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- PDB-2q33: Crystal structure of all-D monellin at 1.8 A resolution -

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Basic information

Entry
Database: PDB / ID: 2q33
TitleCrystal structure of all-D monellin at 1.8 A resolution
Components
  • D-MONELLIN CHAIN A
  • D-MONELLIN CHAIN B
KeywordsDE NOVO PROTEIN / ALPHA/BETA / ALL-D PROTEIN
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHung, L.-W. / Kohmura, M. / Ariyoshi, Y. / Kim, S.-H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structure of an Enantiomeric Protein, D-Monellin at 1.8 A Resolution.
Authors: Hung, L.-W. / Kohmura, M. / Ariyoshi, Y. / Kim, S.-H.
History
DepositionMay 29, 2007Deposition site: RCSB / Processing site: RCSB
SupersessionNov 13, 2007ID: 1N98
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / struct_conn / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Remark 999SEQUENCE THE L-AMINO VERSION OF THE PROTEINS IN CHAINS A AND B CORRESPOND TO THE SEQUENCES IN UNP ...SEQUENCE THE L-AMINO VERSION OF THE PROTEINS IN CHAINS A AND B CORRESPOND TO THE SEQUENCES IN UNP ENTRIES MONA_DIOCU AND MONB_DIOCU RESPECTIVELY

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-MONELLIN CHAIN A
B: D-MONELLIN CHAIN B


Theoretical massNumber of molelcules
Total (without water)10,6922
Polymers10,6922
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.400, 32.940, 41.110
Angle α, β, γ (deg.)90.00, 96.73, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-127-

HOH

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Components

#1: Protein/peptide D-MONELLIN CHAIN A / MONELLIN CHAIN I


Mass: 5098.772 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The enantiomeric protein was chemically synthesized with all D-amino acids. The sequence of the protein is naturally found in Dioscoreophyllum cumminsii.
#2: Protein/peptide D-MONELLIN CHAIN B / MONELLIN CHAIN II


Mass: 5593.396 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The enantiomeric protein was chemically synthesized with all D-amino acids. The sequence of the protein is naturally found in Dioscoreophyllum cumminsii.
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.54 Å3/Da / Density % sol: 51.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 20 MM SODIUM PHOSPHATE BUFFER, 28% PEG 8000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K, pH 7.20
Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mMsodium phosphate1reservoirpH7.2
228 %PEG80001reservoir
310 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1994 / Details: SYNCHROTRON
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.8→35 Å / Num. obs: 9511 / % possible obs: 90 % / Observed criterion σ(I): 3 / Redundancy: 3.5 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 11
Reflection shellResolution: 1.8→1.84 Å / % possible all: 70
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 30 Å / Num. obs: 17490 / Rmerge(I) obs: 0.045

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
MAR345data collection
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→6 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 735264.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED WITH ALL D-AMINO ACIDS. THIS STRUCTURE WAS DETERMINED AND REFINED WITH L-AMINO ACID PARAMETERS. THE ACTUAL ASYMMETRIC UNIT SHOULD CONTAIN THE PROTEIN ...Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED WITH ALL D-AMINO ACIDS. THIS STRUCTURE WAS DETERMINED AND REFINED WITH L-AMINO ACID PARAMETERS. THE ACTUAL ASYMMETRIC UNIT SHOULD CONTAIN THE PROTEIN REPRESENTED BY THIS COORDINATE FILE.
RfactorNum. reflection% reflectionSelection details
Rfree0.215 919 10.6 %RANDOM
Rwork0.175 ---
obs0.175 8665 87.7 %-
Displacement parametersBiso mean: 28.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å20.89 Å2
2--0.21 Å20 Å2
3---0.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms754 0 0 82 836
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.991.5
X-RAY DIFFRACTIONx_mcangle_it3.272
X-RAY DIFFRACTIONx_scbond_it3.482
X-RAY DIFFRACTIONx_scangle_it5.292.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.323 118 10.2 %
Rwork0.243 1040 -
obs--71.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 6 Å / Num. reflection all: 18438 / Num. reflection obs: 17490 / Rfactor Rfree: 0.222 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.61
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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