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- PDB-2trm: THE THREE-DIMENSIONAL STRUCTURE OF ASN102 MUTANT OF TRYPSIN. ROLE... -

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Basic information

Entry
Database: PDB / ID: 2trm
TitleTHE THREE-DIMENSIONAL STRUCTURE OF ASN102 MUTANT OF TRYPSIN. ROLE OF ASP102 IN SERINE PROTEASE CATALYSIS
ComponentsTRYPSIN
KeywordsHYDROLASE (SERINE PROTEINASE)
Function / homology
Function and homology information


Antimicrobial peptides / Alpha-defensins / Activation of Matrix Metalloproteinases / Neutrophil degranulation / collagen catabolic process / trypsin / digestion / response to nutrient / serine-type endopeptidase activity / calcium ion binding ...Antimicrobial peptides / Alpha-defensins / Activation of Matrix Metalloproteinases / 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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin ...: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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 / Anionic trypsin-2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsStroud, R.M. / Finer-Moore, J.
Citation
Journal: Science / Year: 1987
Title: The three-dimensional structure of Asn102 mutant of trypsin: role of Asp102 in serine protease catalysis.
Authors: Sprang, S. / Standing, T. / Fletterick, R.J. / Stroud, R.M. / Finer-Moore, J. / Xuong, N.H. / Hamlin, R. / Rutter, W.J. / Craik, C.S.
#1: Journal: Science / Year: 1987
Title: The Catalytic Role of the Active Site Aspartic Acid in Serine Proteases
Authors: Craik, C.S. / Roczniak, S. / Largman, C. / Rutter, W.J.
History
DepositionApr 25, 1988Processing site: BNL
Revision 1.0Jul 16, 1988Provider: 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 1.4Nov 13, 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 / 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_entry_details.has_protein_modification / _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 / _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

Downloads & links

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Assembly

Deposited unit
A: TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9743
Polymers23,8141
Non-polymers1602
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.380, 124.380, 124.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein TRYPSIN


Mass: 23813.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / References: UniProt: P00763, trypsin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE CATALYTIC SITE, DIFFERS FROM THE CATALYTIC SITE OF NATIVE TRYPSIN BY REPLACEMENT OF ASP 102 ...THE CATALYTIC SITE, DIFFERS FROM THE CATALYTIC SITE OF NATIVE TRYPSIN BY REPLACEMENT OF ASP 102 WITH AN ASN. IN THE MUTANT, ND2 ASN 102 IS A HYDROGEN BOND DONOR TO ND1 HIS 57. THIS HYDROGEN ARRANGEMENT PREVENTS HIS 57 FROM ACCEPTING A HYDROGEN BOND FROM SER 195 AND RESULTS IN A LOSS OF NUCLEOPHILICITY OF SER 195. THE MUTANT IS FOUR ORDERS OF MAGNITUDE LESS ACTIVE THAN NATIVE RAT TRYPSIN.
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: 3.37 Å3/Da / Density % sol: 63.45 %
Crystal growDetails: THE CRYSTALS WERE GROWN AT PH 8 WHICH IS WITHIN THE PH RANGE (7 - 9) WHERE NATIVE TRYPSIN IS OPTIMALLY ACTIVE.
Crystal grow
*PLUS
Method: vapor diffusion

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Data collection

Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 4500 / Num. measured all: 5000

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.8→7 Å / Rfactor obs: 0.157
Refinement stepCycle: LAST / Resolution: 2.8→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1666 0 10 122 1798
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.8
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 7 Å / Rfactor obs: 0.157
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_angle_d

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