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- PDB-3t62: Crystal structure of recombinant Kunitz Type serine protease Inhi... -

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Basic information

Entry
Database: PDB / ID: 3t62
TitleCrystal structure of recombinant Kunitz Type serine protease Inhibitor-1 from the Caribbean Sea anemone Stichodactyla helianthus in complex with bovine chymotrypsin
Components
  • Chymotrypsinogen A
  • Kunitz-type proteinase inhibitor SHPI-1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / chymotrypsin-inhibitor complex / Kunitz-type serine protease inhibitor / secreted / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


nematocyst / chymotrypsin / aspartic-type endopeptidase inhibitor activity / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / serine-type endopeptidase activity / proteolysis / extracellular region
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 ...: / 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 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
Chymotrypsinogen A / PI-stichotoxin-She2a
Similarity search - Component
Biological speciesStichodactyla helianthus (sea anemone)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGarcia-Fernandez, R. / Dominguez, R. / Oberthuer, D. / Pons, T. / Gonzalez-Gonzalez, Y. / Chavez, M.A. / Betzel, C. / Redecke, L.
CitationJournal: To be Published
Title: Structural insights into chymotrypsin inhibition by the Kunitz-type inhibitor-1 from the marine invertebrate Stichodactyla helianthus
Authors: Garcia-Fernandez, R. / Dominguez, R. / Oberthuer, D. / Pons, T. / Gonzalez-Gonzalez, Y. / Chavez, M.A. / Betzel, C. / Redecke, L.
History
DepositionJul 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chymotrypsinogen A
D: Kunitz-type proteinase inhibitor SHPI-1
B: Chymotrypsinogen A
E: Kunitz-type proteinase inhibitor SHPI-1
C: Chymotrypsinogen A
F: Kunitz-type proteinase inhibitor SHPI-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,89213
Polymers95,2206
Non-polymers6727
Water9,962553
1
A: Chymotrypsinogen A
D: Kunitz-type proteinase inhibitor SHPI-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9324
Polymers31,7402
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-37 kcal/mol
Surface area12550 Å2
MethodPISA
2
B: Chymotrypsinogen A
E: Kunitz-type proteinase inhibitor SHPI-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2207
Polymers31,7402
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-79 kcal/mol
Surface area12360 Å2
MethodPISA
3
C: Chymotrypsinogen A
F: Kunitz-type proteinase inhibitor SHPI-1


Theoretical massNumber of molelcules
Total (without water)31,7402
Polymers31,7402
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-14 kcal/mol
Surface area12460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.706, 199.706, 54.572
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Chymotrypsinogen A / alpha-chymotrypsin A


Mass: 25686.037 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: pancreas / References: UniProt: P00766, chymotrypsin
#2: Protein Kunitz-type proteinase inhibitor SHPI-1


Mass: 6053.913 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stichodactyla helianthus (sea anemone) / Production host: Pichia pastoris (fungus) / Strain (production host): KM71H / References: UniProt: P31713
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 553 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.21 Å3/Da / Density % sol: 44.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M ammonium sulfate, 30% PEG8000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 1.5 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 2, 2010
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 1.99→29.216 Å / Num. all: 55522 / Num. obs: 55522 / % possible obs: 99.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 10.2
Reflection shellResolution: 1.99→2.1 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.043 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MTN

1mtn


Resolution: 2→22.508 Å / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8518 / SU ML: 0.26 / σ(F): 1.97 / Phase error: 22.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2329 1968 3.6 %RANDOM
Rwork0.1897 ---
obs0.1913 54651 99.73 %-
all-55522 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.052 Å2 / ksol: 0.316 e/Å3
Displacement parametersBiso max: 268.57 Å2 / Biso mean: 48.4405 Å2 / Biso min: 6.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.439 Å20 Å20 Å2
2---0.439 Å2-0 Å2
3---0.8779 Å2
Refinement stepCycle: LAST / Resolution: 2→22.508 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6540 0 35 553 7128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086798
X-RAY DIFFRACTIONf_angle_d1.0889226
X-RAY DIFFRACTIONf_chiral_restr0.0711045
X-RAY DIFFRACTIONf_plane_restr0.0041170
X-RAY DIFFRACTIONf_dihedral_angle_d12.8322363
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.28671420.248838173959100
2.05-2.10540.29391400.228537193859100
2.1054-2.16730.26881420.220537983940100
2.1673-2.23720.30141390.28337533892100
2.2372-2.31710.4121390.344537393878100
2.3171-2.40980.28581420.225238053947100
2.4098-2.51930.24171410.197837513892100
2.5193-2.65190.21131410.177237683909100
2.6519-2.81780.23651410.176337863927100
2.8178-3.03490.20161410.184237803921100
3.0349-3.33940.24681410.176837633904100
3.3394-3.82060.22611400.177837273867100
3.8206-4.80580.17361400.13293752389299
4.8058-22.50930.18221390.16543725386498
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)
10.61380.07380.26711.2726-0.71781.0272-0.0299-0.0167-0.0020.0080.031-0.0519-0.05290.05780.00130.0493-0.0334-0.01530.0713-0.00170.02537.697636.46022.0702
21.8911-0.1708-0.78940.64710.26661.1052-0.04070.00440.1754-0.05340.05740.06210.0756-0.0168-0.02170.0751-0.0358-0.05870.02270.02320.081312.10919.9143-29.088
37.0656-1.7473-1.55190.96430.26531.1673-0.4642-1.1383-0.9950.13070.2802-0.15840.25420.23170.16760.16610.07330.04860.30220.18440.510877.421322.7124.4821
41.7809-1.00290.06091.50110.33770.12860.3760.9426-0.2494-0.5553-0.29440.077-0.05780.4607-0.0670.20670.10960.09670.5448-0.13860.095353.971529.0663-17.1187
50.8978-0.2619-0.21111.3747-0.49040.1913-0.2817-0.2849-0.05970.78310.0776-0.0582-0.27080.25330.220.32260.03750.01550.14910.05970.036613.45144.1402-8.186
60.43010.62010.06860.8649-0.02550.4501-0.15980.1402-0.5608-0.20910.2861-0.15140.0677-0.3314-0.26870.8691-0.2229-0.01290.7980.361.804563.24050.49093.6767
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 245
2X-RAY DIFFRACTION2chain BB1 - 245
3X-RAY DIFFRACTION3chain CC1 - 245
4X-RAY DIFFRACTION4chain DD3 - 56
5X-RAY DIFFRACTION5chain EE3 - 56
6X-RAY DIFFRACTION6chain FF3 - 56

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