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- PDB-2oqn: High Pressure Cryocooling of Capillary Sample Cryoprotection and ... -

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Basic information

Entry
Database: PDB / ID: 2oqn
TitleHigh Pressure Cryocooling of Capillary Sample Cryoprotection and Diffraction Phasing at Long Wavelengths
ComponentsThaumatin-1
KeywordsPLANT PROTEIN / high pressure cryocooling / capillary cryoprotection / sulfur SAD phasing
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
D(-)-TARTARIC ACID / Thaumatin I
Similarity search - Component
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKim, C.U. / Hao, Q. / Gruner, S.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: High-pressure cryocooling for capillary sample cryoprotection and diffraction phasing at long wavelengths.
Authors: Kim, C.U. / Hao, Q. / Gruner, S.M.
History
DepositionJan 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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 / 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 1.4Nov 13, 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)22,3772
Polymers22,2271
Non-polymers1501
Water7,224401
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.968, 57.968, 150.716
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-TAR / D(-)-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.: 401 / 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: 2.85 Å3/Da / Density % sol: 56.79 %
Crystal growTemperature: 293 K
Method: crystallized in a polycarbonate capillary by vapor diffusion
pH: 7
Details: 0.9 M sodium potassium tartrate, pH 7.0, Crystallized in a polycarbonate capillary by vapor diffusion , temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 1.7463 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7463 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 20909 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.3 % / Biso Wilson estimate: 17.1 Å2 / Rsym value: 0.089 / Net I/σ(I): 32
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 5 / Rsym value: 0.175 / % possible all: 93.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1lxz

1lxz


Resolution: 1.9→28.99 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.92 / SU B: 2.605 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21623 1069 5.1 %RANDOM
Rwork0.17556 ---
obs0.17764 19833 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.117 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1550 0 10 401 1961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221603
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3221.9542178
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4475206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.51423.0366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.22615241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2321512
X-RAY DIFFRACTIONr_chiral_restr0.0950.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021239
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.2833
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21097
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2306
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.248
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8311.51050
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.37921639
X-RAY DIFFRACTIONr_scbond_it2.3273639
X-RAY DIFFRACTIONr_scangle_it3.7064.5539
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.904→1.954 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 79 -
Rwork0.211 1381 -
obs--95.99 %

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