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- PDB-4mtb: Bovine trypsin in complex with small molecule inhibitor -

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Basic information

Entry
Database: PDB / ID: 4mtb
TitleBovine trypsin in complex with small molecule inhibitor
ComponentsCationic trypsin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / METAL-BINDING / DIGESTION / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / 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
Chem-BZY / IMIDAZOLE / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsWagner, S. / Heine, A. / Steinmetzer, T.
CitationJournal: To be Published
Title: X-ray structure of trypsin-inhibitor-complex
Authors: Wagner, S. / Heine, A. / Steinmetzer, T.
History
DepositionSep 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_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: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8314
Polymers23,3241
Non-polymers5073
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.959, 54.959, 108.059
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-733-

HOH

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Components

#1: Protein Cationic trypsin / Beta-trypsin


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-BZY / (2R)-2-amino-N-{(2S)-1-[(4-carbamimidoylbenzyl)amino]-1-oxopropan-2-yl}-4-(4-hydroxyphenyl)butanamide


Mass: 397.471 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N5O3
#4: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.02 Å3/Da / Density % sol: 39.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Ammonium phosphate, 20% PEG 8000, 0.1 M Imidazol, 0.1% Sodium azide, 10 mM Calcium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 18, 2013 / Details: Silicon, active surface 50 nm Rh-coated mirrors
RadiationMonochromator: Si-111 Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.22→40 Å / Num. all: 54536 / Num. obs: 54536 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 11.8 Å2 / Rsym value: 0.048 / Net I/σ(I): 29.7
Reflection shellResolution: 1.22→1.24 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 2647 / Rsym value: 0.422 / % possible all: 93.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.3_1479)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZFS PDB ENTRY

2zfs


Resolution: 1.22→35.715 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 14.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.164 2763 5.07 %random
Rwork0.1353 ---
obs0.1368 54484 95.5 %-
all-54489 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.22→35.715 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1613 0 35 336 1984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091738
X-RAY DIFFRACTIONf_angle_d1.392366
X-RAY DIFFRACTIONf_dihedral_angle_d12.467607
X-RAY DIFFRACTIONf_chiral_restr0.091267
X-RAY DIFFRACTIONf_plane_restr0.007308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2197-1.24080.25421320.23732507X-RAY DIFFRACTION94
1.2408-1.26330.18831420.1622613X-RAY DIFFRACTION98
1.2633-1.28760.22441490.15852612X-RAY DIFFRACTION98
1.2876-1.31390.28011360.21182595X-RAY DIFFRACTION98
1.3139-1.34250.16981390.12912653X-RAY DIFFRACTION98
1.3425-1.37370.16221380.11592622X-RAY DIFFRACTION98
1.3737-1.40810.1771400.11112637X-RAY DIFFRACTION99
1.4081-1.44610.14271480.10952644X-RAY DIFFRACTION99
1.4461-1.48870.16511310.10852655X-RAY DIFFRACTION99
1.4887-1.53680.1381280.09952667X-RAY DIFFRACTION99
1.5368-1.59170.13341620.09522634X-RAY DIFFRACTION99
1.5917-1.65540.13181440.0982682X-RAY DIFFRACTION99
1.6554-1.73070.14921390.1012692X-RAY DIFFRACTION99
1.7307-1.8220.14131760.10692668X-RAY DIFFRACTION100
1.822-1.93610.19671040.14751949X-RAY DIFFRACTION73
1.9361-2.08560.13771340.1192614X-RAY DIFFRACTION95
2.0856-2.29550.17861110.15912029X-RAY DIFFRACTION74
2.2955-2.62750.16241390.14552766X-RAY DIFFRACTION100
2.6275-3.31010.15611410.14982767X-RAY DIFFRACTION100
3.3101-35.72980.16961300.14212715X-RAY DIFFRACTION92

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