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- PDB-3n03: Thaumatin crystals grown from drops -

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Basic information

Entry
Database: PDB / ID: 3n03
TitleThaumatin crystals grown from drops
ComponentsThaumatin-1
KeywordsPLANT PROTEIN / Crystals on loops / Thaumatin
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 / Rigid body with the coordinate for the loop method / Resolution: 1.5 Å
AuthorsMathews, I.I.
Citation
Journal: J.Appl.Crystallogr. / Year: 2010
Title: Diffraction study of protein crystals grown in cryoloops and micromounts.
Authors: Berger, M.A. / Decker, J.H. / Mathews, I.I.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Crystallization in the presence of glycerol displaces water molecules in the structure of thaumatin
Authors: Charron, C. / Kadri, A. / Robert, M.C. / Geige, R. / Lorber, B.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Improving radiation-damage substructures for RIP
Authors: Nanao, M.H. / Sheldrick, G.M. / Ravelli, R.B.G.
History
DepositionMay 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 20, 2013Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...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 / 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
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)22,4563
Polymers22,1561
Non-polymers3002
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.900, 57.900, 150.240
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: 22155.980 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.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.84 Å3/Da / Density % sol: 56.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 0.9M Sodium/potassium tartrate, 0.1M HEPES (pH 7.3), 15% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 25, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→29 Å / Num. all: 41768 / Num. obs: 41768 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 26.3
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 7.7 / Num. unique all: 3042 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: Rigid body with the coordinate for the loop method
Starting model: Coordinate for the structure of the crystals grown in loop (PDB code: 3N02).

3n02


Resolution: 1.5→27.68 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.448 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16335 2083 5 %RANDOM
Rwork0.14624 ---
obs0.14709 39637 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.151 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2--0.19 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.5→27.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1545 0 20 223 1788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221607
X-RAY DIFFRACTIONr_bond_other_d0.0010.021097
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.9612183
X-RAY DIFFRACTIONr_angle_other_deg0.90832656
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5975205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.69523.0366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.57615241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7221512
X-RAY DIFFRACTIONr_chiral_restr0.0970.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211822
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02343
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.941.51017
X-RAY DIFFRACTIONr_mcbond_other0.2691.5423
X-RAY DIFFRACTIONr_mcangle_it1.67221632
X-RAY DIFFRACTIONr_scbond_it2.6713590
X-RAY DIFFRACTIONr_scangle_it4.3074.5551
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.168 150 -
Rwork0.155 2882 -
obs--99.87 %
Refinement TLS params.Method: refined / Origin x: 12.2376 Å / Origin y: 24.0913 Å / Origin z: 32.8354 Å
111213212223313233
T0.007 Å20.0015 Å2-0.0006 Å2-0.0095 Å2-0.003 Å2--0.0074 Å2
L0.1735 °2-0.0191 °2-0.1145 °2-0.3249 °20.3487 °2--0.7022 °2
S-0.0124 Å °-0.0079 Å °-0.0147 Å °0.023 Å °0.0182 Å °-0.0084 Å °0.0069 Å °0.06 Å °-0.0058 Å °

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