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- PDB-3iir: Crystal Structure of Miraculin like protein from seeds of Murraya... -

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Basic information

Entry
Database: PDB / ID: 3iir
TitleCrystal Structure of Miraculin like protein from seeds of Murraya koenigii
ComponentsTrypsin inhibitor
KeywordsHYDROLASE INHIBITOR / beta-trefoil fold / Kunitz trypsin inhibitor
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
Trypsin inhibitor / Trypsin inhibitor
Similarity search - Component
Biological speciesMurraya koenigii (curry leaf)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsGahloth, D. / Selvakumar, P. / Shee, C. / Kumar, P. / Sharma, A.K.
CitationJournal: Arch.Biochem.Biophys. / Year: 2010
Title: Cloning, sequence analysis and crystal structure determination of a miraculin-like protein from Murraya koenigii
Authors: Gahloth, D. / Selvakumar, P. / Shee, C. / Kumar, P. / Sharma, A.K.
History
DepositionAug 3, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trypsin inhibitor
B: Trypsin inhibitor


Theoretical massNumber of molelcules
Total (without water)41,5192
Polymers41,5192
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-12 kcal/mol
Surface area18130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.795, 75.795, 150.848
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Trypsin inhibitor / miraculin like protein


Mass: 20759.291 Da / Num. of mol.: 2 / Fragment: UNP residues 26-215 / Source method: isolated from a natural source / Details: Seeds / Source: (natural) Murraya koenigii (curry leaf) / References: UniProt: D3G8R9, UniProt: D2YW43*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.61 Å3/Da / Density % sol: 52.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 6% PEG 8000, 0.1mM Tris-Cl pH 8.0, 0.08M Sodium Chloride, 0.08M Calcium Chloride, 8% Glycerol , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 26, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.9→25 Å / Num. obs: 10300 / % possible obs: 96.1 % / Observed criterion σ(I): 58581 / Redundancy: 5.6 % / Biso Wilson estimate: 51.9 Å2 / Rmerge(I) obs: 0.146 / Rsym value: 0.146 / Net I/σ(I): 4.7 / Num. measured all: 58581
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 4.7 / Num. unique all: 540 / Rsym value: 0.422 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1AVA

1ava


Resolution: 2.9→10 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.835 / SU B: 17.851 / SU ML: 0.347 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R Free: 0.497 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: weighted full matrix least squares procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.29452 473 4.8 %RANDOM
Rwork0.21618 ---
obs0.21985 9300 97.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.074 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2916 0 0 69 2985
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222982
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6681.9484062
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7945378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.19923.623138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.02515462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0081524
X-RAY DIFFRACTIONr_chiral_restr0.10.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022300
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2570.21206
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.21952
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2146
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3360.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3020.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5271.51918
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.85823024
X-RAY DIFFRACTIONr_scbond_it0.93231207
X-RAY DIFFRACTIONr_scangle_it1.5344.51038
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.969 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 31 -
Rwork0.289 647 -
obs-10300 99.41 %

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