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- PDB-3qy5: Microfluidic crystallization of Thaumatin using the Crystal Former -

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Basic information

Entry
Database: PDB / ID: 3qy5
TitleMicrofluidic crystallization of Thaumatin using the Crystal Former
ComponentsThaumatin-1
KeywordsPLANT PROTEIN
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
L(+)-TARTARIC ACID / Thaumatin I
Similarity search - Component
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsStojanoff, V. / Jankoncic, J. / Sommer, M.O.A.
CitationJournal: TO BE PUBLISHED
Title: Microfluidic crystallization of Thaumatin using the Crystal Former
Authors: Stojanoff, V. / Jankoncic, J. / Sommer, M.O.A.
History
DepositionMar 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 9, 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 / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: Thaumatin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3772
Polymers22,2271
Non-polymers1501
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.914, 57.914, 150.130
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: 22227.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thaumatococcus daniellii (katemfe) / References: UniProt: P02883
#2: Chemical ChemComp-TLA / L(+)-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.: 201 / 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: 56.56 %
Crystal growTemperature: 298 K / pH: 7.5
Details: Microfluidic crystallization using the Crystal Former, 0.1 M HEPES, 0.8 M potassium sodium tartrate tetrahydrate, pH 7.5, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 1, 2008
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.25→25 Å / Num. all: 71681 / Num. obs: 71466 / % possible obs: 99.7 % / Observed criterion σ(F): 1.8 / Observed criterion σ(I): 1.8 / Redundancy: 7.7 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 29.4
Reflection shellResolution: 1.25→1.27 Å / % possible all: 95.9

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Processing

Software
NameVersionClassification
HKL-3000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→23 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.955 / SU ML: 0.019 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.16955 3609 5.1 %RANDOM
Rwork0.1537 ---
all0.1545 67744 --
obs0.1545 67744 100 %-
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: 11.995 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2--0.23 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.25→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1545 0 10 201 1756
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221631
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.9582226
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5885217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.88623.23568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.13615250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.491512
X-RAY DIFFRACTIONr_chiral_restr0.0940.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021267
X-RAY DIFFRACTIONr_nbd_refined0.1980.2750
X-RAY DIFFRACTIONr_nbtor_refined0.310.21136
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2143
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.222
X-RAY DIFFRACTIONr_mcbond_it1.4321.51056
X-RAY DIFFRACTIONr_mcangle_it2.02121668
X-RAY DIFFRACTIONr_scbond_it2.6853654
X-RAY DIFFRACTIONr_scangle_it3.6774.5552
X-RAY DIFFRACTIONr_rigid_bond_restr1.41631710
X-RAY DIFFRACTIONr_sphericity_free7.0473201
X-RAY DIFFRACTIONr_sphericity_bonded4.28131581
LS refinement shellResolution: 1.25→1.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 237 -
Rwork0.206 4783 -
obs--100 %

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