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- PDB-3tjo: HtrA1 catalytic domain, mutationally inactivated -

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Basic information

Entry
Database: PDB / ID: 3tjo
TitleHtrA1 catalytic domain, mutationally inactivated
ComponentsSerine protease HTRA1
KeywordsHYDROLASE / peptidase
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 / Degradation of the extracellular matrix / serine-type peptidase activity / placenta development / molecular function activator activity / 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 / Degradation of the extracellular matrix / serine-type peptidase activity / placenta development / molecular function activator activity / 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 / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Serine protease HTRA1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 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
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine protease HTRA1
B: Serine protease HTRA1
D: Serine protease HTRA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,82514
Polymers75,3953
Non-polymers1,42911
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8810 Å2
ΔGint-59 kcal/mol
Surface area26750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.922, 151.922, 87.536
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-99-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31D

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLUGLUAA160 - 18721 - 48
21METMETGLUGLUBB160 - 18721 - 48
31METMETGLUGLUDC160 - 18721 - 48
12PROPROASNASNAA200 - 21861 - 79
22PROPROASNASNBB200 - 21861 - 79
32PROPROASNASNDC200 - 21861 - 79
13VALVALSERSERAA228 - 36789 - 228
23VALVALSERSERBB228 - 36789 - 228
33VALVALSERSERDC228 - 36789 - 228

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Components

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


Mass: 25131.697 Da / Num. of mol.: 3 / Fragment: protease domain (UNP residues 161-370) / Mutation: S328A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HTRA, HTRA1, PRSS11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q92743, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 3.35 Å3/Da / Density % sol: 63.28 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: ammonium sulfate, LiCl, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 45897 / Num. obs: 44800 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 13 % / Rsym value: 0.12 / Net I/σ(I): 19

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Processing

Software
NameVersionClassification
BOSdata collection
PHASESphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: wild-type homologue

Resolution: 2.301→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.933 / SU B: 9.341 / SU ML: 0.105 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.19 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21616 1052 2.3 %RANDOM
Rwork0.18497 ---
obs0.18566 44800 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.026 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2---0.22 Å2-0 Å2
3---0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.301→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4536 0 90 216 4842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224778
X-RAY DIFFRACTIONr_angle_refined_deg1.1911.9816470
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.075600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.9524.842190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.0915825
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2631521
X-RAY DIFFRACTIONr_chiral_restr0.0860.2775
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213449
X-RAY DIFFRACTIONr_mcbond_it3.3332.52994
X-RAY DIFFRACTIONr_mcangle_it5.35254874
X-RAY DIFFRACTIONr_scbond_it5.0642.51784
X-RAY DIFFRACTIONr_scangle_it7.7351596
Refine LS restraints NCS

Ens-ID: 1 / Number: 1278 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.260.5
2BMEDIUM POSITIONAL0.260.5
3DMEDIUM POSITIONAL0.250.5
1AMEDIUM THERMAL0.792
2BMEDIUM THERMAL0.782
3DMEDIUM THERMAL0.812
LS refinement shellResolution: 2.301→2.425 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.247 147 -
Rwork0.209 6404 -
obs--99.59 %
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)
10.9134-0.31550.26851.1051-0.38240.78760.0046-0.00740.1588-0.0459-0.052-0.0249-0.12170.04170.04740.0675-0.0164-0.00160.0109-0.01450.0946.6237-24.542319.3579
20.51760.1114-0.2281.0475-0.27861.0144-0.0313-0.1712-0.00010.1840.01590.04770.0233-0.00070.01530.1029-0.00130.00190.13030.0020.004247.9122-47.728745.3925
31.4055-0.2915-0.41640.67520.30440.8145-0.0703-0.0183-0.1159-0.02820.0064-0.17940.03280.120.06390.0134-0.01310.02760.10220.02760.114670.9792-49.088819.2094
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A160 - 370
2X-RAY DIFFRACTION2B160 - 370
3X-RAY DIFFRACTION3D160 - 370

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