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- PDB-1mol: TWO CRYSTAL STRUCTURES OF A POTENTLY SWEET PROTEIN: NATURAL MONEL... -

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Basic information

Entry
Database: PDB / ID: 1mol
TitleTWO CRYSTAL STRUCTURES OF A POTENTLY SWEET PROTEIN: NATURAL MONELLIN AT 2.75 ANGSTROMS RESOLUTION AND SINGLE-CHAIN MONELLIN AT 1.7 ANGSTROMS RESOLUTION
ComponentsMONELLIN
KeywordsSWEET-TASTING PROTEIN
Function / homology
Function and homology information


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
Biological speciesDioscoreophyllum cumminsii (serendipity berry)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsSomoza, J.R. / Kim, S.-H.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Two crystal structures of a potently sweet protein. Natural monellin at 2.75 A resolution and single-chain monellin at 1.7 A resolution.
Authors: Somoza, J.R. / Jiang, F. / Tong, L. / Kang, C.H. / Cho, J.M. / Kim, S.H.
#1: Journal: J.Biomol.NMR / Year: 1992
Title: 1H Resonance Assignments, Secondary Structure and General Topology of Single-Chain Monellin in Solution as Determined by 1H-2D-NMR
Authors: Tomic, M.T. / Somoza, J.R. / Wemmer, D.E. / Park, Y.W. / Cho, J.M. / Kim, S.-H.
#2: Journal: Protein Eng. / Year: 1989
Title: Redesigning a Sweet Protein: Increased Stability and Renaturability
Authors: Kim, S.-H. / Kang, C.-H. / Kim, R. / Cho, J.M. / Lee, Y.-B. / Lee, T.-K.
History
DepositionApr 27, 1993Processing site: BNL
Revision 1.0May 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Remark 650HELIX THERE IS A SINGLE RIGHT-HANDED ALPHA-HELIX IN EACH OF THE MONOMERS PRESENT IN THE ASYMMETRIC UNIT.
Remark 700SHEET EACH OF THE MONOMERS IN THE ASYMMETRIC UNIT CONTAINS A SINGLE, FIVE-STRAND ANTIPARALLEL BETA-SHEET.

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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)22,1672
Polymers22,1672
Non-polymers00
Water2,414134
1
A: MONELLIN


Theoretical massNumber of molelcules
Total (without water)11,0841
Polymers11,0841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MONELLIN


Theoretical massNumber of molelcules
Total (without water)11,0841
Polymers11,0841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.360, 49.090, 40.720
Angle α, β, γ (deg.)90.00, 102.86, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO A 40 / 2: CIS PROLINE - PRO A 90 / 3: CIS PROLINE - PRO B 40 / 4: CIS PROLINE - PRO B 90

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Components

#1: Protein MONELLIN


Mass: 11083.628 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry)
References: UniProt: P02882
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: MONB_DIOCU SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE GLU 49 ASN A 49 ASN 50 GLU A 50

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.61 %
Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 mg/mlprotein1drop
210 mMsodium phosphate1drop
34 %(w/v)PEG80001drop
433 %(w/v)PEG80001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.6 Å / Num. obs: 19162 / % possible obs: 82.9 % / Observed criterion σ(I): 0 / Num. measured all: 59663 / Rmerge(I) obs: 0.0638

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.7→6 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.174 -
obs0.174 15053
Refinement stepCycle: LAST / Resolution: 1.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1566 0 0 134 1700
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.86
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection all: 17089 / Rfactor all: 0.188 / Rfactor obs: 0.174 / Rfactor Rwork: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23.6 Å2
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.86

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