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- PDB-1r8n: The Crystal Structure of the Kunitz (STI) Type Inhibitor from See... -

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Basic information

Entry
Database: PDB / ID: 1r8n
TitleThe Crystal Structure of the Kunitz (STI) Type Inhibitor from Seeds of Delonix regia
ComponentsKunitz trypsin inhibitor
KeywordsHYDROLASE INHIBITOR / Kunitz-type trypsin/kallikrein inhibitor / beta-trefoil fold / flamboyant / Delonix regia
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / extracellular region
Similarity search - Function
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 serine protease inhibitor DrTI
Similarity search - Component
Biological speciesDelonix regia (royal poinciana)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsKrauchenco, S. / Pando, S.C. / Marangoni, S. / Polikarpov, I.
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 2003
Title: Crystal structure of the Kunitz (STI)-type inhibitor from Delonix regia seeds.
Authors: Krauchenco, S. / Pando, S.C. / Marangoni, S. / Polikarpov, I.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Purification, crystallization and preliminary crystallographic study of a Kunitz-type trypsin inhibitor from Delonix regia seeds
Authors: Polikarpov, I. / Golubev, A.M. / Perles, L.A. / Pando, S.C. / Novello, J.C. / Marangoni, S.
#2: Journal: Phytochemistry / Year: 2001
Title: Primary sequence determination of a Kunitz inhibitor isolated from Delonix regia seeds
Authors: Pando, S.C. / Oliva, M.L.V. / Sampaio, C.A.M. / Di Ciero, L. / Novello, J.C. / Marangoni, S.
History
DepositionOct 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kunitz trypsin inhibitor


Theoretical massNumber of molelcules
Total (without water)20,1981
Polymers20,1981
Non-polymers00
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.125, 67.249, 72.061
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 Kunitz trypsin inhibitor / STI


Mass: 20197.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Delonix regia (royal poinciana) / References: UniProt: P83667
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 1.93 Å3/Da / Density % sol: 36.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 22% PEG8000, 0.25M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.38 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 19, 2001 / Details: mirrors
RadiationMonochromator: triangular bent crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionResolution: 1.75→19.52 Å / Num. all: 30413 / Num. obs: 23454 / % possible obs: 77.1 % / Observed criterion σ(F): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 9
Reflection shellResolution: 1.75→1.89 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 2.4 / Num. unique all: 813 / % possible all: 35

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AVU

1avu


Resolution: 1.75→19.52 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: CNS bulk solvent model used
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1075 3.5 %RANDOM
Rwork0.215 ---
obs0.215 23454 77.1 %-
all-30413 --
Displacement parametersBiso mean: 35.7 Å2
Baniso -1Baniso -2Baniso -3
1--7.65 Å210.12 Å2-2.47 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 1.75→19.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1417 0 0 183 1600
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_bond_d0.005
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
1.75-1.830.629140.3510.16894524.9
1.83-1.930.336870.3210.036190049.4
1.93-2.050.276950.2590.028282674.7
2.05-2.20.2941630.2520.023334588.1
2.2-2.430.2691630.2260.021353692.8
2.43-19.520.2115530.1990.0151090294.4
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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