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- PDB-4dj1: Thaumatin I by Langmuir-Blodgett Hanging Drop Method at 1.98A res... -

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Basic information

Entry
Database: PDB / ID: 4dj1
TitleThaumatin I by Langmuir-Blodgett Hanging Drop Method at 1.98A resolution for Unique Water Distribution
ComponentsThaumatin I
KeywordsPLANT PROTEIN / Water Distribution / Thin Film / Langmuir Blodgett
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
Thaumatin I / Thaumatin I
Similarity search - Component
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 Å
AuthorsPechkova, E. / Sivozhelezov, V. / Belmonte, L. / Nicolini, C.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Unique water distribution of Langmuir-Blodgett versus classical crystals.
Authors: Pechkova, E. / Sivozhelezov, V. / Belmonte, L. / Nicolini, C.
History
DepositionFeb 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thaumatin I


Theoretical massNumber of molelcules
Total (without water)22,2431
Polymers22,2431
Non-polymers00
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.860, 57.860, 150.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Thaumatin I


Mass: 22243.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thaumatococcus daniellii (katemfe) / References: UniProt: Q8RVT0, UniProt: P02883*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 56.47 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97633 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97633 Å / Relative weight: 1
ReflectionResolution: 1.98→53.992 Å / Num. all: 18634 / Num. obs: 18634 / % possible obs: 100 % / Redundancy: 13 % / Rsym value: 0.119 / Net I/σ(I): 24.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.98-2.0913.30.3371.73543326570.337100
2.09-2.2113.20.2752.13300725090.275100
2.21-2.3712.90.2242.73054323650.224100
2.37-2.5612.40.1823.32760522230.182100
2.56-2.8120.1344.52463920450.134100
2.8-3.1313.90.16.32612518790.1100
3.13-3.6213.80.0758.42312116760.075100
3.62-4.4313.50.0667.51941614350.066100
4.43-6.2613.10.0589.81507611530.058100
6.26-26.65911.60.05510.780296920.05598.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.04 Å26.66 Å
Translation2.04 Å26.66 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→53.99 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.1959 / WRfactor Rwork: 0.1744 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8738 / SU B: 2.825 / SU ML: 0.081 / SU R Cruickshank DPI: 0.1405 / SU Rfree: 0.1253 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1985 948 5.1 %RANDOM
Rwork0.1736 ---
obs0.1749 18544 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 58.13 Å2 / Biso mean: 12.568 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2--0.26 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.98→53.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1552 0 0 171 1723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0221596
X-RAY DIFFRACTIONr_angle_refined_deg1.9281.9532168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6835206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14922.92365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05915244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4121512
X-RAY DIFFRACTIONr_chiral_restr0.1570.2230
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211231
X-RAY DIFFRACTIONr_mcbond_it1.2121.51023
X-RAY DIFFRACTIONr_mcangle_it2.06121641
X-RAY DIFFRACTIONr_scbond_it3.4273573
X-RAY DIFFRACTIONr_scangle_it5.4914.5527
LS refinement shellResolution: 1.98→2.032 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 61 -
Rwork0.162 1272 -
all-1333 -
obs--100 %

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