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- PDB-1krl: Crystal Structure of Racemic DL-monellin in P-1 -

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Basic information

Entry
Database: PDB / ID: 1krl
TitleCrystal Structure of Racemic DL-monellin in P-1
Components
  • MONELLIN, CHAIN A
  • MONELLIN, CHAIN B
KeywordsPLANT PROTEIN / alpha-beta
Function / homology
Function and homology information


N-terminal domain of TfIIb - #130 / Helix Hairpins - #2000 / Monellin, A chain / Monellin, A chain superfamily / Monellin, B chain / : / Monellin / Monellin / N-terminal domain of TfIIb / Cystatin superfamily ...N-terminal domain of TfIIb - #130 / Helix Hairpins - #2000 / Monellin, A chain / Monellin, A chain superfamily / Monellin, B chain / : / Monellin / Monellin / N-terminal domain of TfIIb / Cystatin superfamily / Other non-globular / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
Monellin chain A / Monellin chain B
Similarity search - Component
Biological speciesDioscoreophyllum cumminsii (serendipity berry)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHung, L.W. / Kohmura, M. / Ariyoshi, Y. / Kim, S.H.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Structural differences in D and L-monellin in the crystals of racemic mixture.
Authors: Hung, L.W. / Kohmura, M. / Ariyoshi, Y. / Kim, S.H.
History
DepositionJan 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 28, 2012Group: Other
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MONELLIN, CHAIN A
B: MONELLIN, CHAIN B
C: MONELLIN, CHAIN A
D: MONELLIN, CHAIN B


Theoretical massNumber of molelcules
Total (without water)22,2034
Polymers22,2034
Non-polymers00
Water4,234235
1
A: MONELLIN, CHAIN A
B: MONELLIN, CHAIN B


Theoretical massNumber of molelcules
Total (without water)11,1022
Polymers11,1022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: MONELLIN, CHAIN A
D: MONELLIN, CHAIN B


Theoretical massNumber of molelcules
Total (without water)11,1022
Polymers11,1022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.710, 49.070, 53.120
Angle α, β, γ (deg.)90.55, 94.33, 90.31
Int Tables number2
Space group name H-MP-1

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Components

#1: Protein/peptide MONELLIN, CHAIN A / CHAIN I


Mass: 5259.993 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Dioscoreophyllum cumminsii (serendipity berry)
References: UniProt: P02881
#2: Protein/peptide MONELLIN, CHAIN B / CHAIN II


Mass: 5841.647 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry)
References: UniProt: P02882
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.26 Å3/Da / Density % sol: 45.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: Phosphate buffer, PEG8000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12 mg/mlsynthetic L-monellin1drop
22 mg/mlsynthetic D-monellin1drop
310 mMsodium phosphate1droppH7.2
414 %(w/v)PEG80001drop
510 mMsodium phosphate1reservoirpH7.2
628 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 10, 1994 / Details: Yale mirrors
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→25 Å / Num. all: 36070 / Num. obs: 31453 / % possible obs: 87.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 10.3 Å2 / Rmerge(I) obs: 0.046
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 2.3 / Num. unique all: 31453 / % possible all: 41.8
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 31489

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Single Chain Monellin

Resolution: 1.9→6 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 267815.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.293 2178 9.8 %RANDOM
Rwork0.249 ---
obs-22299 74.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 129.389 Å2 / ksol: 0.795121 e/Å3
Displacement parametersBiso mean: 28.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20.47 Å2-0.48 Å2
2--0.74 Å2-0.67 Å2
3----0.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1532 0 0 235 1767
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.03
X-RAY DIFFRACTIONx_angle_deg2.8
X-RAY DIFFRACTIONx_dihedral_angle_d26.3
X-RAY DIFFRACTIONx_improper_angle_d3.18
X-RAY DIFFRACTIONx_mcbond_it3.721.5
X-RAY DIFFRACTIONx_mcangle_it4.72
X-RAY DIFFRACTIONx_scbond_it4.162
X-RAY DIFFRACTIONx_scangle_it5.152.5
LS refinement shellResolution: 1.9→2.01 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.308 264 9.5 %
Rwork0.306 2517 -
obs--56.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 6 Å / Num. reflection all: 26867 / Num. reflection obs: 23409 / σ(F): 2 / % reflection Rfree: 9.8 % / Rfactor obs: 0.255 / Rfactor Rfree: 0.298
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.76
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg3.18
X-RAY DIFFRACTIONx_mcbond_it3.721.5
X-RAY DIFFRACTIONx_scbond_it4.162
X-RAY DIFFRACTIONx_mcangle_it4.72
X-RAY DIFFRACTIONx_scangle_it5.152.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.308 / % reflection Rfree: 9.5 % / Rfactor Rwork: 0.306

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