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- PDB-3num: Substrate induced remodeling of the active site regulates HtrA1 a... -

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Basic information

Entry
Database: PDB / ID: 3num
TitleSubstrate induced remodeling of the active site regulates HtrA1 activity
ComponentsSerine protease HTRA1
KeywordsHYDROLASE / serine protease / DegP / HtrA / 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 / 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: 2.75 Å
AuthorsTruebestein, L. / Tennstaedt, A. / Hauske, P. / Krojer, T. / Kaiser, M. / Clausen, T. / Ehrmann, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Substrate-induced remodeling of the active site regulates human HTRA1 activity.
Authors: Truebestein, L. / Tennstaedt, A. / Monig, T. / Krojer, T. / Canellas, F. / Kaiser, M. / Clausen, T. / Ehrmann, M.
History
DepositionJul 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine protease HTRA1


Theoretical massNumber of molelcules
Total (without water)36,4261
Polymers36,4261
Non-polymers00
Water0
1
A: Serine protease HTRA1

A: Serine protease HTRA1

A: Serine protease HTRA1


Theoretical massNumber of molelcules
Total (without water)109,2773
Polymers109,2773
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
Buried area5760 Å2
ΔGint-32 kcal/mol
Surface area25900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.476, 109.476, 113.956
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Serine protease HTRA1 / L56 / Serine protease 11


Mass: 36425.629 Da / Num. of mol.: 1 / Fragment: protease and pdz domain (unp residue 158-480) / Mutation: S328A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HTRA1, HTRA, PRSS11 / Plasmid: pET21d / Production host: Escherichia coli (E. coli)
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

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Sample preparation

CrystalDensity Matthews: 3.61 Å3/Da / Density % sol: 65.89 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 1.0M LiSO4, 0.1M sodium citrate pH5.6, 0.5M (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. all: 12716 / Num. obs: 12716 / % possible obs: 95.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.395 / Net I/σ(I): 20.6
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 1.6 / % possible all: 85.5

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.6.0066refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LCY

1lcy


Resolution: 2.75→19.32 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.905 / SU B: 22.494 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.321 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28747 628 4.9 %RANDOM
Rwork0.24243 ---
obs0.24446 12062 95.74 %-
all-12716 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 93.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.03 Å20 Å2
2--0.06 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.75→19.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1407 0 0 0 1407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221428
X-RAY DIFFRACTIONr_bond_other_d0.0010.02915
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.9691942
X-RAY DIFFRACTIONr_angle_other_deg0.89832267
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9845187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.97225.47253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.99915233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.658154
X-RAY DIFFRACTIONr_chiral_restr0.0830.2241
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211580
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02256
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_it0.571.5940
X-RAY DIFFRACTIONr_mcbond_other0.1031.5386
X-RAY DIFFRACTIONr_mcangle_it1.05921517
X-RAY DIFFRACTIONr_scbond_it1.4363488
X-RAY DIFFRACTIONr_scangle_it2.4574.5425
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.746→2.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 37 -
Rwork0.262 787 -
obs--84.77 %
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)
13.1182-2.37060.26210.26472.0513.0828-0.6521-0.8878-0.17261.54230.2498-0.03520.27790.64470.40230.3990.1273-0.06350.54470.11230.293810.7415-3.247512.6201
23.4325-0.5279-3.15451.24840.57696.7098-0.13670.2347-0.57860.107-0.0112-0.31720.93281.08060.14790.52780.3750.10860.4623-0.07410.524219.9009-22.6656-6.8014
312.9651-6.3916-3.02583.12592.50543.3866-0.773-0.7071-1.33890.71150.02430.73161.0282-0.38910.74880.6361-0.1050.09730.36650.15180.4453-0.7718-16.06818.6306
43.3272-1.5449-0.32575.1637-1.36837.1152-0.02150.194-0.3303-0.378-0.1609-0.23890.4741-0.01790.18240.23660.04760.06320.06480.00690.23883.106-11.9147-1.4972
54.932-1.0361.259610.62677.882414.6621-0.4508-1.0163-1.81360.42011.0351.08131.81830.2698-0.58420.80350.05910.10020.35110.23820.95074.1926-29.82851.1717
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A161 - 185
2X-RAY DIFFRACTION2A186 - 263
3X-RAY DIFFRACTION3A264 - 278
4X-RAY DIFFRACTION4A279 - 355
5X-RAY DIFFRACTION5A356 - 369

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