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- PDB-2qh1: Structure of TA289, a CBS-rubredoxin-like protein, in its Fe+2-bo... -

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Basic information

Entry
Database: PDB / ID: 2qh1
TitleStructure of TA289, a CBS-rubredoxin-like protein, in its Fe+2-bound state
ComponentsHypothetical protein Ta0289
KeywordsUNKNOWN FUNCTION / CBS-rubredoxin-like protein / Fe+2 / Hypothetical protein / Structural Genomics / Structural Genomics Consortium / SGC / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Domain of unknown function DUF1936 / Hypothetical protein Ta0289, C-terminal / Domain of unknown function (DUF1936) / Archaeal CBS protein, (ACP)-type metal binding domain / Archaeal CBS proteins (ACP)-type metal binding (MB) domain profile. / : / CBS-domain / CBS-domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily ...Domain of unknown function DUF1936 / Hypothetical protein Ta0289, C-terminal / Domain of unknown function (DUF1936) / Archaeal CBS protein, (ACP)-type metal binding domain / Archaeal CBS proteins (ACP)-type metal binding (MB) domain profile. / : / CBS-domain / CBS-domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
: / CBS domain-containing protein
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSinger, A.U. / Proudfoot, M. / Brown, G. / Xu, L. / Savchenko, A. / Yakunin, A.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Biochemical and structural characterization of a novel family of cystathionine beta-synthase domain proteins fused to a Zn ribbon-like domain.
Authors: Proudfoot, M. / Sanders, S.A. / Singer, A. / Zhang, R. / Brown, G. / Binkowski, A. / Xu, L. / Lukin, J.A. / Murzin, A.G. / Joachimiak, A. / Arrowsmith, C.H. / Edwards, A.M. / Savchenko, A.V. / Yakunin, A.F.
History
DepositionJun 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein Ta0289
B: Hypothetical protein Ta0289
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0434
Polymers44,9322
Non-polymers1122
Water6,215345
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.806, 63.031, 97.474
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hypothetical protein Ta0289 / Cystathionine Beta-Synthase (CBS) domain protein


Mass: 22465.840 Da / Num. of mol.: 2 / Mutation: S109P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Strain: DSM 1728 / Gene: Ta0289 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon-Plus RP / References: UniProt: Q9HLD9
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.01 Å3/Da / Density % sol: 38.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: crystals were grown in a 1:1 solution of protein to resevoir containing 0.1 M Tris HCl (pH 7.8), 0.2 M ammonium formate, 20 % PEG 3350, and 8 % glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 20, 2007 / Details: osmic mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 25194 / Num. obs: 24893 / % possible obs: 98.8 % / Redundancy: 10 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 52.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 13.6 / Num. unique all: 2466 / % possible all: 97.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PVM

1pvm


Resolution: 2→19.67 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1776005.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1194 4.8 %RANDOM
Rwork0.202 ---
all0.204 25113 --
obs0.202 24672 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.1997 Å2 / ksol: 0.311421 e/Å3
Displacement parametersBiso mean: 27.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å20 Å2
2---0.4 Å20 Å2
3----0.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2902 0 2 345 3249
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.81.5
X-RAY DIFFRACTIONc_mcangle_it1.322
X-RAY DIFFRACTIONc_scbond_it1.362
X-RAY DIFFRACTIONc_scangle_it2.092.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.273 204 5.2 %
Rwork0.223 3745 -
obs-3949 96.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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