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- PDB-3mh4: HtrA proteases are activated by a conserved mechanism that can be... -

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Basic information

Entry
Database: PDB / ID: 3mh4
TitleHtrA proteases are activated by a conserved mechanism that can be triggered by distinct molecular cues
ComponentsProtease doPeptidase 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 / chaperone-mediated protein folding / serine-type peptidase activity / protein folding / outer membrane-bounded periplasmic space / peptidase activity / response to heat / response to oxidative stress ...peptidase Do / response to temperature stimulus / protein quality control for misfolded or incompletely synthesized proteins / chaperone-mediated protein folding / serine-type peptidase activity / protein folding / outer membrane-bounded periplasmic space / peptidase activity / 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 / MOLECULAR REPLACEMENT / Resolution: 3.1 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 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease do
B: Protease do


Theoretical massNumber of molelcules
Total (without water)95,8522
Polymers95,8522
Non-polymers00
Water0
1
A: Protease do
x 6


Theoretical massNumber of molelcules
Total (without water)287,5566
Polymers287,5566
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area14880 Å2
ΔGint-68 kcal/mol
Surface area82320 Å2
MethodPISA
2
B: Protease do
x 6


Theoretical massNumber of molelcules
Total (without water)287,5566
Polymers287,5566
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation9_555-x,-x+y,-z1
Buried area20560 Å2
ΔGint-81 kcal/mol
Surface area100630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.708, 120.708, 232.984
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Protease do / Peptidase Do / DegP / HtrA


Mass: 47926.070 Da / Num. of mol.: 2 / Mutation: S210A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: degP / Production host: Escherichia coli (E. coli)
References: UniProt: P0C0V0, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

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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: 2.61 Å3/Da / Density % sol: 52.94 %
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: ESRF / Beamline: ID14-4
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.1→25 Å / Num. all: 18503 / Num. obs: 18503 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 92.7 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 14.9
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1657 / Rsym value: 0.463 / % possible all: 90

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Processing

Software
NameVersionClassification
DNAdata collection
CNSrefinement
PHENIX(phenix.refine)refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KY9

1ky9


Resolution: 3.1→24.068 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.766 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 0 / Phase error: 28.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3088 958 5.19 %RANDOM
Rwork0.2565 ---
all0.2592 18443 --
obs0.2592 18443 97.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 86.581 Å2 / ksol: 0.301 e/Å3
Displacement parametersBiso max: 240.18 Å2 / Biso mean: 138.131 Å2 / Biso min: 53.59 Å2
Baniso -1Baniso -2Baniso -3
1-7.274 Å2-0 Å2-0 Å2
2--7.274 Å20 Å2
3----14.548 Å2
Refinement stepCycle: LAST / Resolution: 3.1→24.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5007 0 0 0 5007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065050
X-RAY DIFFRACTIONf_angle_d0.9366815
X-RAY DIFFRACTIONf_chiral_restr0.061822
X-RAY DIFFRACTIONf_plane_restr0.004893
X-RAY DIFFRACTIONf_dihedral_angle_d17.5761885
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.2630.3561360.2842292242892
3.263-3.4670.321430.25124782621100
3.467-3.7340.2921390.23425092648100
3.734-4.1080.2871470.2225072654100
4.108-4.6980.2061260.1912521264798
4.698-5.9050.2691390.2192560269999
5.905-24.0690.3791280.3172618274694

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