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- PDB-1l1j: Crystal structure of the protease domain of an ATP-independent he... -

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Basic information

Entry
Database: PDB / ID: 1l1j
TitleCrystal structure of the protease domain of an ATP-independent heat shock protease HtrA
Componentsheat shock protease HtrA
KeywordsHYDROLASE / serine proteinase
Function / homology
Function and homology information


serine-type endopeptidase activity
Similarity search - Function
Peptidase S1C, Do / PDZ domain / Peptidase S1C / Trypsin-like peptidase 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 ...Peptidase S1C, Do / PDZ domain / Peptidase S1C / Trypsin-like peptidase 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Heat shock serine protease, periplasmic
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsKim, D.Y. / Kim, D.R. / Ha, S.C. / Lokanath, N.K. / Hwang, H.Y. / Kim, K.K.
CitationJournal: J.BIOL.CHEM. / Year: 2003
Title: Crystal Structure of the Protease Domain of a Heat-shock Protein HtrA from Thermotoga maritima
Authors: Kim, D.Y. / Kim, D.R. / Ha, S.C. / Lokanath, N.K. / Lee, C.J. / Hwang, H.Y. / Kim, K.K.
History
DepositionFeb 18, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: heat shock protease HtrA
B: heat shock protease HtrA


Theoretical massNumber of molelcules
Total (without water)51,8632
Polymers51,8632
Non-polymers00
Water1,04558
1
A: heat shock protease HtrA


Theoretical massNumber of molelcules
Total (without water)25,9311
Polymers25,9311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: heat shock protease HtrA


Theoretical massNumber of molelcules
Total (without water)25,9311
Polymers25,9311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.55, 120.55, 120.55
Angle α, β, γ (deg.)90, 90, 90
Int Tables number198
Space group name H-MP213

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Components

#1: Protein heat shock protease HtrA / heat shock serine protease / periplasmic


Mass: 25931.455 Da / Num. of mol.: 2 / Fragment: protease domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: pET-22b / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WZ41, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: phosphate-citrate, Li2SO4, PEG1000, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMphosphate-citrate1reservoirpH4.4
2110 mM1reservoirLi2SO4
35 %(v/v)PEG10001reservoir

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / Num. obs: 13843 / % possible obs: 95.1 % / Redundancy: 2.43 % / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / % possible obs: 97.2 % / Num. unique obs: 1376 / Rmerge(I) obs: 0.27

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Processing

SoftwareName: CNS / Version: 1 / Classification: refinement
RefinementResolution: 2.8→20 Å
RfactorNum. reflection
Rfree0.278 1347
Rwork0.228 -
obs-13215
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3460 0 0 58 3518
Refinement
*PLUS
Num. reflection all: 13621 / Rfactor Rfree: 0.284 / Rfactor Rwork: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.008
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.53

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