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- PDB-2o9u: Monellin (MNEI) at 1.15 resolution -

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Basic information

Entry
Database: PDB / ID: 2o9u
TitleMonellin (MNEI) at 1.15 resolution
ComponentsMonellin chain B and Monellin chain A
KeywordsPLANT PROTEIN / alternative conformations / 3-10 polyproline II helix
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsHobbs, J.R. / Munger, S.D. / Conn, G.L.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Monellin (MNEI) at 1.15 A resolution
Authors: Hobbs, J.R. / Munger, S.D. / Conn, G.L.
History
DepositionDec 14, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Oct 25, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Monellin chain B and Monellin chain A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8035
Polymers11,4191
Non-polymers3844
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.103, 66.316, 27.154
Angle α, β, γ (deg.)90.000, 111.600, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Monellin chain B and Monellin chain A


Mass: 11419.049 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry)
Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: P02882, UniProt: P02881
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsREFER TO REF. 2 IN UNP DATABASE MONB_DIOCU(P02882).

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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: 1.99 Å3/Da / Density % sol: 38.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M Ammonium sulfate, 30% PEG4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 1, 2004
RadiationMonochromator: Diamond(111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.15→22.44 Å / Num. obs: 27957 / % possible obs: 88.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 9.4 Å2 / Rmerge(I) obs: 0.043
Reflection shellResolution: 1.15→1.21 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 4.5 / Num. unique all: 2513 / % possible all: 54.2

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N98

1n98
PDB Unreleased entry


Resolution: 1.15→22.44 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.234 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.165 1392 5 %RANDOM
Rwork0.131 ---
all0.201 ---
obs0.133 27957 88.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.723 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20.1 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.15→22.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1054 0 20 143 1217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0221121
X-RAY DIFFRACTIONr_bond_other_d0.0010.02999
X-RAY DIFFRACTIONr_angle_refined_deg2.1022.0061554
X-RAY DIFFRACTIONr_angle_other_deg1.23832383
X-RAY DIFFRACTIONr_dihedral_angle_1_deg15.2765149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.45224.42661
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.68115215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.212159
X-RAY DIFFRACTIONr_chiral_restr0.4580.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.021292
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02236
X-RAY DIFFRACTIONr_nbd_refined0.6650.2366
X-RAY DIFFRACTIONr_nbd_other0.3480.21282
X-RAY DIFFRACTIONr_nbtor_refined0.2760.2510
X-RAY DIFFRACTIONr_nbtor_other0.1070.2685
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.4510.2116
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.4110.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4320.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3980.285
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2520.225
X-RAY DIFFRACTIONr_mcbond_it3.5431.5820
X-RAY DIFFRACTIONr_mcbond_other1.4181.5250
X-RAY DIFFRACTIONr_mcangle_it4.36121063
X-RAY DIFFRACTIONr_scbond_it6.0873577
X-RAY DIFFRACTIONr_scangle_it7.3084.5470
X-RAY DIFFRACTIONr_rigid_bond_restr2.92232576
X-RAY DIFFRACTIONr_sphericity_free15.0263143
X-RAY DIFFRACTIONr_sphericity_bonded6.51832067
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.198 43 -
Rwork0.17 1091 -
obs-1134 47.67 %

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