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- PDB-4mon: ORTHORHOMBIC MONELLIN -

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Basic information

Entry
Database: PDB / ID: 4mon
TitleORTHORHOMBIC MONELLIN
Components(MONELLIN) x 2
KeywordsSWEET-TASTING PROTEIN / ORTHORHOMBIC CRYSTALS
Function / homology
Function and homology information


Helix Hairpins - #2000 / N-terminal domain of TfIIb - #130 / Monellin, A chain / Monellin, A chain superfamily / Monellin, B chain / Monellin / Monellin / N-terminal domain of TfIIb / Cystatin superfamily / Other non-globular ...Helix Hairpins - #2000 / N-terminal domain of TfIIb - #130 / 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: 2.3 Å
AuthorsBujacz, G. / Wlodawer, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Structure of monellin refined to 2.3 a resolution in the orthorhombic crystal form.
Authors: Bujacz, G. / Miller, M. / Harrison, R. / Thanki, N. / Gilliland, G.L. / Ogata, C.M. / Kim, S.H. / Wlodawer, A.
History
DepositionMar 4, 1997Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,4984
Polymers22,4984
Non-polymers00
Water3,243180
1
A: MONELLIN
B: MONELLIN


Theoretical massNumber of molelcules
Total (without water)11,2492
Polymers11,2492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-18 kcal/mol
Surface area5830 Å2
MethodPISA
2
C: MONELLIN
D: MONELLIN


Theoretical massNumber of molelcules
Total (without water)11,2492
Polymers11,2492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-17 kcal/mol
Surface area6170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.000, 112.420, 40.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein/peptide MONELLIN /


Mass: 5407.167 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PROTEIN EXTRACTED FROM BERRIES
Source: (natural) Dioscoreophyllum cumminsii (serendipity berry)
References: UniProt: P02881
#2: Protein/peptide MONELLIN /


Mass: 5841.647 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PROTEIN EXTRACTED FROM BERRIES
Source: (natural) Dioscoreophyllum cumminsii (serendipity berry)
References: UniProt: P02882
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPHE 1, RESIDUE PHE 1, NOTED IN SWISS-PROT P02881 AS {VARIANT...MISSING (IN 90% OF THE CHAINS)}, IS ...PHE 1, RESIDUE PHE 1, NOTED IN SWISS-PROT P02881 AS {VARIANT...MISSING (IN 90% OF THE CHAINS)}, IS NOT VISIBLE IN THIS STRUCTURE. THE SEQUENCE OF THE LAST TWO RESIDUES OF THE B/D CHAIN HAS BEEN REMARK 999 GIVEN AS EITHER ASNGLU OR GLUASN, DEPENDING ON THE SOURCE OF THE DATA. THE SEQUENCE USED HERE WAS PREVIOUSLY REPORTED IN THE FILE 3MON, WHICH WAS UTILIZED FOR MOLECULAR REPLACEMENT. WHILE THIS SEQUENCE IS MOST LIKELY INCORRECT (SEE BELOW), IT WAS NOT MODIFIED, SINCE THE ELECTRON DENSITY IN THIS REGION WAS NOT SUFFICIENTLY GOOD TO DISTINGUISH BETWEEN THE TWO POSSIBILITIES AND THE AUTHORS PREFERRED TO REMAIN COMPATIBLE WITH THE PREVIOUS ENTRY.

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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: 2.84 Å3/Da / Density % sol: 54.45 %
Description: REJECTION CRITERIA DEFAULT FOR DATA COLLECTION USING XENGEN IS -3 SIGMA; THIS VALUE WAS NOT ALLOWED BY PDB DEPOSITION SOFTWARE.
Crystal growpH: 7.2
Details: 5-10 MG/ML PROTEIN DISSOLVED IN 100 MM SODIUM PHOSPHATE BUFFER, PH 7.2, DIFFUSED AGAINST 20 W/V % ETHANOL. CRYSTALS UNSTABLE- CROSSLINKED WITH 0.015% GLUTARALDEHYDE FOR 1-1.5 HOURS.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 %(v/v)ethanol1drop
25-10 mgprotein1drop
3100 mMsodium phosphate1reservoirpH7.2

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Sep 1, 1985 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→99 Å / Num. obs: 10602 / % possible obs: 90.9 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.066
Reflection
*PLUS
Num. all: 11667 / Num. measured all: 36281 / Rmerge(I) obs: 0.066

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Processing

Software
NameClassification
MERLOTphasing
PROFFTrefinement
XENGENdata reduction
XENGENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MON

3mon


Resolution: 2.3→8 Å / σ(F): 2
Details: INITIAL REFINEMENT PERFORMED WITH X-PLOR, FOLLOWED BY MODEL BUILDING WITH FRODO AND FURTHER REFINEMENT WITH PROLSQ (PROFFT VERSION).
RfactorNum. reflection% reflection
Rwork0.15 --
obs-7607 66.8 %
Displacement parametersBiso mean: 44.25 Å2
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1568 0 0 180 1748
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0330.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0390.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.5681.5
X-RAY DIFFRACTIONp_mcangle_it2.7512
X-RAY DIFFRACTIONp_scbond_it2.1482
X-RAY DIFFRACTIONp_scangle_it5.083
X-RAY DIFFRACTIONp_plane_restr0.0110.018
X-RAY DIFFRACTIONp_chiral_restr0.0960.1
X-RAY DIFFRACTIONp_singtor_nbd0.2340.5
X-RAY DIFFRACTIONp_multtor_nbd0.3180.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2830.5
X-RAY DIFFRACTIONp_planar_tor5.47.5
X-RAY DIFFRACTIONp_staggered_tor24.110
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor15.410
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Lowest resolution: 8 Å / Rfactor obs: 0.15 / Rfactor Rwork: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS

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