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- PDB-1qqu: CRYSTAL STRUCTURE OF PORCINE BETA TRYPSIN WITH BOUND ACETATE ION -

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Basic information

Entry
Database: PDB / ID: 1qqu
TitleCRYSTAL STRUCTURE OF PORCINE BETA TRYPSIN WITH BOUND ACETATE ION
ComponentsBETA TRYPSIN
KeywordsHYDROLASE / SERINE PROTEASE
Function / homology
Function and homology information


trypsin / digestion / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
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
ACETATE ION / Trypsin
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLCEMENT / Resolution: 1.63 Å
AuthorsJohnson, A. / Gautham, N. / Pattabhi, V.
Citation
Journal: Biochim.Biophys.Acta / Year: 1999
Title: Crystal structure at 1.63 A resolution of the native form of porcine beta-trypsin: revealing an acetate ion binding site and functional water network.
Authors: Johnson, A. / Gautham, N. / Pattabhi, V.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: The First Crystal Structure at 1.8 Angstroms Resolution of an Active Autolysate Form of Porcine Alpha Trypsin
Authors: Johnson, A. / Krishnaswamy, S. / Sundaram, P.V. / Pattabhi, V.
History
DepositionJun 9, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: BETA TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5913
Polymers23,4921
Non-polymers992
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.000, 53.900, 47.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BETA TRYPSIN


Mass: 23491.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P00761, trypsin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE 223 AMINO ACIDS OF TRYPSIN ARE IDENTIFIED BY THE RESIDUE NUMBERS OF THE HOMOLOGOUS CHYMOTRYPSINOGEN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.81 %
Crystal growpH: 6.7 / Details: pH 6.70
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and precipitant solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115 mg/mlprotein1drop
20.05 Msodium acetate1drop
320 mM1dropCaCl2
40.7 Mammonium sulfate1dropprecipitant
51.5 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 13, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.63→23.62 Å / Num. obs: 21149 / % possible obs: 83.2 % / Observed criterion σ(I): 0 / Redundancy: 3.83 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 19.96
Reflection shellResolution: 1.63→1.7 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.77 / % possible all: 80.6
Reflection shell
*PLUS
% possible obs: 80.6 %

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Processing

Software
NameClassification
XDSdata scaling
AUTOMARdata reduction
X-PLORmodel building
X-PLORrefinement
REFMACrefinement
XDSdata reduction
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLCEMENT
Starting model: 1AKS

1aks


Resolution: 1.63→8 Å / Cross valid method: FREE R / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1082 5.11 %RANDOM R VALUE (WORKING + TEST SET) : 0.195
Rwork0.193 ---
obs0.193 21149 83.2 %-
Refinement stepCycle: LAST / Resolution: 1.63→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1642 0 5 149 1796
Software
*PLUS
Name: 'X-PLOR,REFMAC,CNS 0.9' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg2.13
X-RAY DIFFRACTIONx_dihedral_angle_deg28
X-RAY DIFFRACTIONx_improper_angle_deg2.03

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