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- PDB-8sdm: HTRA-1 PDSA bound to CKP 3B3 -

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Basic information

Entry
Database: PDB / ID: 8sdm
TitleHTRA-1 PDSA bound to CKP 3B3
Components
  • Cysteine-containing peptide 3B3
  • Serine protease HTRA1
KeywordsPEPTIDE BINDING PROTEIN / Protease / Complex / Cysteine Knot peptide
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 / Peptidase S1, PA clan
Similarity search - Domain/homology
Serine protease HTRA1
Similarity search - Component
Biological speciesHomo sapiens (human)
Ecballium elaterium (jumping cucumber)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsUltsch, M.H. / Kirchhofer, D. / Wei, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: HTRA-1 PDSA bound to CKP 3B3
Authors: Ultsch, M.H.
History
DepositionApr 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
I: Cysteine-containing peptide 3B3
X: Cysteine-containing peptide 3B3
Y: Cysteine-containing peptide 3B3


Theoretical massNumber of molelcules
Total (without water)90,4936
Polymers90,4936
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9540 Å2
ΔGint-58 kcal/mol
Surface area27360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.694, 84.607, 201.799
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 26060.838 Da / Num. of mol.: 3 / Mutation: S328A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HTRA1, HTRA, PRSS11 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q92743, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein/peptide Cysteine-containing peptide 3B3


Mass: 4103.597 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Ecballium elaterium (jumping cucumber)
Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 46.72 % / Description: Block
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8 / Details: 15% PEG 20000, 0.1M HEPES pH 7.5 / PH range: 7.0-9.0

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.01→77.819 Å / Num. obs: 7422 / % possible obs: 82.4 % / Redundancy: 5.5 % / Biso Wilson estimate: 69.03 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.168 / Rrim(I) all: 0.203 / Net I/σ(I): 3.9
Reflection shellResolution: 3.01→3.156 Å / Redundancy: 4 % / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 358 / CC1/2: 0.682 / Rpim(I) all: 0.596 / Rrim(I) all: 0.956 / % possible all: 45.2

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→50.45 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2947 380 5.12 %
Rwork0.2599 --
obs0.2616 7422 45.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.05→50.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4705 0 0 0 4705
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034788
X-RAY DIFFRACTIONf_angle_d0.7426563
X-RAY DIFFRACTIONf_dihedral_angle_d4.814698
X-RAY DIFFRACTIONf_chiral_restr0.048809
X-RAY DIFFRACTIONf_plane_restr0.004857
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.490.4529360.3979406X-RAY DIFFRACTION8
3.49-4.390.3807880.33611647X-RAY DIFFRACTION32
4.39-50.450.27042560.24174989X-RAY DIFFRACTION93
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)
12.53920.0189-0.22942.72191.93453.63630.22750.1380.40570.1775-0.2392-0.0177-0.3729-0.22410.00140.34120.12180.14290.40940.12510.5253-15.3096-11.6749-23.1078
21.64620.12470.08721.24440.23751.84280.24530.0375-0.3598-0.02980.0624-0.16120.31990.17230.00010.6524-0.2018-0.0130.5055-0.08050.6297-18.3996-44.4137-11.1256
30.8403-1.18970.03481.91150.56930.92550.04190.4983-0.2835-0.7508-0.4795-0.35650.0814-0.3408-0.00230.7968-0.01690.02460.9142-0.18650.5407-16.2239-38.8855-45.7301
40.3225-0.1458-0.20890.07530.15560.50420.60751.5039-0.17760.00540.2724-0.3342-1.1613-0.04530.04610.7318-0.12930.07580.6034-0.04790.75322.0506-15.6131-31.9982
50.0533-0.08650.08150.1422-0.18140.27330.03750.69250.8576-0.1579-0.0126-0.422-0.12430.7925-0.00010.3566-0.2629-0.05441.17030.06510.9652-1.5211-35.6963-6.2691
60.32730.9190.46912.57351.31370.6725-0.20010.3451-1.19441.2973-0.2104-1.28840.9501-0.7375-0.06320.7610.09420.03111.15270.11131.1466-0.1926-47.8401-36.7409
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 164 through 370)
2X-RAY DIFFRACTION2(chain 'B' and resid 164 through 370)
3X-RAY DIFFRACTION3(chain 'C' and resid 164 through 370)
4X-RAY DIFFRACTION4(chain 'I' and resid 4 through 36)
5X-RAY DIFFRACTION5(chain 'X' and resid 4 through 37)
6X-RAY DIFFRACTION6(chain 'Y' and resid 3 through 37)

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