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- PDB-1a0j: CRYSTAL STRUCTURE OF A NON-PSYCHROPHILIC TRYPSIN FROM A COLD-ADAP... -

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Basic information

Entry
Database: PDB / ID: 1a0j
TitleCRYSTAL STRUCTURE OF A NON-PSYCHROPHILIC TRYPSIN FROM A COLD-ADAPTED FISH SPECIES.
ComponentsTRYPSIN
KeywordsSERINE PROTEASE / SERINE PROTEINASE / TRYPSIN / HYDROLASE
Function / homology
Function and homology information


trypsin / digestion / serine-type endopeptidase activity / 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
BENZAMIDINE / Trypsin-3
Similarity search - Component
Biological speciesSalmo salar (Atlantic salmon)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSchroeder, H.-K. / Willassen, N.P. / Smalaas, A.O.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structure of a non-psychrophilic trypsin from a cold-adapted fish species.
Authors: Schroder, H.K. / Willassen, N.P. / Smalas, A.O.
History
DepositionDec 1, 1997Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / software / struct_conn / 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_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_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
C: TRYPSIN
D: TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,69619
Polymers95,2154
Non-polymers1,48115
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
D: TRYPSIN
hetero molecules

A: TRYPSIN
B: TRYPSIN
C: TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,69619
Polymers95,2154
Non-polymers1,48115
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation4_556x+1/2,-y+1/2,-z+11
identity operation1_555x,y,z1
Buried area10040 Å2
ΔGint-162 kcal/mol
Surface area31150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.907, 83.107, 154.787
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.57345, -0.321655, 0.753454), (-0.367037, -0.721359, -0.587303), (0.73242, -0.613334, 0.295604)25.56022, 120.9744, 41.0547
2given(-0.054285, -0.335982, -0.940303), (-0.413757, -0.849473, 0.327415), (-0.908767, 0.406831, -0.092901)107.68916, 66.42438, 85.58722
3given(-0.504313, 0.863056, 0.028337), (-0.835345, -0.479281, -0.269237), (-0.218785, -0.159451, 0.962657)-16.28458, 72.87833, 48.48168
4given(-0.569275, 0.814531, -0.111647), (0.757198, 0.572348, 0.314752), (0.320276, 0.094642, -0.942585)28.27138, -35.09442, 104.65495
5given(0.032942, -0.454114, -0.890334), (0.430334, 0.81046, -0.397452), (0.902069, -0.370048, 0.222119)74.37251, -19.85422, 61.08286
6given(-0.28924, -0.515202, 0.806788), (0.459541, 0.664614, 0.589161), (-0.839739, 0.541161, 0.044524)-19.95494, -71.18546, 99.16763

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Components

#1: Protein
TRYPSIN /


Mass: 23803.662 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: BENZAMIDINE INHIBITOR IN THE ACTIVE SITE. THE AMINO ACID NUMBERING SCHEME USED IS ADOPTED FROM CHYMOTRYPSINOGEN.
Source: (natural) Salmo salar (Atlantic salmon) / Organ: PANCREAS / References: UniProt: P35033, trypsin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-BEN / BENZAMIDINE / Benzamidine


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


Mass: 18.015 Da / Num. of mol.: 379 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AMINO ACID NUMBERING SCHEME USED IS ADOPTED FROM CHYMOTRYPSINOGEN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44 %
Crystal growpH: 4.6 / Details: pH 4.6
Crystal grow
*PLUS
Temperature: 310 K / Method: vapor diffusion
Details: drop contained 1:1 mixture of protein and reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
260 mMbenzamidine1drop
31.60-1.75 Mammonium sulfate1reservoir
40.1 Macetate1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.7→28 Å / Num. obs: 76357 / % possible obs: 81.2 % / Observed criterion σ(I): 1 / Redundancy: 5.9 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 3.6
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 2.9 / % possible all: 52.3
Reflection
*PLUS
Num. measured all: 451079
Reflection shell
*PLUS
% possible obs: 52.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
XDSdata scaling
SCALAdata scaling
Agrovatadata reduction
CCP4data reduction
AMoREphasing
X-PLOR3.8refinement
XDSdata reduction
CCP4(AGROVATAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PTB BOVINE TRYPSIN, WITH CORRECT AMINO ACID SEQUENCE SUPERIMPOSED ONTO ANIONIC SALMON TRYPSIN 2TBS.

3ptb

2tbs


Resolution: 1.7→8 Å / Cross valid method: THROUGHOUT / σ(F): 3
Details: NCS RESTRAINTS WERE INCLUDED IN THE FIRST REFINEMENT ROUNDS, THEN LEFT OUT. THE ELECTRON DENSITY INDICATES A CALCIUM ION FOR ONLY ONE OF THE FOUR MOLECULES (MOL A). THE ELECTRON DENSITY ...Details: NCS RESTRAINTS WERE INCLUDED IN THE FIRST REFINEMENT ROUNDS, THEN LEFT OUT. THE ELECTRON DENSITY INDICATES A CALCIUM ION FOR ONLY ONE OF THE FOUR MOLECULES (MOL A). THE ELECTRON DENSITY INDICATES A CALCIUM ION FOR ONLY ONE OF THE FOUR MOLECULES (MOL A).
RfactorNum. reflection% reflectionSelection details
Rfree0.215 3866 5 %RANDOM
Rwork0.173 ---
obs0.173 68062 73.061 %-
Displacement parametersBiso mean: 22.93 Å2
Refine analyzeLuzzati coordinate error free: 0.18 Å / Luzzati sigma a free: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6640 0 87 379 7106
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg2.697
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.35
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.087
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.7→1.76 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2121 163 5 %
Rwork0.2347 2986 -
obs--34.21 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARAM19X.PRO
X-RAY DIFFRACTION2
X-RAY DIFFRACTION4TOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.35
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.087
LS refinement shell
*PLUS
Rfactor obs: 0.2347

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