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- PDB-1c9t: COMPLEX OF BDELLASTASIN WITH BOVINE TRYPSIN -

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Basic information

Entry
Database: PDB / ID: 1c9t
TitleCOMPLEX OF BDELLASTASIN WITH BOVINE TRYPSIN
Components
  • BDELLASTASIN
  • TRYPSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / COMPLEX (HYDROLASE-INHIBITOR) / HYDROLASE / INHIBITOR / ANTISTASIN / PLASMIN / 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 / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Antistasin; domain 1 / Antistasin; domain 1 / Antistasin-like domain / Antistasin family / Antistasin-like domain profile. / Hirudin/antistatin / Ribbon / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family ...Antistasin; domain 1 / Antistasin; domain 1 / Antistasin-like domain / Antistasin family / Antistasin-like domain profile. / Hirudin/antistatin / Ribbon / 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 / Mainly Beta
Similarity search - Domain/homology
: / Serine protease 1 / Bdellastasin
Similarity search - Component
Biological speciesHirudo medicinalis (medicinal leech)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 3.3 Å
AuthorsRester, U. / Bode, W. / Moser, M. / Parry, M.A. / Huber, R. / Auerswald, E.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Structure of the complex of the antistasin-type inhibitor bdellastasin with trypsin and modelling of the bdellastasin-microplasmin system.
Authors: Rester, U. / Bode, W. / Moser, M. / Parry, M.A. / Huber, R. / Auerswald, E.
#1: Journal: Eur.J.Biochem. / Year: 1998
Title: Bdellastasin, a serine protease inhibitor of the antistasin family from the medical leech (Hirudo medicinalis)-primary structure, expression in yeast, and characterisation of native and recombinant inhibitor
Authors: Moser, M. / Auerswald, E. / Mentele, R. / Eckerskorn, C. / Fritz, E. / Fink, H.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: L-Isoaspartate 115 of porcine beta-trypsin promotes crystallization of its complex with bdellastasin
Authors: Rester, U. / Moser, M. / Huber, R. / Bode, W.
History
DepositionAug 3, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRYPSIN
B: TRYPSIN
C: TRYPSIN
D: TRYPSIN
E: TRYPSIN
F: TRYPSIN
G: BDELLASTASIN
H: BDELLASTASIN
I: BDELLASTASIN
J: BDELLASTASIN
K: BDELLASTASIN
L: BDELLASTASIN


Theoretical massNumber of molelcules
Total (without water)178,05312
Polymers178,05312
Non-polymers00
Water2,630146
1
A: TRYPSIN
G: BDELLASTASIN


Theoretical massNumber of molelcules
Total (without water)29,6752
Polymers29,6752
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-8 kcal/mol
Surface area11890 Å2
MethodPISA
2
B: TRYPSIN
H: BDELLASTASIN


Theoretical massNumber of molelcules
Total (without water)29,6752
Polymers29,6752
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-9 kcal/mol
Surface area11790 Å2
MethodPISA
3
C: TRYPSIN
I: BDELLASTASIN


Theoretical massNumber of molelcules
Total (without water)29,6752
Polymers29,6752
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-9 kcal/mol
Surface area11780 Å2
MethodPISA
4
D: TRYPSIN
J: BDELLASTASIN


Theoretical massNumber of molelcules
Total (without water)29,6752
Polymers29,6752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-8 kcal/mol
Surface area11760 Å2
MethodPISA
5
E: TRYPSIN
K: BDELLASTASIN


Theoretical massNumber of molelcules
Total (without water)29,6752
Polymers29,6752
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-9 kcal/mol
Surface area11910 Å2
MethodPISA
6
F: TRYPSIN
L: BDELLASTASIN


Theoretical massNumber of molelcules
Total (without water)29,6752
Polymers29,6752
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-9 kcal/mol
Surface area11810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.22, 108.78, 95.71
Angle α, β, γ (deg.)90, 93.7, 90
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein
TRYPSIN / / E.C.3.4.21.4


Mass: 23324.287 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Secretion: SALIVA / References: UniProt: P00760, trypsin
#2: Protein
BDELLASTASIN


Mass: 6351.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hirudo medicinalis (medicinal leech) / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: TrEMBL: P82107, UniProt: P82107*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.7855.71
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, sitting drop5.650MM MES, 2.0M AMMONIUM SULFATE, 10MM MAGNESIM CHLORIDE, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
2932vapor diffusion, sitting drop5.650MM MES, 2.2M AMMONIUM SULFATE, 10MM MAGNESIM CHLORIDE, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
2150 mMsodium chloride1drop
32.2 Mammonium sulfate1reservoir
410 mMmagnesium chloride1reservoir
550 mMMES1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12771
22771
Diffraction source
SourceTypeIDWavelength
ROTATING ANODERIGAKU RU20011.5418
ROTATING ANODERIGAKU RU20021.5418
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEApr 17, 1997
MARRESEARCH2IMAGE PLATEOct 19, 1997
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21
ReflectionResolution: 3.3→47 Å / Num. all: 52903 / Num. obs: 52903 / % possible obs: 81.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 55.5 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 4.3
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.29 / % possible all: 77
Reflection
*PLUS
Num. obs: 23797
Reflection shell
*PLUS
% possible obs: 77 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
Agrovatadata reduction
AMoREphasing
X-PLOR3.851refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementResolution: 3.3→8 Å / Cross valid method: THROUGHOUT / σ(I): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.287 2351 10.7 %RANDOM
Rwork0.208 ---
obs0.208 21951 --
Refinement stepCycle: LAST / Resolution: 3.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12078 0 0 146 12224
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d0.01
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.561
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.36
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.321

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