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- PDB-1pyt: TERNARY COMPLEX OF PROCARBOXYPEPTIDASE A, PROPROTEINASE E, AND CH... -

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Basic information

Entry
Database: PDB / ID: 1pyt
TitleTERNARY COMPLEX OF PROCARBOXYPEPTIDASE A, PROPROTEINASE E, AND CHYMOTRYPSINOGEN C
Components
  • (PROCARBOXYPEPTIDASE ...) x 2
  • CHYMOTRYPSINOGEN C
  • PROPROTEINASE E
KeywordsTERNARY COMPLEX (ZYMOGEN) / SERINE PROTEINASE / C-TERMINAL PEPTIDASE
Function / homology
Function and homology information


Cobalamin (Cbl, vitamin B12) transport and metabolism / chymotrypsin C / carboxypeptidase A / leukotriene metabolic process / metallocarboxypeptidase activity / digestion / serine-type endopeptidase activity / proteolysis / extracellular space / zinc ion binding
Similarity search - Function
Metallocarboxypeptidase-like / Carboxypeptidase A, carboxypeptidase domain / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / Zinc carboxypeptidases, zinc-binding region 2 signature. / Zinc carboxypeptidases, zinc-binding region 1 signature. / Peptidase family M14 domain profile. / Zn_pept / Peptidase M14, carboxypeptidase A ...Metallocarboxypeptidase-like / Carboxypeptidase A, carboxypeptidase domain / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / Zinc carboxypeptidases, zinc-binding region 2 signature. / Zinc carboxypeptidases, zinc-binding region 1 signature. / Peptidase family M14 domain profile. / Zn_pept / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase / Zn peptidases / Aminopeptidase / 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 / Alpha-Beta Plaits / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Carboxypeptidase A1 / Proproteinase E / Chymotrypsin-C
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.35 Å
AuthorsGomis-Ruth, F.X. / Gomez, M. / Bode, W. / Huber, R. / Aviles, F.X.
Citation
Journal: EMBO J. / Year: 1995
Title: The three-dimensional structure of the native ternary complex of bovine pancreatic procarboxypeptidase A with proproteinase E and chymotrypsinogen C.
Authors: Gomis-Ruth, F.X. / Gomez, M. / Bode, W. / Huber, R. / Aviles, F.X.
#1: Journal: To be Published
Title: Procarboxypeptidase A-S6 : Detailed Structure Analysis of the Constituting Subunits and Implications for Their Activation
Authors: Gomis-Ruth, F.X. / Gomez, M. / Vendrell, J. / Ventura, S. / Bode, W. / Huber, R. / Aviles, F.X.
History
DepositionJun 21, 1995Processing site: BNL
Revision 1.0Jan 27, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROCARBOXYPEPTIDASE A
B: PROCARBOXYPEPTIDASE A
C: PROPROTEINASE E
D: CHYMOTRYPSINOGEN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,4236
Polymers100,3174
Non-polymers1052
Water6,864381
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)188.500, 188.500, 82.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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PROCARBOXYPEPTIDASE ... , 2 types, 2 molecules AB

#1: Protein PROCARBOXYPEPTIDASE A


Mass: 10801.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P00730, carboxypeptidase A
#2: Protein PROCARBOXYPEPTIDASE A


Mass: 34793.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P00730, carboxypeptidase A

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Protein , 2 types, 2 molecules CD

#3: Protein PROPROTEINASE E


Mass: 27336.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P05805
#4: Protein CHYMOTRYPSINOGEN C / TC / PCPA-TC


Mass: 27385.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: Q7M3E1*PLUS

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Non-polymers , 3 types, 383 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE ACTIVATION PEPTIDE (UP TO ARG 715) OF CTGC IS TWO RESIDUES SHORTER (701-712+715) THAN THE ...THE ACTIVATION PEPTIDE (UP TO ARG 715) OF CTGC IS TWO RESIDUES SHORTER (701-712+715) THAN THE CORRESPONDING PART IN CTGA, THE ACTIVATION PEPTIDE OF BPE IS 4 RESIDUES SHORTER AND STARTS AT COUNT 405 (405 - 415).
Sequence detailsFOR RATIONALITY REASONS AND IN ORDER TO PRESERVE THE CHYMOTRYPSINOGEN A (CTGA) NUMBERING FOR BOTH ...FOR RATIONALITY REASONS AND IN ORDER TO PRESERVE THE CHYMOTRYPSINOGEN A (CTGA) NUMBERING FOR BOTH SERINE PROPROTEINASES, 400 COUNTS AND THE CHAIN IDENTIFIER C HAVE BEEN ADDED TO THE (EQUIVALENT) RESIDUES OF PROPROTEINASE E (BPE) AND 700 PLUS THE CHAIN IDENTIFIER D HAVE BEEN ADDED TO THE CHYMOTRYPSINOGEN C (CTGC) RESIDUES. THEREFORE, THE CATALYTIC TRIAD SER 195, ASP 102, AND HIS 57 OF CHYMOTRYPSINOGEN A IS EQUIVALENT TO SER C 595, ASP C 502, AND HIS C 457 OF BPE AND SER D 895, ASP D 802, AND HIS D 757 OF CTGC. THE PROCARBOXYPEPTIDASE A(PCPA) NUMBERING HAS BEEN TAKEN FROM PDB ENTRY 1PCA (GUASCH ET AL., 1992), THAT IS, THE RESIDUES FROM THE PCPA ACTIVATION PEPTIDE HAVE BEEN LABELED A 4 TO A 99 (WITH A TWO RESIDUE INSERTION AT POSITIONS 34B AND 34C, AND A 4-RESIDUE DELETION [A 43 - A 46]).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.24 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.1 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.1 M1dropCaCl2
20.05 MHEPES1drop
315 %(v/v)PEG4001drop
415 mg/mlprotein1drop
50.1 M1reservoirCaCl2
60.05 MHEPES1reservoir
715 %(v/v)PEG4001reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→20 Å / Num. obs: 39633 / % possible obs: 87.2 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.078

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Processing

Software
NameClassification
MOSFLMdata reduction
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.35→6 Å
Details: NO PROPER DENSITY WAS OBSERVED FOR SEGMENTS 712 - 716, 846 - 847, AND 888 - 889 OF CTGC. THESE 16 RESIDUES AND SOME SURFACE-LOCATED SIDE-CHAINS (709, 710, 711, 770, 810, 848, 892, 943) HAVE ...Details: NO PROPER DENSITY WAS OBSERVED FOR SEGMENTS 712 - 716, 846 - 847, AND 888 - 889 OF CTGC. THESE 16 RESIDUES AND SOME SURFACE-LOCATED SIDE-CHAINS (709, 710, 711, 770, 810, 848, 892, 943) HAVE BEEN TENTATIVELY TRACED IN ORDER TO PRESERVE CHAIN CONTINUITY AND SET TO ZERO OCCUPANCY (B = 20.0). NO PROPER DENSITY WAS OBSERVED FOR SEGMENT 405 - 409 OF BPE. THIS SEGMENT HAS NOT BEEN TRACED NOR INCLUDED IN THIS MODEL.
RfactorNum. reflection
Rfree0.283 -
Rwork0.192 -
obs0.192 30541
Displacement parametersBiso mean: 45.4 Å2
Refinement stepCycle: LAST / Resolution: 2.35→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7028 0 2 381 7411
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.822
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

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