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- PDB-1tbr: CRYSTAL STRUCTURE OF INSECT DERIVED DOUBLE DOMAIN KAZAL INHIBITOR... -

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Basic information

Entry
Database: PDB / ID: 1tbr
TitleCRYSTAL STRUCTURE OF INSECT DERIVED DOUBLE DOMAIN KAZAL INHIBITOR RHODNIIN IN COMPLEX WITH THROMBIN
Components
  • (THROMBIN) x 2
  • RHODNIIN
KeywordsCOMPLEX (SERINE PROTEASE/INHIBITOR) / COMPLEX (SERINE PROTEASE-INHIBITOR) / KAZAL-TYPE INHIBITOR / THROMBIN / COMPLEX (SERINE PROTEASE-INHIBITOR) complex
Function / homology
Function and homology information


fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / acute-phase response / serine-type endopeptidase inhibitor activity / platelet activation / : / serine-type endopeptidase activity / calcium ion binding ...fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / acute-phase response / serine-type endopeptidase inhibitor activity / platelet activation / : / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region
Similarity search - Function
Serine protease inhibitor Kazal-type 4-like / Epsilon-Thrombin; Chain L / Thrombin light chain domain / Kazal serine protease inhibitors family signature. / Kazal-type serine protease inhibitor domain / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain ...Serine protease inhibitor Kazal-type 4-like / Epsilon-Thrombin; Chain L / Thrombin light chain domain / Kazal serine protease inhibitors family signature. / Kazal-type serine protease inhibitor domain / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Kringle-like fold / Few Secondary Structures / Irregular / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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
Prothrombin / Thrombin inhibitor rhodniin
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsVan De Locht, A. / Lamba, D. / Bode, W.
Citation
Journal: EMBO J. / Year: 1995
Title: Two heads are better than one: crystal structure of the insect derived double domain Kazal inhibitor rhodniin in complex with thrombin.
Authors: van de Locht, A. / Lamba, D. / Bauer, M. / Huber, R. / Friedrich, T. / Kroger, B. / Hoffken, W. / Bode, W.
#1: Journal: J.Biol.Chem. / Year: 1993
Title: A Kazal-Type Inhibitor with Thrombin Specificity from Rhodnius Prolixus
Authors: Friedrich, T. / Kroger, B. / Bialojan, S. / Lemaire, H.G. / Hoffken, H.W. / Reuschenbach, P. / Otte, M. / Dodt, J.
#2: Journal: Protein Sci. / Year: 1992
Title: The Refined 1.9-A X-Ray Crystal Structure of D-Phe-Pro-Arg Chloromethylketone-Inhibited Human Alpha-Thrombin: Structure Analysis, Overall Structure, Electrostatic Properties, Detailed Active- ...Title: The Refined 1.9-A X-Ray Crystal Structure of D-Phe-Pro-Arg Chloromethylketone-Inhibited Human Alpha-Thrombin: Structure Analysis, Overall Structure, Electrostatic Properties, Detailed Active-Site Geometry, and Structure-Function Relationships
Authors: Bode, W. / Turk, D. / Karshikov, A.
#3: Journal: J.Mol.Biol. / Year: 1991
Title: Refined Structure of the Hirudin-Thrombin Complex
Authors: Rydel, T.J. / Tulinsky, A. / Bode, W. / Huber, R.
#4: Journal: Embo J. / Year: 1990
Title: Crystal Structure of the Thrombin-Hirudin Complex: A Novel Mode of Serine Protease Inhibition
Authors: Grutter, M.G. / Priestle, J.P. / Rahuel, J. / Grossenbacher, H. / Bode, W. / Hofsteenge, J. / Stone, S.R.
#5: Journal: Science / Year: 1990
Title: The Structure of a Complex of Recombinant Hirudin and Human Alpha-Thrombin
Authors: Rydel, T.J. / Ravichandran, K.G. / Tulinsky, A. / Bode, W. / Huber, R. / Roitsch, C. / Fenton II, J.W.
#6: Journal: Embo J. / Year: 1989
Title: The Refined 1.9 A Crystal Structure of Human Alpha-Thrombin: Interaction with D-Phe-Pro-Arg Chloromethylketone and Significance of the Tyr-Pro-Pro-Trp Insertion Segment
Authors: Bode, W. / Mayr, I. / Baumann, U. / Huber, R. / Stone, S.R. / Hofsteenge, J.
History
DepositionMar 3, 1995Processing site: BNL
Revision 1.0Oct 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 16, 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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: THROMBIN
H: THROMBIN
J: THROMBIN
K: THROMBIN
R: RHODNIIN
S: RHODNIIN


Theoretical massNumber of molelcules
Total (without water)93,1986
Polymers93,1986
Non-polymers00
Water3,657203
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
L: THROMBIN
H: THROMBIN
R: RHODNIIN


Theoretical massNumber of molelcules
Total (without water)46,5993
Polymers46,5993
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-31 kcal/mol
Surface area18330 Å2
MethodPISA
3
J: THROMBIN
K: THROMBIN
S: RHODNIIN


Theoretical massNumber of molelcules
Total (without water)46,5993
Polymers46,5993
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-28 kcal/mol
Surface area18130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.735, 112.297, 92.069
Angle α, β, γ (deg.)90.00, 94.97, 90.00
Int Tables number5
Space group name H-MC121
DetailsTHIS ENTRY CONTAINS TWO THROMBIN MOLECULES AND TWO RHODNIIN MOLECULES. THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN IDENTIFIERS *L* AND *J* ARE USED FOR RESIDUES 1U - 15 OF THROMBIN AND CHAIN IDENTIFIERS *H* AND *K* ARE USED FOR RESIDUES 16 - 247 OF THROMBIN. CHAIN IDENTIFIERS *R* AND *S* ARE USED FOR RHODNIIN.

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Components

#1: Protein/peptide THROMBIN


Mass: 5735.240 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: PLASMA / References: UniProt: P00735, thrombin
#2: Protein THROMBIN


Mass: 29772.422 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: PLASMA / References: UniProt: P00735, thrombin
#3: Protein RHODNIIN


Mass: 11091.089 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodnius prolixus (insect) / Gene: PRPTI / Organ: PLASMA / Plasmid: PR2C / Gene (production host): PRPTI / Production host: Escherichia coli (E. coli) / References: UniProt: Q06684
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsCHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ...CHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF CHYMOTRYPSINOGEN (H.BRANDSTETTER ET AL., 1992, J.MOL.BIOL., V. 226, 1085).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 60 %
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 %PEG40001reservoir
2300 mMphosphate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 10, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→999 Å / Num. obs: 33844 / Observed criterion σ(I): 3 / Redundancy: 2.64 % / Rmerge(I) obs: 0.065
Reflection
*PLUS
% possible obs: 94.5 % / Num. measured all: 89438 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.66 Å / % possible obs: 78.2 %

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Processing

Software
NameClassification
MOSFLMdata reduction
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.6→8 Å / σ(F): 2
Details: AN OCCUPANCY OF 0.0 SIGNIFIES AN ATOM THAT WAS NOT LOCATED IN THE ELECTRON DENSITY MAPS.
RfactorNum. reflection% reflection
Rfree0.263 -10 %
Rwork0.189 --
obs0.189 30087 91.3 %
Displacement parametersBiso mean: 38.88 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6530 0 0 203 6733
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.66
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 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.64 Å / Rfactor Rfree: 0.262
Solvent computation
*PLUS
Displacement parameters
*PLUS

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