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

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Basic information

Entry
Database: PDB / ID: 3nwu
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 / molecular function activator activity / negative regulation of transforming growth factor beta receptor signaling pathway / placenta development ...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 / molecular function activator activity / negative regulation of transforming growth factor beta receptor signaling pathway / placenta development / 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: 3.2 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 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: Serine protease HTRA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9176
Polymers74,6293
Non-polymers2883
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6450 Å2
ΔGint-75 kcal/mol
Surface area23270 Å2
MethodPISA
2
A: Serine protease HTRA1
B: Serine protease HTRA1
C: Serine protease HTRA1
hetero molecules

A: Serine protease HTRA1
B: Serine protease HTRA1
C: Serine protease HTRA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,83512
Polymers149,2586
Non-polymers5766
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area20060 Å2
ΔGint-219 kcal/mol
Surface area39370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.671, 153.671, 89.835
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B
32C
/ NCS ensembles :
ID
1
2

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Components

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


Mass: 24876.395 Da / Num. of mol.: 3 / Fragment: HtrA1 protease domain (unp residues 158-375)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HTRA, HTRA1, PRSS11 / Production host: Escherichia coli (E. coli)
References: UniProt: Q92743, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4

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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: 3.55 Å3/Da / Density % sol: 65.38 %
Crystal growTemperature: 292 K / pH: 4.6
Details: 2.0M Ammonium sulfate, 0.1M Sodium acetate, pH 4.6, 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: 3.2→19.9 Å / Num. obs: 17660 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 58.3 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 15.2
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 2.9 / % possible all: 97.8

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.6.0066refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→19.9 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.935 / SU B: 13.467 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.209 900 5.1 %RANDOM
Rwork0.172 ---
obs0.174 16741 96.3 %-
all-17641 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.2 Å2
Baniso -1Baniso -2Baniso -3
1--3.22 Å20 Å20 Å2
2---3.22 Å20 Å2
3---6.43 Å2
Refinement stepCycle: LAST / Resolution: 3.2→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4133 0 15 0 4148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224209
X-RAY DIFFRACTIONr_bond_other_d0.0020.022712
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.9785726
X-RAY DIFFRACTIONr_angle_other_deg0.99536724
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1055548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.46525.43151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.6615699
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1391512
X-RAY DIFFRACTIONr_chiral_restr0.0880.2714
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214620
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02748
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A753tight positional0.030.05
12B753tight positional0.030.05
13C753tight positional0.040.05
21A151tight positional0.030.05
22B151tight positional0.030.05
23C151tight positional0.030.05
11A812medium positional0.030.5
12B812medium positional0.030.5
13C812medium positional0.030.5
21A153medium positional0.040.5
22B153medium positional0.030.5
23C153medium positional0.040.5
11A753tight thermal8.980.5
12B753tight thermal7.550.5
13C753tight thermal11.550.5
21A151tight thermal5.840.5
22B151tight thermal5.170.5
23C151tight thermal5.720.5
11A812medium thermal9.612
12B812medium thermal7.842
13C812medium thermal11.872
21A153medium thermal5.412
22B153medium thermal4.562
23C153medium thermal6.062
LS refinement shellResolution: 3.2→3.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 43 -
Rwork0.28 1197 -
obs--94.58 %

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