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- PDB-2g4y: structure of thaumatin at 2.0 A wavelength -

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Basic information

Entry
Database: PDB / ID: 2g4y
Titlestructure of thaumatin at 2.0 A wavelength
ComponentsThaumatin-1
KeywordsPLANT PROTEIN / thaumatin structure at a wavelength of 2 A
Function / homology
Function and homology information


cytoplasmic vesicle
Similarity search - Function
Thaumatin / Thaumatin / Thaumatin, conserved site / Thaumatin family signature. / Thaumatin family / Thaumatin family / Thaumatin family profile. / Thaumatin family / Osmotin/thaumatin-like superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
D(-)-TARTARIC ACID / Thaumatin I
Similarity search - Component
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.98 Å
AuthorsMueller-Dieckmann, C. / Weiss, M.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: On the routine use of soft X-rays in macromolecular crystallography. Part IV. Efficient determination of anomalous substructures in biomacromolecules using longer X-ray wavelengths.
Authors: Mueller-Dieckmann, C. / Panjikar, S. / Schmidt, A. / Mueller, S. / Kuper, J. / Geerlof, A. / Wilmanns, M. / Singh, R.K. / Tucker, P.A. / Weiss, M.S.
History
DepositionFeb 22, 2006Deposition site: RCSB / Processing site: RCSB
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 1.3Nov 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 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THERE ARE TWO ISOFORMS OF THAUMATION, I AND II. LYS46 FROM THE FORM I IS USED BECAUSE THE ...SEQUENCE THERE ARE TWO ISOFORMS OF THAUMATION, I AND II. LYS46 FROM THE FORM I IS USED BECAUSE THE CRYSTALLIZATION MATERIAL CONTAINS A MIXTURE OF LYS AND ASN. ASP IS USED AT POSITION 113 AS SUGGESTED BY KO ET AL., ACTA CRYST. D50,813(1994)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thaumatin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3932
Polymers22,2431
Non-polymers1501
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.900, 57.900, 150.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Thaumatin-1 / Thaumatin I


Mass: 22243.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thaumatococcus daniellii (katemfe) / References: UniProt: P02883
#2: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.83 Å3/Da / Density % sol: 56.57 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 2 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2 Å / Relative weight: 1
ReflectionResolution: 1.98→30 Å / Num. obs: 18622 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
CCP4(SCALA)data scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.98→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.378 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24311 385 2.1 %RANDOM
Rwork0.1939 ---
obs0.19493 18237 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20 Å2
2--0.5 Å20 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.98→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1557 0 10 100 1667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0221611
X-RAY DIFFRACTIONr_bond_other_d0.0010.021389
X-RAY DIFFRACTIONr_angle_refined_deg1.9671.962190
X-RAY DIFFRACTIONr_angle_other_deg0.95833246
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.535208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.83222.92365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55715246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1911512
X-RAY DIFFRACTIONr_chiral_restr0.1340.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021828
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02345
X-RAY DIFFRACTIONr_nbd_refined0.2030.2301
X-RAY DIFFRACTIONr_nbd_other0.1890.21344
X-RAY DIFFRACTIONr_nbtor_refined0.1850.2769
X-RAY DIFFRACTIONr_nbtor_other0.0920.2887
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.288
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2790.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2920.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4260.29
X-RAY DIFFRACTIONr_mcbond_it1.6731.51284
X-RAY DIFFRACTIONr_mcbond_other0.3621.5429
X-RAY DIFFRACTIONr_mcangle_it2.122.51648
X-RAY DIFFRACTIONr_scbond_it5.0245706
X-RAY DIFFRACTIONr_scangle_it6.59710541
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.196 23 -
Rwork0.235 1311 -
obs--100 %

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