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- PDB-3gk5: Crystal structure of rhodanese-related protein (TVG0868615) from ... -

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Basic information

Entry
Database: PDB / ID: 3gk5
TitleCrystal structure of rhodanese-related protein (TVG0868615) from Thermoplasma volcanium, Northeast Structural Genomics Consortium Target TvR109A
ComponentsUncharacterized rhodanese-related protein TVG0868615
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Rhodanese domain-containing protein
Similarity search - Component
Biological speciesThermoplasma volcanium GSS1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsForouhar, F. / Su, M. / Seetharaman, J. / Mao, L. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Belote, R.L. / Everett, J.K. / Nair, R. ...Forouhar, F. / Su, M. / Seetharaman, J. / Mao, L. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Belote, R.L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of rhodanese-related protein (TVG0868615) from Thermoplasma volcanium, Northeast Structural Genomics Consortium Target TvR109A
Authors: Forouhar, F. / Su, M. / Seetharaman, J. / Mao, L. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Belote, R.L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionMar 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 6, 2023Group: 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 / 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: Uncharacterized rhodanese-related protein TVG0868615


Theoretical massNumber of molelcules
Total (without water)12,3751
Polymers12,3751
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.446, 89.446, 34.554
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Uncharacterized rhodanese-related protein TVG0868615


Mass: 12374.956 Da / Num. of mol.: 1 / Fragment: UNP residues 101-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma volcanium GSS1 (archaea) / Strain: GSS1 / DSM 4299 / IFO 15438 / JCM 9571 / Gene: TV0844, TVG0868615 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q97AG6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.15 Å3/Da / Density % sol: 42.78 %
Crystal growTemperature: 291 K / Method: microbatch under oil / pH: 6.5
Details: Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM Sodium chloride, 5 mM DTT. Reservoir solution: 100 mM Bis-Tris pH 6.5, 45% PEG 400., MICROBATCH UNDER OIL, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97853 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 18, 2009 / Details: mirrors
RadiationMonochromator: Si(111) CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 8057 / Num. obs: 6253 / % possible obs: 77.6 % / Observed criterion σ(I): 1.5 / Redundancy: 3.2 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.057 / Net I/σ(I): 28.54
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.072 / Mean I/σ(I) obs: 13.63 / Num. unique all: 810 / Rsym value: 0.097 / % possible all: 60

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
COMOphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3EME

3eme
PDB Unreleased entry


Resolution: 2.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: Program XtalView has also been used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.243 331 4.1 %RANDOM
Rwork0.187 ---
all0.189 8039 --
obs0.187 6239 77.6 %-
Solvent computationBsol: 42.432 Å2
Displacement parametersBiso mean: 30.337 Å2
Baniso -1Baniso -2Baniso -3
1--2.59 Å20 Å20 Å2
2---2.59 Å20 Å2
3---5.181 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms797 0 0 47 844
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it4.4711.5
X-RAY DIFFRACTIONc_scbond_it7.3542
X-RAY DIFFRACTIONc_mcangle_it6.0622
X-RAY DIFFRACTIONc_scangle_it9.2832.5
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree error: 0.054
RfactorNum. reflection% reflection
Rfree0.246 21 -
Rwork0.248 --
obs-461 59.8 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param

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