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- PDB-5mjg: Single-shot pink beam serial crystallography: Thaumatin -

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Basic information

Entry
Database: PDB / ID: 5mjg
TitleSingle-shot pink beam serial crystallography: Thaumatin
ComponentsThaumatin-1
KeywordsPLANT PROTEIN / Thaumatin / Serial Crystallography / Pink beam
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
S,R MESO-TARTARIC ACID / Thaumatin I
Similarity search - Component
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMeents, A. / Oberthuer, D. / Lieske, J. / Srajer, V.
Citation
Journal: To Be Published
Title: Single-shot pink beam serial crystallography: Thaumatin
Authors: Meents, A. / Oberthuer, D. / Lieske, J. / Srajer, V.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart /
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
History
DepositionDec 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thaumatin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4003
Polymers22,2271
Non-polymers1732
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-10 kcal/mol
Surface area9670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.400, 58.400, 152.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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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-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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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: 2.92 Å3/Da / Density % sol: 57.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Sodium Tartrate

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.1-1.3
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Jul 10, 2016
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
21.31
ReflectionResolution: 1.98→30 Å / Num. obs: 6850 / % possible obs: 36.6 % / Observed criterion σ(F): 3 / Redundancy: 1 % / Biso Wilson estimate: 8.04 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 38.2
Reflection shellResolution: 2.1→2.2 Å / Num. measured obs: 3728 / Num. unique all: 245 / % possible all: 12.7

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Processing

Software
NameVersionClassification
PHENIX1.11_2567refinement
PHASERphasing
Epinormdata reduction
Precognitiondata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KWN

1kwn
PDB Unreleased entry


Resolution: 2.1→14.98 Å / SU ML: 0.167403583403 / Cross valid method: FREE R-VALUE / σ(F): 0.316734975762 / Phase error: 13.7032148611
RfactorNum. reflection% reflectionSelection details
Rfree0.199583762888 340 4.96785505552 %imported from 1KWN
Rwork0.154264418754 ---
obs0.15638687993 6844 42.5727792983 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.3601988224 Å2
Refinement stepCycle: LAST / Resolution: 2.1→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1550 0 11 168 1729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002422950402241616
X-RAY DIFFRACTIONf_angle_d0.4944061638592198
X-RAY DIFFRACTIONf_chiral_restr0.0410658259748234
X-RAY DIFFRACTIONf_plane_restr0.00240187973756289
X-RAY DIFFRACTIONf_dihedral_angle_d9.23771926237973
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1003-2.64370.195885034329950.1660955590161852X-RAY DIFFRACTION24.7615413964
2.6437-14.9680.2006478817592450.1509607309674652X-RAY DIFFRACTION59.646772229
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.425731670228-0.1661524426380.2426997186290.864321932082-0.07818335281920.3952721229810.07737501217270.144982740523-0.0584003752548-0.07393043964520.0577276181128-0.1189598601660.1137645284650.1848049752190.2293556527710.09804058914390.0278697844142-0.004830713459950.114223923208-0.02300833840180.077580856335517.808978099522.714526940527.5256886485
20.3997939766120.217173219091-0.1060206430910.9059548454110.4729984670310.8601982014140.0666338294570.0493834682554-0.0393155754709-0.05943844475070.02828478666120.1516515310460.0407513326356-0.03825152394180.2488564336410.07987241207520.0232783785361-0.0237511395110.0792498462365-0.01286366583130.08529476567426.6158768093328.717584877240.2057801184
30.103556697149-0.0483265883687-0.07124184669450.2622651463920.1146747107410.1565105342560.1098606219970.00507071191995-0.08143332251270.07817507700820.023874606236-0.07365081236490.1034607139380.101160578530.6086282485750.2239611467760.0348814627699-0.0747823991250.0770038304643-0.06144320374660.1012035382857.4804437917914.734745365728.6809683237
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 103 )
2X-RAY DIFFRACTION2chain 'A' and (resid 104 through 190 )
3X-RAY DIFFRACTION3chain 'A' and (resid 191 through 207 )

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