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- PDB-4ri0: Serine Protease HtrA3, mutationally inactivated -

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Basic information

Entry
Database: PDB / ID: 4ri0
TitleSerine Protease HtrA3, mutationally inactivated
ComponentsSerine protease HTRA3
KeywordsHYDROLASE / structural genomics / PSI-BIOLOGY / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / National Science Center - Poland / protease
Function / homology
Function and homology information


negative regulation of BMP signaling pathway / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / negative regulation of transforming growth factor beta receptor signaling pathway / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular region / identical protein binding
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 / Kazal type serine protease inhibitors / Peptidase S1C / Kazal domain superfamily / Trypsin-like peptidase domain ...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 / Kazal type serine protease inhibitors / Peptidase S1C / Kazal domain superfamily / Trypsin-like peptidase domain / Kazal domain / Kazal domain profile. / Thrombin, subunit H - #120 / PDZ domain / Pdz3 Domain / 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 / Roll / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Serine protease HTRA3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.272 Å
AuthorsOsipiuk, J. / Glaza, P. / Wenta, T. / Lipinska, B. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Plos One / Year: 2015
Title: Structural and Functional Analysis of Human HtrA3 Protease and Its Subdomains.
Authors: Glaza, P. / Osipiuk, J. / Wenta, T. / Zurawa-Janicka, D. / Jarzab, M. / Lesner, A. / Banecki, B. / Skorko-Glonek, J. / Joachimiak, A. / Lipinska, B.
History
DepositionOct 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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 HTRA3
B: Serine protease HTRA3
C: Serine protease HTRA3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,1275
Polymers108,9373
Non-polymers1902
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-32 kcal/mol
Surface area31710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.981, 118.981, 167.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resid 135 through 344 )
21chain B and (resid 135 through 344 )
31chain C and (resid 135 through 344 )

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resid 135 through 344 )A0
211chain B and (resid 135 through 344 )B0
311chain C and (resid 135 through 344 )C0
Detailsbiological unit is the same as asymmetric unit

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Components

#1: Protein Serine protease HTRA3 / High-temperature requirement factor A3 / Pregnancy-related serine protease


Mass: 36312.293 Da / Num. of mol.: 3 / Fragment: Residues 130-453 / Mutation: S305A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HTRA3, PRSP / Plasmid: pET-coco2 modified / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)del_clpP
References: UniProt: P83110, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.73 Å3/Da / Density % sol: 54.89 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 1 M potassium/sodium phosphate buffer, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2013
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.27→40.76 Å / Num. all: 18953 / Num. obs: 18953 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Biso Wilson estimate: 109.44 Å2 / Rmerge(I) obs: 0.085 / Χ2: 1.195 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
3.27-3.339.70.8552.729271.06899.8
3.33-3.399.60.7799401.10199.7
3.39-3.459.70.689431.07999.6
3.45-3.529.70.5169291.1299.4
3.52-3.69.70.4569571.09999.7
3.6-3.689.70.4069221.10699.2
3.68-3.779.80.3149121.08799.2
3.77-3.889.70.2489631.12699.3
3.88-3.999.60.2019311.10499.3
3.99-4.129.70.1489491.13798.9
4.12-4.279.80.1119291.15998.5
4.27-4.449.60.0919421.23398.9
4.44-4.649.70.0799461.27598.5
4.64-4.889.60.0769441.29398.4
4.88-5.199.50.0739531.40898.5
5.19-5.599.60.0819511.45797.9
5.59-6.159.50.089571.44197.8
6.15-7.049.20.0599671.27897.3
7.04-8.8690.0359811.20497
8.86-508.70.02810101.11592.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.15data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NZI

3nzi


Resolution: 3.272→40.758 Å / SU ML: 0.35 / σ(F): 1.35 / σ(I): 0 / Phase error: 24.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2327 935 4.95 %RANDOM
Rwork0.1993 ---
obs0.201 18907 98.36 %-
all-18907 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 235.04 Å2 / Biso mean: 112.6819 Å2 / Biso min: 61.62 Å2
Refinement stepCycle: LAST / Resolution: 3.272→40.758 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5367 0 10 3 5380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035473
X-RAY DIFFRACTIONf_angle_d0.8297426
X-RAY DIFFRACTIONf_chiral_restr0.031878
X-RAY DIFFRACTIONf_plane_restr0.004958
X-RAY DIFFRACTIONf_dihedral_angle_d13.4172008
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2648X-RAY DIFFRACTION13.827TORSIONAL
12B2648X-RAY DIFFRACTION13.827TORSIONAL
13C2648X-RAY DIFFRACTION13.827TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.272-3.44440.3171320.26592505263799
3.4444-3.66010.30861180.25292571268999
3.6601-3.94250.29111350.23882532266799
3.9425-4.33880.23791190.19212565268499
4.3388-4.96570.21490.16642553270299
4.9657-6.25270.2291460.19562587273398
6.2527-40.76130.20921360.18932659279596
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)
13.3519-1.3129-0.59771.79431.77691.4656-0.4382-0.36380.40370.5050.3618-0.1045-0.241-0.1060.10221.08610.0295-0.04370.99160.1740.77339.327955.822424.1509
24.84830.3709-1.35925.70480.02392.6352-0.363-0.88270.00240.51180.4372-0.1906-0.0049-0.17290.05690.89870.0805-0.1071.08620.17750.771449.399645.865724.549
38.0924-1.0172.33416.34771.04146.32420.0377-0.147-0.1887-0.08230.2170.028-0.1880.0977-0.14080.69230.04330.08940.80490.16250.736433.669649.420415.4328
42.7007-2.547-1.60632.13931.7220.9529-0.6903-0.5949-1.07070.47030.62620.53980.01740.06140.20850.9066-0.07930.01071.14060.42241.099247.829132.335120.4359
55.8743-1.58852.1328.4391-0.66217.92760.2649-0.25121.3007-0.66090.12140.45-0.133-0.3190.14540.8575-0.0791-0.02751.04850.24371.263770.949344.46858.6526
66.3037-1.8843-1.12378.0251-2.64674.9589-0.0168-0.20560.0393-0.01180.06170.36610.0277-0.0021-0.20380.7613-0.0752-0.20821.08070.22740.970774.312534.637511.2914
72.1282.6021-0.06044.3061-2.5294.77630.53110.23330.4934-0.941-0.7710.34920.4671-1.5639-0.32021.10350.10540.00011.1160.09341.095518.247945.514127.6468
82.72860.3865-1.19821.72870.55574.6516-0.7039-0.1991-1.02630.3260.26480.76541.07360.3501-0.41240.8699-0.0144-0.10160.82150.11011.040516.11642.87960.5233
92.4819-1.4384-3.6784.3532.39665.28470.33210.618-0.2605-0.49260.0025-0.03780.5037-0.6984-0.09511.11080.0542-0.37230.93860.0931.099217.815242.3628-14.0931
101.50370.0217-2.05781.1068-0.34995.7133-0.490.04940.40140.5053-0.16290.9628-0.277-1.0320.52911.0252-0.0482-0.27671.3321-0.09381.45612.816738.9163-10.8913
113.52833.1638-0.28664.68810.85386.4842-0.4132-0.23240.0178-0.6551-0.06371.03160.2848-0.74050.32280.8914-0.0674-0.15461.1572-0.111.20166.900145.6476-5.9016
121.88942.56391.21515.14991.63435.7186-0.6178-0.4296-0.64150.9321-0.23371.630.5427-0.82350.23020.86580.0961-0.00731.15280.04771.069216.265752.56545.0602
133.13632.297-1.83914.00190.83294.971-0.4754-0.37690.16390.2950.19030.0335-0.5260.36710.05751.09120.18370.01331.08710.18440.812617.627561.31732.7793
146.81382.5971.43914.97431.73263.88040.9948-0.48150.0726-0.1738-0.45960.4209-0.3872-0.3752-0.07240.88340.1041-0.03940.9350.10040.842317.681952.9792.8804
154.29382.1073-1.03993.2946-0.21934.2730.27560.2590.2974-0.0521-0.47160.4932-1.1213-0.88010.47730.96590.2179-0.21211.10160.06351.048412.301458.3149-5.2308
160.96531.3019-0.03143.65230.5863.2642-0.0655-0.13960.50260.17920.3831.6669-0.4623-0.8137-0.23081.03420.3326-0.08191.01690.0911.279315.479870.933212.5546
173.9708-0.70780.01473.3484-2.91372.6078-0.14550.36560.26320.33340.25850.2931-0.3661-0.0270.09171.14350.0538-0.19260.7535-0.06680.851624.680588.86-0.8396
183.4120.4031-3.76982.0204-1.34734.91540.43770.14330.46810.7698-0.05690.4469-1.188-0.0738-0.2681.57250.1331-0.08071.0349-0.14651.173525.894289.03176.5736
194.2021-0.60581.27694.30081.99841.4234-0.4344-0.40820.73551.06580.33590.0247-0.6429-0.55860.2911.25040.0826-0.03371.00750.01260.940123.682279.194715.6434
204.74291.6733-0.88295.22342.87683.0816-0.3358-0.19390.19920.79960.0484-0.20280.3793-0.02990.15790.9267-0.0257-0.05380.9320.18530.741629.193569.838615.2262
214.22552.9882-1.67532.1226-0.7823.7538-0.72180.91592.10260.09710.70380.5269-1.54761.14610.46821.4252-0.0505-0.17631.04620.11610.804631.552274.359313.7077
221.71581.6381-0.49482.526-1.28550.83760.3531-1.21790.20481.2848-1.3732-1.099-1.65270.0816-0.15552.0657-0.1888-0.3751.2770.21531.169434.609480.073219.9186
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 135 through 179 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 180 through 246 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 247 through 328 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 329 through 356 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 357 through 400 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 401 through 459 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 130 through 141 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 142 through 162 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 163 through 201 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 202 through 223 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 224 through 246 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 247 through 267 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 268 through 296 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 297 through 315 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 316 through 344 )B0
16X-RAY DIFFRACTION16chain 'C' and (resid 134 through 161 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 162 through 181 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 182 through 223 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 224 through 267 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 268 through 315 )C0
21X-RAY DIFFRACTION21chain 'C' and (resid 316 through 323 )C0
22X-RAY DIFFRACTION22chain 'C' and (resid 327 through 344 )C0

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