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- PDB-1iv7: Crystal Structure of Single Chain Monellin -

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Basic information

Entry
Database: PDB / ID: 1iv7
TitleCrystal Structure of Single Chain Monellin
ComponentsMonellin
KeywordsPLANT PROTEIN / ALPHA+BETA
Function / homology
Function and homology information


Monellin, A chain / Monellin, A chain superfamily / Monellin, B chain / : / Monellin / Monellin / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Monellin chain A / Monellin chain B
Similarity search - Component
Biological speciesDioscoreophyllum cumminsii (serendipity berry)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsTamada, T. / Kato, Y. / Kuroki, R.
CitationJournal: To be Published
Title: The Effect of Single Chain Derivatization on the Structure and Stability of the Monellin
Authors: Kato, Y. / Tamada, T. / Sone, H. / Iijima, H. / Kuroki, R.
History
DepositionMar 15, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Monellin
B: Monellin


Theoretical massNumber of molelcules
Total (without water)22,5762
Polymers22,5762
Non-polymers00
Water1,910106
1
A: Monellin


Theoretical massNumber of molelcules
Total (without water)11,2881
Polymers11,2881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Monellin


Theoretical massNumber of molelcules
Total (without water)11,2881
Polymers11,2881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.650, 36.260, 46.380
Angle α, β, γ (deg.)90.00, 91.10, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein Monellin


Mass: 11287.853 Da / Num. of mol.: 2 / Mutation: E49N, N50E, E149N, N150E
Source method: isolated from a genetically manipulated source
Details: fusion protein concerning chain A comprise residues 1-50 (MONELLIN, CHAIN B) and 52-96 (MONELLIN, CHAIN A), Including glysine linker. fusion protein concerning chain B comprise residues 101- ...Details: fusion protein concerning chain A comprise residues 1-50 (MONELLIN, CHAIN B) and 52-96 (MONELLIN, CHAIN A), Including glysine linker. fusion protein concerning chain B comprise residues 101-150 (MONELLIN, CHAIN B) and 152-196 (MONELLIN, CHAIN A), Including glysine linker.
Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry)
Plasmid: pST6311 / Species (production host): Escherichia coli
Production host: Escherichia coli str. K12 substr. W3110 (bacteria)
Strain (production host): W3110 / References: UniProt: P02882, UniProt: P02881
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.51 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 7.2
Details: PEG8000, potassium phosphate, pH 7.2, micro batch, temperature 277K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200H / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 19, 1998
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→60 Å / Num. all: 18113 / Num. obs: 17026 / % possible obs: 94 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.067

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
REFMAC5refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MOL

1mol


Resolution: 1.82→15 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.762 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24084 870 5.1 %RANDOM
Rwork0.19983 ---
obs0.20202 16119 93.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.272 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å20.54 Å2
2--0.35 Å2-
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.82→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1596 0 0 106 1702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0221636
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2321.9672200
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9553190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.05615314
X-RAY DIFFRACTIONr_chiral_restr0.1540.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021278
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2670.3613
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.5164
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.331
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.513
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.4931.5954
X-RAY DIFFRACTIONr_mcangle_it2.67521540
X-RAY DIFFRACTIONr_scbond_it4.6253682
X-RAY DIFFRACTIONr_scangle_it7.4144.5660
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.824→1.871 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.363 59
Rwork0.349 1044

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