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- PDB-4u30: Human mesotrypsin complexed with bikunin Kunitz domain 2 -

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Basic information

Entry
Database: PDB / ID: 4u30
TitleHuman mesotrypsin complexed with bikunin Kunitz domain 2
Components
  • Trypsin-3
  • Trypstatin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / serine protease / protease inhibitor / protein-protein interaction / protein degradation / proteolysis / substrate specificity / enzyme kinetics / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


Oxidoreductases; Acting on NADH or NADPH; With a heme protein as acceptor / calcium oxalate binding / Uptake of dietary cobalamins into enterocytes / IgA binding / heme catabolic process / negative regulation of immune response / negative regulation of JNK cascade / antimicrobial humoral response / Alpha-defensins / zymogen activation ...Oxidoreductases; Acting on NADH or NADPH; With a heme protein as acceptor / calcium oxalate binding / Uptake of dietary cobalamins into enterocytes / IgA binding / heme catabolic process / negative regulation of immune response / negative regulation of JNK cascade / antimicrobial humoral response / Alpha-defensins / zymogen activation / Antimicrobial peptides / endothelial cell migration / trypsin / calcium channel inhibitor activity / Scavenging of heme from plasma / digestion / serine-type peptidase activity / female pregnancy / serine-type endopeptidase inhibitor activity / tertiary granule lumen / carbohydrate binding / nuclear membrane / collagen-containing extracellular matrix / mitochondrial inner membrane / blood microparticle / oxidoreductase activity / cell adhesion / serine-type endopeptidase activity / calcium ion binding / heme binding / Neutrophil degranulation / cell surface / endoplasmic reticulum / protein homodimerization activity / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane / cytosol
Similarity search - Function
Protein AMBP / Alpha-1-microglobulin / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Lipocalin family conserved site / 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 ...Protein AMBP / Alpha-1-microglobulin / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Lipocalin family conserved site / 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 / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Few Secondary Structures / Irregular / Serine proteases, trypsin family, histidine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Lipocalin signature. / 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
Protein AMBP / Trypsin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsWang, R. / Soares, A.S. / Radisky, E.S.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Sequence and Conformational Specificity in Substrate Recognition: SEVERAL HUMAN KUNITZ PROTEASE INHIBITOR DOMAINS ARE SPECIFIC SUBSTRATES OF MESOTRYPSIN.
Authors: Pendlebury, D. / Wang, R. / Henin, R.D. / Hockla, A. / Soares, A.S. / Madden, B.J. / Kazanov, M.D. / Radisky, E.S.
History
DepositionJul 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Database references
Revision 1.2Dec 10, 2014Group: Database references
Revision 1.3Jan 7, 2015Group: Database references
Revision 1.4Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / refine_hist / struct_conn / struct_ref_seq_dif
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trypsin-3
B: Trypsin-3
C: Trypsin-3
D: Trypsin-3
X: Trypstatin
Y: Trypstatin
Z: Trypstatin
W: Trypstatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,00812
Polymers122,8488
Non-polymers1604
Water5,242291
1
A: Trypsin-3
X: Trypstatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7523
Polymers30,7122
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-19 kcal/mol
Surface area12140 Å2
MethodPISA
2
B: Trypsin-3
Z: Trypstatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7523
Polymers30,7122
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-18 kcal/mol
Surface area12160 Å2
MethodPISA
3
C: Trypsin-3
W: Trypstatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7523
Polymers30,7122
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-19 kcal/mol
Surface area12150 Å2
MethodPISA
4
D: Trypsin-3
Y: Trypstatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7523
Polymers30,7122
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-19 kcal/mol
Surface area12200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.000, 164.000, 81.021
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

#1: Protein
Trypsin-3 / / Brain trypsinogen / Mesotrypsinogen / Serine protease 3 / Serine protease 4 / Trypsin III / Trypsin IV


Mass: 24257.457 Da / Num. of mol.: 4 / Mutation: S195A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRSS3, PRSS4, TRY3, TRY4 / Production host: Escherichia coli (E. coli) / References: UniProt: P35030, trypsin
#2: Protein
Trypstatin


Mass: 6454.507 Da / Num. of mol.: 4 / Fragment: BPTI/Kunitz inhibitor 2 residues 285-338
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AMBP, HCP, ITIL / Production host: Komagataella pastoris (fungus) / References: UniProt: P02760
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 4.94 Å3/Da / Density % sol: 75 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1 M HEPES pH 7.0 and 1 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Type: OTHER / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 80120 / % possible obs: 99 % / Redundancy: 5.2 % / Net I/σ(I): 2

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Processing

SoftwareName: REFMAC / Version: 5.7.0029 / Classification: refinement
RefinementResolution: 2.5→44.75 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.862 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22284 4207 5 %RANDOM
Rwork0.18776 ---
obs0.18954 80120 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.669 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0.35 Å20 Å2
2---0.35 Å20 Å2
3---1.14 Å2
Refinement stepCycle: 1 / Resolution: 2.5→44.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8471 0 4 291 8766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0198704
X-RAY DIFFRACTIONr_bond_other_d0.0010.028136
X-RAY DIFFRACTIONr_angle_refined_deg1.9281.94511832
X-RAY DIFFRACTIONr_angle_other_deg0.9123.00718668
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.93751104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97424.409372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.503151376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3931540
X-RAY DIFFRACTIONr_chiral_restr0.1180.21264
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02110028
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022020
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.635 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.324 573 -
Rwork0.26 11729 -
obs--99.99 %

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