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- PDB-2pka: REFINED 2 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF PORCINE PANCREATIC... -

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Basic information

Entry
Database: PDB / ID: 2pka
TitleREFINED 2 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF PORCINE PANCREATIC KALLIKREIN A, A SPECIFIC TRYPSIN-LIKE SERINE PROTEINASE. CRYSTALLIZATION, STRUCTURE DETERMINATION, CRYSTALLOGRAPHIC REFINEMENT, STRUCTURE AND ITS COMPARISON WITH BOVINE TRYPSIN
Components(KALLIKREIN A) x 2
KeywordsSERINE PROTEINASE
Function / homology
Function and homology information


tissue kallikrein / regulation of systemic arterial blood pressure / zymogen activation / secretory granule / serine-type endopeptidase activity
Similarity search - Function
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 ...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
BENZAMIDINE / Glandular kallikrein
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.05 Å
AuthorsBode, W. / Chen, Z.
Citation
Journal: J.Mol.Biol. / Year: 1983
Title: Refined 2 A X-ray crystal structure of porcine pancreatic kallikrein A, a specific trypsin-like serine proteinase. Crystallization, structure determination, crystallographic refinement, ...Title: Refined 2 A X-ray crystal structure of porcine pancreatic kallikrein A, a specific trypsin-like serine proteinase. Crystallization, structure determination, crystallographic refinement, structure and its comparison with bovine trypsin.
Authors: Bode, W. / Chen, Z. / Bartels, K. / Kutzbach, C. / Schmidt-Kastner, G. / Bartunik, H.
#1: Journal: J.Mol.Biol. / Year: 1983
Title: Refined 2.5 Angstroms X-Ray Crystal Structure of the Complex Formed by Porcine Kallikrein a and the Bovine Pancreatic Trypsin Inhibitor. Crystallization, Patterson Search, Structure ...Title: Refined 2.5 Angstroms X-Ray Crystal Structure of the Complex Formed by Porcine Kallikrein a and the Bovine Pancreatic Trypsin Inhibitor. Crystallization, Patterson Search, Structure Determination, Refinement, Structure and Comparison with its Components and with the Bovine Trypsin-Pancreatic Trypsin Inhibitor Complex
Authors: Chen, Z. / Bode, W.
History
DepositionMay 21, 1984Processing site: BNL
Revision 1.0Jul 19, 1984Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _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: KALLIKREIN A
B: KALLIKREIN A
X: KALLIKREIN A
Y: KALLIKREIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5026
Polymers51,2614
Non-polymers2402
Water1,53185
1
A: KALLIKREIN A
B: KALLIKREIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7513
Polymers25,6312
Non-polymers1201
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-41 kcal/mol
Surface area10580 Å2
MethodPISA
2
X: KALLIKREIN A
Y: KALLIKREIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7513
Polymers25,6312
Non-polymers1201
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint-44 kcal/mol
Surface area10320 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13900 Å2
ΔGint-93 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.200, 90.200, 159.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Atom site foot note1: RESIDUES PRO B 147, PRO B 219, PRO Y 147, PRO Y 219 ARE CIS-PROLINES.
2: SEE REMARK 5.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.3872, -0.83477, 0.39152), (0.68544, 0.54462, 0.48328), (-0.61662, 0.08124, 0.78303)
Vector: 36.314, -49.058, 24.735)
DetailsTHE TRANSFORMATION GIVING OPTIMAL SUPERPOSITION OF MOLECULE 1 (CHAIN INDICATORS *A* AND *B*) ONTO MOLECULE 2 (CHAIN INDICATORS *X* AND *Y*) IS GIVEN IN THE MTRIX RECORDS BELOW.

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Components

#1: Protein KALLIKREIN A


Mass: 9119.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P00752, tissue kallikrein
#2: Protein KALLIKREIN A


Mass: 16511.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P00752, tissue kallikrein
#3: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.08 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 Mammonium sulfate1drop
20.1 Mphosphate1drop
310 mMbenzamidine1drop
460 mg/mlprotein1drop

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Data collection

Reflection
*PLUS
Highest resolution: 2.05 Å / Num. obs: 35517 / % possible obs: 86.8 % / Observed criterion σ(I): 2 / Num. measured all: 198249 / Rmerge(I) obs: 0.102

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Processing

SoftwareName: EREF / Classification: refinement
RefinementRfactor Rwork: 0.22 / Highest resolution: 2.05 Å
Details: AN OCCUPANCY OF 0.0 INDICATES THAT NO SIGNIFICANT ELECTRON DENSITY WAS FOUND IN THE FINAL FOURIER MAP AND THAT THE COORDINATES WERE GENERATED USING STEREOCHEMICAL CRITERIA.
Refinement stepCycle: LAST / Highest resolution: 2.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3598 0 18 85 3701
Refinement
*PLUS
Rfactor obs: 0.22 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS

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