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- PDB-4bnr: Extremely stable complex of crayfish trypsin with bovine trypsin ... -

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Basic information

Entry
Database: PDB / ID: 4bnr
TitleExtremely stable complex of crayfish trypsin with bovine trypsin inhibitor
Components
  • HEPATOPANCREAS TRYPSIN
  • PANCREATIC TRYPSIN INHIBITOR
KeywordsHYDOLASE/INHIBITOR / HYDOLASE-INHIBITOR COMPLEX / PROTEASE / INHIBITION / ARTHROPODA / HEAT STABILITY / COMPLEX FORMATION
Function / homology
Function and homology information


trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / negative regulation of platelet aggregation / potassium channel inhibitor activity / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity ...trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / negative regulation of platelet aggregation / potassium channel inhibitor activity / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity / protease binding / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Few Secondary Structures ...Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Few Secondary Structures / Irregular / 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
Pancreatic trypsin inhibitor / Hepatopancreas trypsin
Similarity search - Component
Biological speciesPONTASTACUS LEPTODACTYLUS (narrow-clawed crayfish)
BOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMolnar, T. / Voros, J. / Szeder, B. / Takats, K. / Kardos, J. / Katona, G. / Graf, L.
CitationJournal: FEBS J. / Year: 2013
Title: Comparison of Complexes Formed by a Crustacean and a Vertebrate Trypsin with Bovine Pancreatic Trypsin Inhibitor - the Key to Achieving Extreme Stability?
Authors: Molnar, T. / Voros, J. / Szeder, B. / Takats, K. / Kardos, J. / Katona, G. / Graf, L.
History
DepositionMay 17, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Nov 13, 2013Group: Database references
Revision 2.0May 8, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Experimental preparation / Other
Category: atom_site / database_PDB_rev ...atom_site / database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.pdbx_auth_atom_name / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 2.1Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEPATOPANCREAS TRYPSIN
B: HEPATOPANCREAS TRYPSIN
I: PANCREATIC TRYPSIN INHIBITOR
J: PANCREATIC TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,32910
Polymers71,9764
Non-polymers3526
Water8,521473
1
B: HEPATOPANCREAS TRYPSIN
J: PANCREATIC TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1645
Polymers35,9882
Non-polymers1763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-47.2 kcal/mol
Surface area12630 Å2
MethodPISA
2
A: HEPATOPANCREAS TRYPSIN
I: PANCREATIC TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1645
Polymers35,9882
Non-polymers1763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-46.4 kcal/mol
Surface area12630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.980, 138.980, 93.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.668892, 0.740995, 0.059254), (0.742066, -0.670304, 0.005566), (0.043843, 0.040247, -0.998227)-37.7844, 87.4027, -18.6793
2given(0.632592, 0.772309, 0.058024), (0.773817, -0.633381, -0.005947), (0.032159, 0.048662, -0.998297)-40.9699, 86.8351, -19.4031

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Components

#1: Protein HEPATOPANCREAS TRYPSIN


Mass: 25072.434 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) PONTASTACUS LEPTODACTYLUS (narrow-clawed crayfish)
Organ: STOMACH / References: UniProt: Q52V24, trypsin
#2: Protein PANCREATIC TRYPSIN INHIBITOR / BOVINE PANCREATIC TRYPSIN INHIBITOR / APROTININ / BASIC PROTEASE INHIBITOR / BPI / BPTI


Mass: 10915.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: PANCREAS / References: UniProt: P00974
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / 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: 2.76 Å3/Da / Density % sol: 55.4 % / Description: NONE
Crystal growTemperature: 293 K / pH: 5.6
Details: 10.6 MG/ML PROTEIN, 33 (W/V)% PEG 4000, 0.1 M SODIUM CITRATE PH 5.6, 0.2 M AMMONIUM ACETATE, 1:1 MIXING, 20 C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 29, 2008 / Details: SAGITALLY FOCUSING GE(220) AND A MULTILAYER
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.99→40.9 Å / Num. obs: 45201 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.3
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2 / % possible all: 83.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2F91

2f91


Resolution: 2→40.896 Å / SU ML: 0.19 / σ(F): 2 / Phase error: 17.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1822 2257 5.1 %
Rwork0.1494 --
obs0.1511 44678 98.34 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.2 Å2
Refinement stepCycle: LAST / Resolution: 2→40.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4434 0 14 473 4921
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054560
X-RAY DIFFRACTIONf_angle_d0.9026188
X-RAY DIFFRACTIONf_dihedral_angle_d12.4151594
X-RAY DIFFRACTIONf_chiral_restr0.056668
X-RAY DIFFRACTIONf_plane_restr0.003822
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04350.25891140.22682288X-RAY DIFFRACTION84
2.0435-2.0910.23041250.20622468X-RAY DIFFRACTION92
2.091-2.14330.22721360.18982677X-RAY DIFFRACTION98
2.1433-2.20130.20541340.17522678X-RAY DIFFRACTION100
2.2013-2.2660.19591270.15842738X-RAY DIFFRACTION100
2.266-2.33920.18011390.14942648X-RAY DIFFRACTION100
2.3392-2.42280.19181390.14962716X-RAY DIFFRACTION100
2.4228-2.51980.17671550.15822694X-RAY DIFFRACTION100
2.5198-2.63440.20861800.15972654X-RAY DIFFRACTION100
2.6344-2.77330.21111360.16222712X-RAY DIFFRACTION100
2.7733-2.9470.20481510.15532680X-RAY DIFFRACTION100
2.947-3.17450.20091370.16062713X-RAY DIFFRACTION100
3.1745-3.49380.16991590.14852686X-RAY DIFFRACTION100
3.4938-3.99890.18331280.13052699X-RAY DIFFRACTION100
3.9989-5.03680.13221480.11332701X-RAY DIFFRACTION100
5.0368-40.90460.17151490.15282669X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.4077-0.56290.12892.0466-0.57521.7672-0.2093-0.41830.0940.20220.2650.0503-0.2134-0.2065-0.1020.25370.10080.01940.26620.03040.1712-17.649122.89433.4483
21.6766-0.4743-0.06172.65970.00811.7601-0.0797-0.163-0.1353-0.05420.1169-0.1272-0.04010.01930.00620.17570.06670.02710.18030.03130.1969-11.503217.3296-1.5301
31.68790.17060.75530.9398-0.03511.6228-0.1692-0.46-0.46090.09740.31860.47320.1981-0.4602-0.10330.29690.02440.09330.3730.2010.3532-26.924310.90262.52
41.3245-0.21070.38731.69620.05380.62560.0098-0.0959-0.6582-0.4950.11940.36820.1637-0.2439-0.11480.3843-0.0371-0.05350.31260.09060.4859-29.17066.4199-8.3358
51.20450.134-0.20321.8592-0.18551.0858-0.0936-0.2083-0.3997-0.06570.16590.21890.2688-0.1026-0.05780.30090.01490.01030.20640.10790.3302-20.28747.7574-3.1872
62.1820.528-0.63222.31080.2652.0534-0.03680.07710.0683-0.15420.2254-0.0271-0.1826-0.1567-0.16530.27750.0423-0.02380.22350.04930.2632-33.426259.077-21.2859
71.95280.3667-0.70861.67450.44281.12580.2431-0.09360.47110.07850.15010.1367-0.4779-0.0215-0.19430.38930.09630.05730.17540.05370.2987-33.657367.1044-15.9362
81.57910.2476-0.32891.71450.12451.8634-0.04620.0330.21950.04120.12830.6012-0.3043-0.6801-0.03240.3190.1739-0.03230.45250.11740.4784-50.930761.1837-15.9569
91.68210.69780.46440.88560.13910.661-0.1695-0.03590.7675-0.09860.31020.6463-0.6631-0.2595-0.17220.59110.13960.06750.33240.02440.538-41.444573.1453-12.596
101.3487-0.07740.12641.2247-0.31211.0079-0.0693-0.04420.0384-0.04590.10270.1543-0.0451-0.1452-0.03330.20630.0055-0.01370.17210.04220.1866-31.605630.7973-15.7207
112.2729-0.7140.30492.1327-0.83773.2677-0.0433-0.02360.1372-0.16550.0287-0.1733-0.31860.01990.02780.3067-0.0136-0.00620.20270.0150.1977-26.337933.5187-18.9139
120.4574-0.02740.271.2291-0.5391.23020.03210.0329-0.0537-0.02850.05130.1820.1054-0.1043-0.06860.24490.04230.01630.27450.03230.2199-37.351342.8357-2.8681
130.6790.40680.76452.1-1.37333.0430.1219-0.01870.21150.0385-0.1135-0.0202-0.3774-0.0109-0.04010.25970.05470.03910.29910.02720.2103-36.382749.4484-0.6884
145.6706-0.05070.66473.94871.1524.22060.34470.2975-0.6097-0.0330.0191-0.5380.44720.551-0.08290.27450.0806-0.00470.3274-0.00970.293-26.743340.23112.2159
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 16 THROUGH 80 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 81 THROUGH 123 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 124 THROUGH 164 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 165 THROUGH 196 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 197 THROUGH 244 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 16 THROUGH 80 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 81 THROUGH 123 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 124 THROUGH 225 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 227 THROUGH 244 )
10X-RAY DIFFRACTION10CHAIN I AND (RESID 1 THROUGH 35 )
11X-RAY DIFFRACTION11CHAIN I AND (RESID 36 THROUGH 58 )
12X-RAY DIFFRACTION12CHAIN J AND (RESID 1 THROUGH 35 )
13X-RAY DIFFRACTION13CHAIN J AND (RESID 36 THROUGH 47 )
14X-RAY DIFFRACTION14CHAIN J AND (RESID 48 THROUGH 58 )

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