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- PDB-1amh: UNCOMPLEXED RAT TRYPSIN MUTANT WITH ASP 189 REPLACED WITH SER (D189S) -

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Basic information

Entry
Database: PDB / ID: 1amh
TitleUNCOMPLEXED RAT TRYPSIN MUTANT WITH ASP 189 REPLACED WITH SER (D189S)
ComponentsANIONIC TRYPSIN
KeywordsHYDROLASE / SERINE PROTEASE / ACTIVATION DOMAIN / SUBSTRATE SPECIFICITY HYDROLASE
Function / homology
Function and homology information


Antimicrobial peptides / Alpha-defensins / Activation of Matrix Metalloproteinases / Collagen degradation / Neutrophil degranulation / collagen catabolic process / trypsin / digestion / response to nutrient / serine-type endopeptidase activity ...Antimicrobial peptides / Alpha-defensins / Activation of Matrix Metalloproteinases / Collagen degradation / Neutrophil degranulation / collagen catabolic process / trypsin / digestion / response to nutrient / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region
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
Biological speciesRattus rattus (black rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSzabo, E. / Bocskei, Z.S. / Naray-Szabo, G. / Graf, L.
Citation
Journal: Eur.J.Biochem. / Year: 1999
Title: The three-dimensional structure of Asp189Ser trypsin provides evidence for an inherent structural plasticity of the protease.
Authors: Szabo, E. / Bocskei, Z. / Naray-Szabo, G. / Graf, L.
#1: Journal: Biochemistry / Year: 1994
Title: Exogenous Acetate Reconstitutes the Enzymatic Activity of Trypsin Asp189Ser
Authors: Perona, J.J. / Hedstrom, L. / Wagner, R.L. / Rutter, W.J. / Craik, C.S. / Fletterick, R.J.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1988
Title: Electrostatic Complementarity within the Substrate-Binding Pocket of Trypsin
Authors: Graf, L. / Jancso, A. / Szilagyi, L. / Hegyi, G. / Pinter, K. / Naray-Szabo, G. / Hepp, J. / Medzihradszky, K. / Rutter, W.J.
#3: Journal: Acc.Chem.Res. / Year: 1978
Title: Structural Basis of the Activation and Action of Trypsin
Authors: Huber, R. / Bode, W.
History
DepositionJun 17, 1997Processing site: BNL
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_conn_angle / software / 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_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _software.name / _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
Revision 1.4Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANIONIC TRYPSIN
B: ANIONIC TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6544
Polymers47,5742
Non-polymers802
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-23 kcal/mol
Surface area17020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.920, 49.790, 89.880
Angle α, β, γ (deg.)90.00, 97.34, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (0.739109, 0.012922, -0.673462), (0.015672, -0.999875, -0.001986), (-0.673404, -0.009087, -0.739219)
Vector: 17.0746, 21.6473, 44.7529)

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Components

#1: Protein ANIONIC TRYPSIN


Mass: 23786.828 Da / Num. of mol.: 2 / Mutation: D189S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus rattus (black rat) / Organ: PANCREAS / Plasmid: PYES2 / Cellular location (production host): SECRETION / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): INVSC1 / References: UniProt: P00763, trypsin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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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: 2.07 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 277 K / pH: 5.6
Details: CRYSTALLIZED AT 277 K FROM 10 MG/ML PROTEIN SOLUTION USING 22% PEG 3350, 10 MM CACL2 AND 0.15M NH4CL AS PRECIPITANT AT PH=5.6 (0.1 M SODIUM CITRATE).
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
20.1 Msodium citrate1reservoir
310 mM1reservoirCaCl2
422 %PEG33501reservoir
50.15 Mammonium chloride1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Dec 1, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.52→100 Å / Num. obs: 13312 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 36.25 Å2 / Rmerge(I) obs: 0.12 / Rsym value: 0.131 / Net I/σ(I): 7.7
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 2.63 / Rsym value: 0.312 / % possible all: 91.9
Reflection shell
*PLUS
Highest resolution: 2.54 Å / Lowest resolution: 2.59 Å / % possible obs: 91.9 % / Num. unique obs: 470 / Mean I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
bioteXdata collection
bioteXdata reduction
X-PLOR3.851model building
X-PLOR3.851refinement
bioteXdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BRB

1brb


Resolution: 2.5→100 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1183 5 %RANDOM
Rwork0.182 ---
obs0.182 13312 85 %-
Displacement parametersBiso mean: 18.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.369 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.438 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.5→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3328 0 2 131 3461
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.369
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.17
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.304
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.8941.5
X-RAY DIFFRACTIONx_mcangle_it3.0152
X-RAY DIFFRACTIONx_scbond_it2.9592
X-RAY DIFFRACTIONx_scangle_it4.1062.5
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Weight Biso : 3

Ens-IDDom-IDNCS model detailsRms dev Biso (Å2)Rms dev position (Å)Weight position
11RESTRAINTS1.8710.134820
222.0940.198310
LS refinement shellResolution: 2.54→2.59 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 38 8.1 %
Rwork0.259 470 -
obs--67.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARAM.CATOP.CA
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 12103
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.17
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.304
LS refinement shell
*PLUS
Rfactor obs: 0.259

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