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- PDB-3rdz: Crystal Structure of rBTI-trypsin complex at 2.26 angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 3rdz
TitleCrystal Structure of rBTI-trypsin complex at 2.26 angstrom resolution
Components
  • BWI-1=PROTEASE inhibitor/trypsin inhibitor
  • Cationic trypsin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / serine protease inhibitor / potato inhibitor I / trypsin inhibitor / trypsin / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / response to wounding / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Trypsin Inhibitor V, subunit A / Proteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / Trypsin Inhibitor V; Chain A / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. ...Trypsin Inhibitor V, subunit A / Proteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / Trypsin Inhibitor V; Chain A / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Serine protease 1 / Proteinase inhibitor
Similarity search - Component
Biological speciesFagopyrum esculentum (common buckwheat)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.262 Å
AuthorsWang, L.F. / Li, M. / Chang, W.R.
CitationJournal: Plos One / Year: 2011
Title: Conformational Changes of rBTI from Buckwheat upon Binding to Trypsin: Implications for the Role of the P(8)' Residue in the Potato Inhibitor I Family
Authors: Wang, L.F. / Zhao, F. / Li, M. / Zhang, H. / Gao, Y. / Cao, P. / Pan, X. / Wang, Z. / Chang, W.R.
History
DepositionApr 2, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Cationic trypsin
C: BWI-1=PROTEASE inhibitor/trypsin inhibitor
B: Cationic trypsin
D: BWI-1=PROTEASE inhibitor/trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7676
Polymers64,6874
Non-polymers802
Water5,405300
1
A: Cationic trypsin
C: BWI-1=PROTEASE inhibitor/trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3843
Polymers32,3442
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-7 kcal/mol
Surface area12120 Å2
MethodPISA
2
B: Cationic trypsin
D: BWI-1=PROTEASE inhibitor/trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3843
Polymers32,3442
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-7 kcal/mol
Surface area12120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.709, 50.236, 84.492
Angle α, β, γ (deg.)90.00, 95.06, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 1:96 or resseq 100:223 )A1 - 96
121chain A and (resseq 1:96 or resseq 100:223 )A100 - 223
211chain B and (resseq 1:96 or resseq 100:223 )B1 - 96
221chain B and (resseq 1:96 or resseq 100:223 )B100 - 223
112chain C and (resseq 13:79 )C13 - 79
212chain D and (resseq 13:79 )D13 - 79

NCS ensembles :
ID
1
2

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Components

#1: Protein Cationic trypsin / Beta-trypsin / Alpha-trypsin chain 1 / Alpha-trypsin chain 2


Mass: 23324.287 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Purchased from AppliChem / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin
#2: Protein BWI-1=PROTEASE inhibitor/trypsin inhibitor / Proteinase inhibitor


Mass: 9019.240 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fagopyrum esculentum (common buckwheat)
Gene: BWI-1, Edn1 / Plasmid: QIA express pQE-31 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q9S9F3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.18 Å3/Da / Density % sol: 43.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15% (w/v) PEG 3350, 200mM magnesium chloride, 100mM Tris-HCl (pH 9.0), VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 20, 2009
RadiationMonochromator: X-Ray Generator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.26→20 Å / Num. all: 26331 / Num. obs: 26279 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 34.9 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 181.7
Reflection shellResolution: 2.26→2.34 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 31 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
MrBUMPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2CMY, 1VBW

2cmy

1vbw


Resolution: 2.262→20 Å / FOM work R set: 0.8267 / SU ML: 0.31 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 24.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2265 1328 5.05 %random
Rwork0.1817 ---
all0.184 26331 --
obs0.1834 26279 51.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.032 Å2 / ksol: 0.399 e/Å3
Displacement parametersBiso mean: 30.9 Å2
Baniso -1Baniso -2Baniso -3
1--3.2197 Å20 Å25.1647 Å2
2---7.319 Å20 Å2
3---10.5386 Å2
Refinement stepCycle: LAST / Resolution: 2.262→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4245 0 2 300 4547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074335
X-RAY DIFFRACTIONf_angle_d1.0775860
X-RAY DIFFRACTIONf_dihedral_angle_d16.3641530
X-RAY DIFFRACTIONf_chiral_restr0.074662
X-RAY DIFFRACTIONf_plane_restr0.005757
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1597X-RAY DIFFRACTIONPOSITIONAL0.048
12B1597X-RAY DIFFRACTIONPOSITIONAL0.048
21C524X-RAY DIFFRACTIONPOSITIONAL0.069
22D524X-RAY DIFFRACTIONPOSITIONAL0.069
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.262-2.35240.29291170.22332720X-RAY DIFFRACTION50
2.3524-2.45930.27231650.20882754X-RAY DIFFRACTION51
2.4593-2.58870.29071540.19532722X-RAY DIFFRACTION51
2.5887-2.75050.27851380.20292790X-RAY DIFFRACTION51
2.7505-2.96220.26561510.20092748X-RAY DIFFRACTION51
2.9622-3.25910.26281420.18342781X-RAY DIFFRACTION52
3.2591-3.72790.19921570.17412771X-RAY DIFFRACTION52
3.7279-4.68640.19161400.14532823X-RAY DIFFRACTION52
4.6864-19.73020.15721640.15482842X-RAY DIFFRACTION53

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