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- PDB-9p15: Thaumatin Room-Temperature In-Situ, Shipped -

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Basic information

Entry
Database: PDB / ID: 9p15
TitleThaumatin Room-Temperature In-Situ, Shipped
ComponentsThaumatin I
KeywordsPLANT PROTEIN / monomer
Function / homology
Function and homology information


cytoplasmic vesicle
Similarity search - Function
Thaumatin, conserved site / Thaumatin family signature. / Thaumatin family / Thaumatin family / Thaumatin family profile. / Thaumatin family / Osmotin/thaumatin-like superfamily
Similarity search - Domain/homology
L(+)-TARTARIC ACID / Thaumatin I
Similarity search - Component
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsSnell, M.E. / Campomizzi, C.S. / Mikolajek, H. / Sandy, J. / Sanchez-Weatherby, J. / Budziszewski, G.R. / Hough, M.A. / Bowman, S.E.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM141273 United States
CitationJournal: Biorxiv / Year: 2025
Title: Does crossing the pond affect crystal quality?
Authors: Campomizzi, C.S. / Snell, M.E. / Mikolajek, H. / Sandy, J. / Sanchez-Weatherby, J. / Budziszewski, G.R. / Russi, S. / Howells Jr., R. / Cohen, A. / Hough, M.A. / Bowman, S.E.J.
History
DepositionJun 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thaumatin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3782
Polymers22,2281
Non-polymers1501
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.202, 58.202, 150.459
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Thaumatin I / Thaumatin-1


Mass: 22228.043 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.: 149 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.87 Å3/Da / Density % sol: 57.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.59 M di-ammonium tartrate

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: VMXi / Wavelength: 0.7749 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Oct 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.67→54.2 Å / Num. obs: 31026 / % possible obs: 100 % / Redundancy: 14.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.052 / Rrim(I) all: 0.157 / Net I/σ(I): 11.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.99-54.2812.30.0282571810.010.03
1.67-1.75.91.89514530.3721.1592.236

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
MOLREPphasing
Cootmodel building
xia2.multiplexdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→54.2 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.874 / SU ML: 0.057 / Cross valid method: FREE R-VALUE / ESU R: 0.071 / ESU R Free: 0.073
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1777 1539 4.974 %
Rwork0.1522 29401 -
all0.153 --
obs-30940 99.987 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.717 Å2
Baniso -1Baniso -2Baniso -3
1-0.456 Å20 Å20 Å2
2--0.456 Å20 Å2
3----0.912 Å2
Refinement stepCycle: LAST / Resolution: 1.67→54.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1519 0 10 149 1678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121606
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161425
X-RAY DIFFRACTIONr_angle_refined_deg1.9351.7962198
X-RAY DIFFRACTIONr_angle_other_deg0.7021.7283304
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9185221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.959
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34110235
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.5291064
X-RAY DIFFRACTIONr_chiral_restr0.0930.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021959
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02379
X-RAY DIFFRACTIONr_nbd_refined0.2510.2308
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.21371
X-RAY DIFFRACTIONr_nbtor_refined0.1940.2841
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0940.2893
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.4760.2116
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3070.25
X-RAY DIFFRACTIONr_nbd_other0.170.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.10.212
X-RAY DIFFRACTIONr_mcbond_it2.0572.052839
X-RAY DIFFRACTIONr_mcbond_other2.0522.051839
X-RAY DIFFRACTIONr_mcangle_it2.9383.6671051
X-RAY DIFFRACTIONr_mcangle_other2.9433.6691052
X-RAY DIFFRACTIONr_scbond_it3.5832.37767
X-RAY DIFFRACTIONr_scbond_other3.5852.37766
X-RAY DIFFRACTIONr_scangle_it5.4274.1741139
X-RAY DIFFRACTIONr_scangle_other5.4274.1741139
X-RAY DIFFRACTIONr_lrange_it6.44721.4371850
X-RAY DIFFRACTIONr_lrange_other6.33320.811825
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.7140.3071020.3172152X-RAY DIFFRACTION99.9557
1.714-1.760.3241070.2922066X-RAY DIFFRACTION99.954
1.76-1.8110.252970.2632018X-RAY DIFFRACTION100
1.811-1.8670.2251000.231954X-RAY DIFFRACTION100
1.867-1.9280.2211000.1931907X-RAY DIFFRACTION99.9502
1.928-1.9960.21720.1741873X-RAY DIFFRACTION100
1.996-2.0710.162980.1561799X-RAY DIFFRACTION100
2.071-2.1560.1621020.1471702X-RAY DIFFRACTION100
2.156-2.2510.197950.1511633X-RAY DIFFRACTION100
2.251-2.3610.183740.1431602X-RAY DIFFRACTION100
2.361-2.4880.196940.141502X-RAY DIFFRACTION100
2.488-2.6390.192690.1421450X-RAY DIFFRACTION100
2.639-2.8210.164820.1351335X-RAY DIFFRACTION99.9295
2.821-3.0460.16750.141277X-RAY DIFFRACTION100
3.046-3.3360.163590.1431177X-RAY DIFFRACTION100
3.336-3.7280.14540.1211085X-RAY DIFFRACTION100
3.728-4.3010.125400.1971X-RAY DIFFRACTION100
4.301-5.2590.144450.099832X-RAY DIFFRACTION100
5.259-7.4030.155490.148653X-RAY DIFFRACTION100
7.403-54.20.159250.161413X-RAY DIFFRACTION100

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