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- PDB-3tjn: HtrA1 catalytic domain, apo form -

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Basic information

Entry
Database: PDB / ID: 3tjn
TitleHtrA1 catalytic domain, apo form
ComponentsSerine protease HTRA1
KeywordsHYDROLASE / protease
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 / 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: 3 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 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)74,2123
Polymers74,2123
Non-polymers00
Water0
1
A: Serine protease HTRA1

A: Serine protease HTRA1

A: Serine protease HTRA1


Theoretical massNumber of molelcules
Total (without water)74,2123
Polymers74,2123
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area5730 Å2
ΔGint-22 kcal/mol
Surface area25210 Å2
MethodPISA
2
B: Serine protease HTRA1

B: Serine protease HTRA1

B: Serine protease HTRA1


Theoretical massNumber of molelcules
Total (without water)74,2123
Polymers74,2123
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area6290 Å2
ΔGint-32 kcal/mol
Surface area26670 Å2
MethodPISA
3
D: Serine protease HTRA1

D: Serine protease HTRA1

D: Serine protease HTRA1


Theoretical massNumber of molelcules
Total (without water)74,2123
Polymers74,2123
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area6100 Å2
ΔGint-27 kcal/mol
Surface area25640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.495, 108.495, 234.435
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
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
11SERSERHISHISAA164 - 18525 - 46
21SERSERHISHISBB164 - 18525 - 46
31SERSERHISHISDC164 - 18525 - 46
12VALVALTHRTHRAA199 - 22360 - 84
22VALVALTHRTHRBB199 - 22360 - 84
32VALVALTHRTHRDC199 - 22360 - 84
13ARGARGGLYGLYAA227 - 28388 - 144
23ARGARGGLYGLYBB227 - 28388 - 144
33ARGARGGLYGLYDC227 - 28388 - 144
14ASNASNTHRTHRAA290 - 300151 - 161
24ASNASNTHRTHRBB290 - 300151 - 161
34ASNASNTHRTHRDC290 - 300151 - 161
15ASPASPILEILEAA315 - 323176 - 184
25ASPASPILEILEBB315 - 323176 - 184
35ASPASPILEILEDC315 - 323176 - 184
16GLYGLYTHRTHRAA330 - 344191 - 205
26GLYGLYTHRTHRBB330 - 344191 - 205
36GLYGLYTHRTHRDC330 - 344191 - 205
17SERSERLYSLYSAA352 - 362213 - 223
27SERSERLYSLYSBB352 - 362213 - 223
37SERSERLYSLYSDC352 - 362213 - 223

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Components

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


Mass: 24737.268 Da / Num. of mol.: 3 / Fragment: protease domain (UNP residues 161-367)
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

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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: 2.68 Å3/Da / Density % sol: 54.17 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7
Details: ammonium acetate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 17102 / Num. obs: 16292 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 11 % / Rsym value: 0.077 / Net I/σ(I): 27

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LCY

1lcy


Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.894 / SU B: 44.554 / SU ML: 0.372 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(I): -2 / ESU R Free: 0.465 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29372 799 4.7 %RANDOM
Rwork0.2421 ---
obs0.24449 16292 99.85 %-
all-17102 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 89.021 Å2
Baniso -1Baniso -2Baniso -3
1-2.07 Å21.03 Å2-0 Å2
2--2.07 Å2-0 Å2
3----3.1 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4373 0 0 0 4373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224446
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1711.9726013
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9545566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.14824.737171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.55915795
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.231520
X-RAY DIFFRACTIONr_chiral_restr0.0860.2730
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213210
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4782.52842
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.35554617
X-RAY DIFFRACTIONr_scbond_it2.6992.51604
X-RAY DIFFRACTIONr_scangle_it4.55851396
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1098 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.50.5
2BMEDIUM POSITIONAL0.450.5
3DMEDIUM POSITIONAL0.420.5
1AMEDIUM THERMAL19.2850
2BMEDIUM THERMAL5.4150
3DMEDIUM THERMAL21.4650
LS refinement shellResolution: 3→3.162 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.362 124 -
Rwork0.286 2287 -
obs--99.46 %
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)
10.75830.738-0.18091.7521-0.19730.67420.0431-0.06180.1068-0.01220.0056-0.0252-0.08260.0777-0.04870.1806-0.0194-0.01690.1777-0.03910.2005-43.8365-13.7294-47.0186
21.08970.7525-0.74171.24230.0692.88490.00150.0232-0.1050.0887-0.10010.12510.3116-0.23340.09860.2346-0.08560.03710.1328-0.03350.1952-64.66614.828-31.1187
30.24120.1893-0.68761.061-0.73453.2997-0.053-0.2338-0.03070.2898-0.1809-0.2052-0.19620.30760.23390.3659-0.0826-0.14160.51060.0520.0693-37.2347-21.4334-6.8155
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A164 - 367
2X-RAY DIFFRACTION2B163 - 367
3X-RAY DIFFRACTION3D164 - 367

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