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- PDB-6jbp: Structure of MP-4 from Mucuna pruriens at 2.22 Angstroms -

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Basic information

Entry
Database: PDB / ID: 6jbp
TitleStructure of MP-4 from Mucuna pruriens at 2.22 Angstroms
ComponentsKunitz-type trypsin inhibitor-like 2 protein
KeywordsPLANT PROTEIN / Protease Inhibitor / Mucuna pruriens
Function / homology
Function and homology information


endopeptidase inhibitor activity
Similarity search - Function
Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature. / Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Kunitz inhibitor STI-like superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
Kunitz-type trypsin inhibitor-like 2 protein
Similarity search - Component
Biological speciesMucuna pruriens (plant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.217 Å
AuthorsJain, A. / Shikhi, M. / Kumar, A. / Kumar, A. / Nair, D.T. / Salunke, D.M.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2020
Title: The structure of MP-4 from Mucuna pruriens at 2.22 angstrom resolution.
Authors: Jain, A. / Kumar, A. / Shikhi, M. / Kumar, A. / Nair, D.T. / Salunke, D.M.
#1: Journal: J. Biol. Chem. / Year: 2016
Title: MP-4 Contributes to Snake Venom Neutralization by Mucuna pruriens Seeds through an Indirect Antibody-mediated Mechanism.
Authors: Kumar, A. / Gupta, C. / Nair, D.T. / Salunke, D.M.
History
DepositionJan 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Kunitz-type trypsin inhibitor-like 2 protein


Theoretical massNumber of molelcules
Total (without water)20,1101
Polymers20,1101
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9040 Å2
Unit cell
Length a, b, c (Å)75.460, 75.460, 94.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Kunitz-type trypsin inhibitor-like 2 protein


Mass: 20110.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mucuna pruriens (plant) / References: UniProt: A0A371E4L6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 3.85 Å3/Da / Density % sol: 68.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 50mM Tris-HCl pH 9.5, 1.5M ammonium sulfate

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: Xenocs GeniX 3D Cu HF / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.21→53.7 Å / Num. obs: 15843 / % possible obs: 99.2 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.026 / Rrim(I) all: 0.072 / Net I/σ(I): 23.8
Reflection shellResolution: 2.21→2.33 Å / Redundancy: 7 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 5.9 / Num. unique obs: 2151 / Rpim(I) all: 0.129 / Rrim(I) all: 0.348 / % possible all: 94.2

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DSS

5dss


Resolution: 2.217→38.218 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / Phase error: 19.87
RfactorNum. reflection% reflectionSelection details
Rfree0.2203 771 4.86 %Random Selection
Rwork0.1795 ---
obs0.1814 15811 99.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.217→38.218 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1414 0 0 88 1502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061449
X-RAY DIFFRACTIONf_angle_d0.7731968
X-RAY DIFFRACTIONf_dihedral_angle_d9.266863
X-RAY DIFFRACTIONf_chiral_restr0.051210
X-RAY DIFFRACTIONf_plane_restr0.005262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2167-2.29590.28771160.21542721X-RAY DIFFRACTION95
2.2959-2.38780.23911530.20442780X-RAY DIFFRACTION100
2.3878-2.49650.29081570.20112833X-RAY DIFFRACTION100
2.4965-2.62810.28451790.20742828X-RAY DIFFRACTION100
2.6281-2.79270.21871360.19952837X-RAY DIFFRACTION100
2.7927-3.00830.24471450.20392820X-RAY DIFFRACTION100
3.0083-3.31080.20631460.18982833X-RAY DIFFRACTION100
3.3108-3.78950.21791260.1612861X-RAY DIFFRACTION100
3.7895-4.7730.15711610.14032797X-RAY DIFFRACTION100
4.773-38.22360.21631200.17262881X-RAY DIFFRACTION100

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