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- PDB-3tc2: Crystal structure of potato serine protease inhibitor. -

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Basic information

Entry
Database: PDB / ID: 3tc2
TitleCrystal structure of potato serine protease inhibitor.
ComponentsKunitz-type proteinase inhibitor P1H5
KeywordsHydrolase Inhibitor / beta-trefoil fold / Protease inhibitor
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity
Similarity search - Function
Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature. / Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Kunitz inhibitor STI-like superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
Kunitz-type inhibitor B
Similarity search - Component
Biological speciesSolanum tuberosum (potato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMeulenbroek, E.M. / Thomassen, E.A.J. / Pannu, N.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structure of a post-translationally processed heterodimeric double-headed Kunitz-type serine protease inhibitor from potato.
Authors: Meulenbroek, E.M. / Thomassen, E.A. / Pouvreau, L. / Abrahams, J.P. / Gruppen, H. / Pannu, N.S.
History
DepositionAug 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kunitz-type proteinase inhibitor P1H5
B: Kunitz-type proteinase inhibitor P1H5
C: Kunitz-type proteinase inhibitor P1H5


Theoretical massNumber of molelcules
Total (without water)60,9723
Polymers60,9723
Non-polymers00
Water9,026501
1
A: Kunitz-type proteinase inhibitor P1H5


Theoretical massNumber of molelcules
Total (without water)20,3241
Polymers20,3241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Kunitz-type proteinase inhibitor P1H5


Theoretical massNumber of molelcules
Total (without water)20,3241
Polymers20,3241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Kunitz-type proteinase inhibitor P1H5


Theoretical massNumber of molelcules
Total (without water)20,3241
Polymers20,3241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.822, 93.920, 55.442
Angle α, β, γ (deg.)90.00, 100.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Kunitz-type proteinase inhibitor P1H5


Mass: 20323.883 Da / Num. of mol.: 3 / Fragment: UNP residues 21-221 / Source method: isolated from a natural source / Source: (natural) Solanum tuberosum (potato) / Strain: cv Elkana / References: UniProt: Q8S380
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 501 / 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: 2.22 Å3/Da / Density % sol: 44.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 10% PEG 8000, 8% ethylene glycol, 9 mM 1-s-octyl-beta-D-thioglucoside, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.94644 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Sep 13, 2002
RadiationMonochromator: Si(311) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94644 Å / Relative weight: 1
ReflectionResolution: 1.6→54.23 Å / Num. all: 50787 / Num. obs: 50787 / % possible obs: 70 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 14
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.37 / % possible all: 18.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
REFMAC5.6.0116refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→54.23 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.799 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22108 2533 5 %RANDOM
Rwork0.16796 ---
obs0.17061 48229 69.89 %-
all-48229 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.91 Å2
Baniso -1Baniso -2Baniso -3
1--1.34 Å2-0 Å20.34 Å2
2---0.23 Å2-0 Å2
3---1.69 Å2
Refinement stepCycle: LAST / Resolution: 1.6→54.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4113 0 0 501 4614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0224246
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3161.9555764
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4055540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.64524.333180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92115687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.8931518
X-RAY DIFFRACTIONr_chiral_restr0.1990.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213218
X-RAY DIFFRACTIONr_gen_planes_other
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
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 45 -
Rwork0.328 788 -
obs--15.6 %
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)
11.05930.18180.11240.85120.04251.1126-0.06890.0077-0.02430.0294-0.0048-0.00310.01720.03250.07370.16540.01770.03260.06740.00750.01152.90368.632-27.372
22.0160.32780.36981.1905-0.04891.91170.2194-0.32540.06260.1968-0.05670.12540.1196-0.1788-0.16270.2258-0.03950.0390.155-0.00510.03186.23241.8282.145
31.43110.181-0.13191.01460.18221.2861-0.0255-0.0102-0.0374-0.03630.0183-0.0223-0.0348-0.00950.00720.15690.0010.01360.06170.00080.0024-21.2346.537-18.693
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 187
2X-RAY DIFFRACTION2B4 - 187
3X-RAY DIFFRACTION3C5 - 187

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