DIFFRACTIONf_chiral_restr0.055467
X-RAY DIFFRACTIONf_plane_restr0.003515
X-RAY DIFFRACTIONf_dihedral_angle_d18.7621086
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.6-3.790.4431430.4282706284994
4.12-5.1860.2821420.2542687282992
5.186-28.7040.2621380.2142692283087

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