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- PDB-3tjq: N-domain of HtrA1 -

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Basic information

Entry
Database: PDB / ID: 3tjq
TitleN-domain of HtrA1
ComponentsSerine protease HTRA1
KeywordsHYDROLASE
Function / homology
Function and homology information


chorionic trophoblast cell differentiation / programmed cell death / growth factor binding / negative regulation of BMP signaling pathway / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / Degradation of the extracellular matrix / molecular function activator activity / placenta development / negative regulation of transforming growth factor beta receptor signaling pathway ...chorionic trophoblast cell differentiation / programmed cell death / growth factor binding / negative regulation of BMP signaling pathway / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / Degradation of the extracellular matrix / molecular function activator activity / placenta development / negative regulation of transforming growth factor beta receptor signaling pathway / collagen-containing extracellular matrix / positive regulation of apoptotic process / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Insulin-like growth factor binding protein / Insulin-like growth factor-binding protein, IGFBP / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain profile. / Insulin growth factor-binding protein homologues / Kazal-type serine protease inhibitor domain / PDZ domain 6 / Kazal type serine protease inhibitors / PDZ domain / Peptidase S1C / Kazal domain superfamily ...Insulin-like growth factor binding protein / Insulin-like growth factor-binding protein, IGFBP / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain profile. / Insulin growth factor-binding protein homologues / Kazal-type serine protease inhibitor domain / PDZ domain 6 / Kazal type serine protease inhibitors / PDZ domain / Peptidase S1C / Kazal domain superfamily / Trypsin-like peptidase domain / Kazal domain / Kazal domain profile. / Growth factor receptor cysteine-rich domain superfamily / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Peptidase S1, PA clan
Similarity search - Domain/homology
: / THIOCYANATE ION / Serine protease HTRA1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.001 Å
AuthorsEigenbrot, C. / Ultsch, M.
CitationJournal: Structure / Year: 2012
Title: Structural and Functional Analysis of HtrA1 and Its Subdomains.
Authors: Eigenbrot, C. / Ultsch, M. / Lipari, M.T. / Moran, P. / Lin, S.J. / Ganesan, R. / Quan, C. / Tom, J. / Sandoval, W. / van Lookeren Campagne, M. / Kirchhofer, D.
History
DepositionAug 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Jun 27, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine protease HTRA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,57914
Polymers14,6511
Non-polymers92713
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.085, 72.085, 41.289
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Serine protease HTRA1 / High-temperature requirement A serine peptidase 1 / L56 / Serine protease 11


Mass: 14651.489 Da / Num. of mol.: 1 / Fragment: N-terminal part (UNP residues 36-155)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HTRA, HTRA1, PRSS11 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): T. ni
References: UniProt: Q92743, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

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Non-polymers , 5 types, 51 molecules

#2: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pt
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CNS
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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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: 2.11 Å3/Da / Density % sol: 41.81 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: potassium thiocyanate, sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 8555 / Num. obs: 7676 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 9.8 % / Rsym value: 0.106 / Net I/σ(I): 19

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Processing

Software
NameVersionClassification
BOSdata collection
PHENIXmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.001→40 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.91 / SU B: 7.584 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2696 859 10.1 %RANDOM
Rwork0.21677 ---
obs0.22212 7676 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.153 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å20.78 Å2-0 Å2
2--1.55 Å2-0 Å2
3----2.33 Å2
Refinement stepCycle: LAST / Resolution: 2.001→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms753 0 26 38 817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021798
X-RAY DIFFRACTIONr_angle_refined_deg1.2331.9961077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6335106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.63622.35334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15715114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3351511
X-RAY DIFFRACTIONr_chiral_restr0.0720.2110
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022626
X-RAY DIFFRACTIONr_mcbond_it3.8572.5540
X-RAY DIFFRACTIONr_mcangle_it5.6745847
X-RAY DIFFRACTIONr_scbond_it4.6672.5258
X-RAY DIFFRACTIONr_scangle_it6.7115230
LS refinement shellResolution: 2.001→2.109 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.323 111 -
Rwork0.265 1053 -
obs--94.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.81481.12441.04841.74821.11451.59090.1362-0.2336-0.09310.1364-0.13860.07930.04330.01950.00240.0456-0.0302-0.00540.05960.01240.0236-6.162937.029419.7618
20.6334-0.7083-0.44211.0813-0.08481.58390.0994-0.00240.1153-0.0625-0.0775-0.1719-0.16230.0582-0.02190.0914-0.04370.00410.07490.02070.031310.915344.688617.2118
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 65
2X-RAY DIFFRACTION2A66 - 154

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