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- PDB-1aal: STRUCTURAL EFFECTS INDUCED BY MUTAGENESIS AFFECTED BY CRYSTAL PAC... -

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Basic information

Entry
Database: PDB / ID: 1aal
TitleSTRUCTURAL EFFECTS INDUCED BY MUTAGENESIS AFFECTED BY CRYSTAL PACKING FACTORS: THE STRUCTURE OF A 30-51 DISULFIDE MUTANT OF BASIC PANCREATIC TRYPSIN INHIBITOR
ComponentsBOVINE PANCREATIC TRYPSIN INHIBITOR
KeywordsSERINE PROTEASE INHIBITOR
Function / homology
Function and homology information


trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity ...trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity / protease binding / calcium ion binding / extracellular space
Similarity search - Function
: / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily ...: / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
PHOSPHATE ION / Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsEigenbrot, C. / Randal, M. / Kossiakoff, A.A.
Citation
Journal: Proteins / Year: 1992
Title: Structural effects induced by mutagenesis affected by crystal packing factors: the structure of a 30-51 disulfide mutant of basic pancreatic trypsin inhibitor.
Authors: Eigenbrot, C. / Randal, M. / Kossiakoff, A.A.
#1: Journal: Protein Eng. / Year: 1990
Title: Structural Effects Induced by Removal of a Disulfide Bridge: The X-Ray Structure of the C30A(Slash)C51A Mutant of Basic Pancreatic Trypsin Inhibitor at 1.6 Angstroms
Authors: Eigenbrot, C. / Randal, M. / Kossiakoff, A.A.
History
DepositionApr 9, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_entry_details.has_protein_modification / _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: BOVINE PANCREATIC TRYPSIN INHIBITOR
B: BOVINE PANCREATIC TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0783
Polymers12,9832
Non-polymers951
Water2,270126
1
A: BOVINE PANCREATIC TRYPSIN INHIBITOR


Theoretical massNumber of molelcules
Total (without water)6,4911
Polymers6,4911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BOVINE PANCREATIC TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5862
Polymers6,4911
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.280, 89.580, 48.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: THE FOLLOWING RESIDUES MODELLED WITH 2 SIDE CHAIN CONFORMATIONS: GLU A 7, ARG A 17, ARG A 39, GLU A 49, ASP B 3, ARG B 17, ARG B 39, ARG B 42, GLU B 49.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.785512, -0.594349, -0.172394), (-0.528944, -0.789422, 0.311497), (-0.321229, -0.153498, -0.934479)
Vector: 46.50912, 117.36581, 50.15519)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL GENERATE APPROXIMATE COORDINATES FOR CHAIN B WHEN APPLIED TO CHAIN A.

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Components

#1: Protein BOVINE PANCREATIC TRYPSIN INHIBITOR


Mass: 6491.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P00974
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHERE IS A UNIQUE SALT-BRIDGE BETWEEN THE N AND C TERMINALS OF MOLECULES WITH RESIDUE NUMBERS 1 - ...THERE IS A UNIQUE SALT-BRIDGE BETWEEN THE N AND C TERMINALS OF MOLECULES WITH RESIDUE NUMBERS 1 - 58, WHICH HAS BEEN SEEN IN SOLUTION (NMR) BUT NEVER CRYSTALLOGRAPHICALLY.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal grow
*PLUS
pH: 10 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
Conc.: 0.7 M / Chemical formula: NaKPO4

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 8 Å / Num. obs: 16638 / Rmerge(I) obs: 0.131

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.6→8 Å / σ(I): 1 /
RfactorNum. reflection
obs0.179 15473
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms945 0 5 126 1076
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.0560.05
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0630.06
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it22
X-RAY DIFFRACTIONp_mcangle_it2.93
X-RAY DIFFRACTIONp_scbond_it32.5
X-RAY DIFFRACTIONp_scangle_it4.94
X-RAY DIFFRACTIONp_plane_restr0.0160.02
X-RAY DIFFRACTIONp_chiral_restr0.1540.125
X-RAY DIFFRACTIONp_singtor_nbd0.1930.5
X-RAY DIFFRACTIONp_multtor_nbd0.2630.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2180.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.45
X-RAY DIFFRACTIONp_staggered_tor19.860
X-RAY DIFFRACTIONp_orthonormal_tor20.645
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 8 Å / Num. reflection obs: 15473 / σ(I): 1 / Rfactor obs: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS

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