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- PDB-3zc9: Crystal Structure of Murraya koenigii Miraculin-Like Protein at 2... -

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Basic information

Entry
Database: PDB / ID: 3zc9
TitleCrystal Structure of Murraya koenigii Miraculin-Like Protein at 2.2 A resolution at pH 4.6
ComponentsTRYPSIN INHIBITOR
KeywordsHYDROLASE INHIBITOR / BETA-TREFOIL FOLD / KUNITZ SUPER-FAMILY
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
Biological speciesMURRAYA KOENIGII (curry leaf)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsSelvakumar, P. / Sharma, N. / Tomar, P.P.S. / Kumar, P. / Sharma, A.K.
CitationJournal: Proteins / Year: 2014
Title: Structural Insights Into the Aggregation Behavior of Murraya Koenigii Miraculin-Like Protein Below Ph 7.5.
Authors: Selvakumar, P. / Sharma, N. / Tomar, P.P.S. / Kumar, P. / Sharma, A.K.
History
DepositionNov 19, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Oct 16, 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


Theoretical massNumber of molelcules
Total (without water)20,7591
Polymers20,7591
Non-polymers00
Water1,24369
1
A: TRYPSIN INHIBITOR

A: TRYPSIN INHIBITOR


Theoretical massNumber of molelcules
Total (without water)41,5192
Polymers41,5192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1640 Å2
ΔGint-10.3 kcal/mol
Surface area15780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.620, 45.420, 38.790
Angle α, β, γ (deg.)90.00, 94.87, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein TRYPSIN INHIBITOR / MIRACULIN-LIKE PROTEIN


Mass: 20759.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MURRAYA KOENIGII (curry leaf) / Organ: SEEDS / References: UniProt: D2YW43
#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: 2.12 Å3/Da / Density % sol: 42.12 % / Description: NONE
Crystal growpH: 4.6
Details: 4M AMMONIUM ACETATE, 0.1M SODIUM ACETATE TRIHYDRATE PH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER / Wavelength: 1.54
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.21→50.63 Å / Num. obs: 7985 / % possible obs: 90 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.7
Reflection shellResolution: 2.21→2.33 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5.7 / % possible all: 60.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IIR

3iir


Resolution: 2.24→50.63 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.877 / SU B: 6.12 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.418 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES REFINED INDIVIDUALLY. RESIDUES 183-190 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.23798 384 4.8 %RANDOM
Rwork0.19127 ---
obs0.19352 7599 92.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.901 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å20 Å2-0.53 Å2
2--1.05 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.24→50.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1409 0 0 69 1478
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191442
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.9481965
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3885181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.05723.52968
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70115224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9981512
X-RAY DIFFRACTIONr_chiral_restr0.0810.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211114
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.8681.877727
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.62.813907
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.6211.874714
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: 2.236→2.294 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 30 -
Rwork0.249 505 -
obs--83.59 %

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