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- PDB-1trm: THE THREE-DIMENSIONAL STRUCTURE OF ASN102 MUTANT OF TRYPSIN. ROLE... -

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Basic information

Entry
Database: PDB / ID: 1trm
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 rattus (black rat)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsSprang, S. / Standing, T. / Fletterick, R.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
DepositionOct 21, 1987Processing 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 1.4Oct 23, 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_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

Downloads & links

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Assembly

Deposited unit
A: TRYPSIN
B: TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9486
Polymers47,6282
Non-polymers3204
Water4,143230
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.400, 92.000, 127.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: SEE REMARK 5.

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Components

#1: Protein TRYPSIN


Mass: 23813.854 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus rattus (black rat) / 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: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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 NECLEOPHILICITY 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: 2.48 Å3/Da / Density % sol: 50.45 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDCommon nameCrystal-IDSol-ID
1benzamidine1drop
2PEG1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 22000 / Num. measured all: 90000 / Rmerge F obs: 0.05

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.3→6 Å / Rfactor obs: 0.16
Details: THE A AND B CONFORMATIONS OF THE RESIDUE HIS 57 IN BOTH CHAINS WERE OBSERVED IN DIFFERENCE MAPS AFTER REFINEMENT WITH THIS SIDE CHAIN OMITTED FROM THE MODEL. THE POSSIBILITY THAT ONE OF THE ...Details: THE A AND B CONFORMATIONS OF THE RESIDUE HIS 57 IN BOTH CHAINS WERE OBSERVED IN DIFFERENCE MAPS AFTER REFINEMENT WITH THIS SIDE CHAIN OMITTED FROM THE MODEL. THE POSSIBILITY THAT ONE OF THE POSITIONS WOULD CORRESPOND TO AN ORDERED WATER MOLECULE WAS TESTED AND FOUND TO BE INCORRECT. THE RELATIVE OCCUPANCY OF THE TWO CONFORMATIONS WAS ESTIMATED BY COMPARING THE ELECTRON DENSITY AT POSITIONS WHERE THE TWO SIDE CHAINS DO NOT OVERLAP. THE OCCUPANCY OF THE TWO POSITIONS WAS NOT REFINED. THE B CONFORMATION CORRESPONDS TO THAT FOUND IN WILD TYPE TRYPSIN.
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3344 0 20 230 3594
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.03
X-RAY DIFFRACTIONp_angle_d0.05
X-RAY DIFFRACTIONp_angle_deg
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: 2.3 Å / Lowest resolution: 6 Å / Rfactor obs: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS

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