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- PDB-5zj3: Textilinin-1, A Kunitz-Type Serine Protease Inhibitor From pichia... -

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Basic information

Entry
Database: PDB / ID: 5zj3
TitleTextilinin-1, A Kunitz-Type Serine Protease Inhibitor From pichia expression system
ComponentsKunitz-type serine protease inhibitor textilinin-1
KeywordsHYDROLASE INHIBITOR / Textilinin-1 / A Kunitz-Type Serine Protease Inhibitor From
Function / homology
Function and homology information


venom-mediated blood coagulation / serine-type endopeptidase inhibitor activity / toxin activity / extracellular space
Similarity search - Function
: / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily ...: / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Kunitz-type serine protease inhibitor textilinin-1
Similarity search - Component
Biological speciesPseudonaja textilis textilis (cobra)
MethodX-RAY DIFFRACTION / Resolution: 1.88 Å
AuthorsOu, X.J. / li, N.
CitationJournal: To Be Published
Title: Textilinin-1, A Kunitz-Type Serine Protease Inhibitor expressed from picha system by LIAONING GRAND NUOKANG BIOPHARMACEUTICAL CO.,LTD
Authors: Ou, X.J. / Li, N.
History
DepositionMar 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kunitz-type serine protease inhibitor textilinin-1
B: Kunitz-type serine protease inhibitor textilinin-1
C: Kunitz-type serine protease inhibitor textilinin-1


Theoretical massNumber of molelcules
Total (without water)20,0953
Polymers20,0953
Non-polymers00
Water4,486249
1
A: Kunitz-type serine protease inhibitor textilinin-1


Theoretical massNumber of molelcules
Total (without water)6,6981
Polymers6,6981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kunitz-type serine protease inhibitor textilinin-1


Theoretical massNumber of molelcules
Total (without water)6,6981
Polymers6,6981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Kunitz-type serine protease inhibitor textilinin-1


Theoretical massNumber of molelcules
Total (without water)6,6981
Polymers6,6981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.752, 98.752, 80.206
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11B-104-

HOH

21C-175-

HOH

31C-185-

HOH

41C-206-

HOH

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Components

#1: Protein Kunitz-type serine protease inhibitor textilinin-1 / Txln-1


Mass: 6698.442 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudonaja textilis textilis (cobra) / Production host: Pichia (fungus) / References: UniProt: Q90WA1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O
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: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 0.1M Na HEPES, 2%(v/v) PEG 400, Mammonium sulfate, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RAYONIX SX-165mm / Detector: CCD / Date: Mar 1, 2017
RadiationMonochromator: double mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 16431 / % possible obs: 100 % / Redundancy: 14 % / Net I/σ(I): 6.4
Reflection shellResolution: 1.88→1.91 Å / Num. unique obs: 808 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.7_650refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.88→38.686 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.57
RfactorNum. reflection% reflection
Rfree0.2231 830 5.05 %
Rwork0.1879 --
obs0.1897 16424 99.85 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Bsol: 40.24 Å2 / ksol: 0.397 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.9329 Å2-0 Å20 Å2
2---0.9329 Å20 Å2
3---1.8659 Å2
Refinement stepCycle: LAST / Resolution: 1.88→38.686 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1352 0 0 249 1601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071397
X-RAY DIFFRACTIONf_angle_d1.1041876
X-RAY DIFFRACTIONf_dihedral_angle_d15.962524
X-RAY DIFFRACTIONf_chiral_restr0.081182
X-RAY DIFFRACTIONf_plane_restr0.006261
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8802-1.9980.29711460.22332506X-RAY DIFFRACTION99
1.998-2.15220.22761340.16332567X-RAY DIFFRACTION100
2.1522-2.36880.25621530.17062566X-RAY DIFFRACTION100
2.3688-2.71150.17861300.18732574X-RAY DIFFRACTION100
2.7115-3.41580.23231370.19242623X-RAY DIFFRACTION100
3.4158-38.69450.20281300.19172758X-RAY DIFFRACTION100

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