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- PDB-2pe7: Thaumatin from Thaumatococcus Danielli in complex with tris-dipic... -

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Basic information

Entry
Database: PDB / ID: 2pe7
TitleThaumatin from Thaumatococcus Danielli in complex with tris-dipicolinate Europium
ComponentsPreprothaumatin I
KeywordsPLANT PROTEIN / Thaumatin / Tris-dipicolinate Europium
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
EUROPIUM ION / PYRIDINE-2,6-DICARBOXYLIC ACID / L(+)-TARTARIC ACID / Thaumatin I / Thaumatin I
Similarity search - Component
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.46 Å
AuthorsPompidor, G. / Vicat, J. / Kahn, R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: A dipicolinate lanthanide complex for solving protein structures using anomalous diffraction.
Authors: Pompidor, G. / Maury, O. / Vicat, J. / Kahn, R.
History
DepositionApr 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Aug 30, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _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

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Assembly

Deposited unit
A: Preprothaumatin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1827
Polymers22,2281
Non-polymers9536
Water6,323351
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.550, 57.550, 149.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-601-

EU

21A-602-

PDC

31A-602-

PDC

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Components

#1: Protein Preprothaumatin I


Mass: 22228.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thaumatococcus daniellii (katemfe) / References: UniProt: A1IIJ1, UniProt: P02883*PLUS
#2: Chemical ChemComp-EU / EUROPIUM ION / Europium


Mass: 151.964 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Eu
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-PDC / PYRIDINE-2,6-DICARBOXYLIC ACID / DIPICOLINIC ACID / Dipicolinic acid


Mass: 167.119 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H5NO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsACCORDING TO AUTHORS THE LIGAND PDC IS IN THE BASIC (DEPROTONATED) FORM (C7H3N1O4)
Sequence detailsTHERE ARE TWO ISOFORMS OF THAUMATIN, I AND II. CRYSTALLIZATION MATERIAL CONTAINS A MIXTURE OF LYS46 ...THERE ARE TWO ISOFORMS OF THAUMATIN, I AND II. CRYSTALLIZATION MATERIAL CONTAINS A MIXTURE OF LYS46 AND ASN46. ASN46 FROM THE FORM II IS USED.

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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: 2.78 Å3/Da / Density % sol: 55.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.7 M Sodium Potassium Tatrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM30A11.776211, 0.920134
ESRF BM30A2
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 25, 2004 / Details: Si(111)
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.7762111
20.9201341
ReflectionResolution: 1.456→45.596 Å / Num. obs: 44812 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 12.3 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 5.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.46-1.537.70.391.14783862180.3996.7
1.53-1.6312.80.2162.87837561260.216100
1.63-1.7413.10.1593.67524757600.159100
1.74-1.8813.30.12557107953560.125100
1.88-2.0613.10.0976.26540549820.097100
2.06-2.3130.0817.25911245440.081100
2.3-2.6613.10.06395225340000.063100
2.66-3.2613.50.04711.24674134510.047100
3.26-4.613.20.0538.83621927390.053100
4.6-45.6120.0518.11959516360.05199.9

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Phasing

PhasingMethod: MAD
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
13.6493.6490EU18.60.26
21.6622.2220.663EU18.580.02
37.775.612-0.096EU18.580.02
452.53252.5140EU18.60.02
5-1.0431.278-1.732EU18.660.01
66.2332.40EU18.60.01
74.5222.1011.146EU18.610.01
846.2012.155-1.981EU18.790.02
93.2944.8194.775EU18.620.04
10-0.1674.7313.347EU18.60.06
117.8973.7011.966EU18.650.02
120.0063.9822.898EU18.60.03

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
SHARPphasing
SOLOMONphasing
REFMACrefinement
PDB_EXTRACT2data extraction
BM30Abeamline softwaredata collection
XDSdata reduction
RefinementMethod to determine structure: MAD
Starting model: 1RQW

1rqw


Resolution: 1.46→53.68 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.176 2259 5.1 %RANDOM
Rwork0.152 ---
obs0.153 44636 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.078 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.46→53.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1551 0 57 351 1959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221698
X-RAY DIFFRACTIONr_bond_other_d00.021433
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.9892312
X-RAY DIFFRACTIONr_angle_other_deg3.97533359
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6865216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.72923.14370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.8315260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2051513
X-RAY DIFFRACTIONr_chiral_restr0.0830.2241
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021940
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02363
X-RAY DIFFRACTIONr_nbd_refined0.2060.2326
X-RAY DIFFRACTIONr_nbd_other0.230.21457
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2862
X-RAY DIFFRACTIONr_nbtor_other0.1180.2857
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2238
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.280.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.236
X-RAY DIFFRACTIONr_mcbond_it1.111.51042
X-RAY DIFFRACTIONr_mcbond_other0.6721.5434
X-RAY DIFFRACTIONr_mcangle_it1.64221682
X-RAY DIFFRACTIONr_scbond_it2.1923656
X-RAY DIFFRACTIONr_scangle_it3.0644.5626
X-RAY DIFFRACTIONr_rigid_bond_restr1.21233131
X-RAY DIFFRACTIONr_sphericity_free4.8843352
X-RAY DIFFRACTIONr_sphericity_bonded1.43933083
LS refinement shellResolution: 1.456→1.494 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 156 -
Rwork0.323 2842 -
obs-2998 91.96 %

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