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- PDB-1sbw: CRYSTAL STRUCTURE OF MUNG BEAN INHIBITOR LYSINE ACTIVE FRAGMENT C... -

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Basic information

Entry
Database: PDB / ID: 1sbw
TitleCRYSTAL STRUCTURE OF MUNG BEAN INHIBITOR LYSINE ACTIVE FRAGMENT COMPLEX WITH BOVINE BETA-TRYPSIN AT 1.8A RESOLUTION
Components
  • PROTEIN (BETA-TRYPSIN)
  • PROTEIN (MUNG BEAN INHIBITOR LYSIN ACTIVE FRAGMENT)
KeywordsHYDROLASE/HYDROLASE INHIBITOR / COMPLEX(PROTEINASE-INHIBITOR) / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Bowman-Birk serine protease inhibitor family / Bowman-Birk serine protease inhibitors family signature. / Proteinase inhibitor I12, Bowman-Birk / Bowman-Birk type proteinase inhibitor / Bowman-Birk type proteinase inhibitor / : / 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. ...Bowman-Birk serine protease inhibitor family / Bowman-Birk serine protease inhibitors family signature. / Proteinase inhibitor I12, Bowman-Birk / Bowman-Birk type proteinase inhibitor / Bowman-Birk type proteinase inhibitor / : / 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
Serine protease 1 / Bowman-Birk type trypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (cattle)
Vigna radiata (mung bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHuang, Q. / Zhu, Y. / Chi, C. / Tang, Y.
CitationJournal: J.Biomol.Struct.Dyn. / Year: 1999
Title: Crystal structure of mung bean inhibitor lysine active fragment complex with bovine beta-trypsin at 1.8A resolution.
Authors: Zhu, Y. / Huang, Q. / Chi, C.
History
DepositionApr 29, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0May 6, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_ref_seq_dif / 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_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_ref_seq_dif.details / _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: PROTEIN (BETA-TRYPSIN)
I: PROTEIN (MUNG BEAN INHIBITOR LYSIN ACTIVE FRAGMENT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4074
Polymers27,2712
Non-polymers1362
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-29 kcal/mol
Surface area9220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.270, 63.550, 69.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN (BETA-TRYPSIN) / EC 3.4.21.4


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREATIC / References: UniProt: P00760, trypsin
#2: Protein/peptide PROTEIN (MUNG BEAN INHIBITOR LYSIN ACTIVE FRAGMENT)


Mass: 3946.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: P01062
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 3 Å3/Da / Density % sol: 57 %
Crystal growpH: 6 / Details: pH 6.0

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 1, 1997
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→70 Å / Num. obs: 23601 / % possible obs: 88.8 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 12
Reflection shellResolution: 1.8→1.88 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.038 / % possible all: 70.7

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Processing

SoftwareName: X-PLOR / Version: 3.8 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TLD

1tld


Resolution: 1.8→70 Å / Isotropic thermal model: RESTRAINED / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1137 4.82 %RANDOM
Rwork0.164 ---
obs-23601 88.8 %-
Displacement parametersBiso mean: 19.48 Å2
Refinement stepCycle: LAST / Resolution: 1.8→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1734 0 6 272 2012
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.45
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.17
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
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 1.8→1.88 Å / Total num. of bins used: 127
RfactorNum. reflection% reflection
Rfree0.224 127 11.1 %
Rwork0.173 2307 -
obs--74.64 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARHCSDX.PROTOPHCSDX.PRO

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