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- PDB-1pvm: Crystal Structure of a Conserved CBS Domain Protein TA0289 of Unk... -

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Basic information

Entry
Database: PDB / ID: 1pvm
TitleCrystal Structure of a Conserved CBS Domain Protein TA0289 of Unknown Function from Thermoplasma acidophilum
Componentsconserved hypothetical protein Ta0289
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / CBS domain / PSI / 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 / Archaeal CBS protein, (ACP)-type metal binding domain / Domain of unknown function (DUF1936) / Archaeal CBS proteins (ACP)-type metal binding (MB) domain profile. / CBS-domain / CBS-domain / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain ...Domain of unknown function DUF1936 / Hypothetical protein Ta0289, C-terminal / Archaeal CBS protein, (ACP)-type metal binding domain / Domain of unknown function (DUF1936) / Archaeal CBS proteins (ACP)-type metal binding (MB) domain profile. / CBS-domain / CBS-domain / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
: / CBS domain-containing protein
Similarity search - Component
Biological speciesThermoplasma acidophilum DSM 1728 (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsZhang, R. / Joachimiak, A. / Edwards, A. / Savchenko, A. / Xu, L. / 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 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: conserved hypothetical protein Ta0289
B: conserved hypothetical protein Ta0289
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2624
Polymers41,8602
Non-polymers4012
Water9,044502
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-14 kcal/mol
Surface area16200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.735, 62.838, 97.278
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer consists of chain A (Mol.A) and chain B (Mol.B).

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Components

#1: Protein conserved hypothetical protein Ta0289


Mass: 20930.186 Da / Num. of mol.: 2 / Fragment: CBS DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum DSM 1728 (acidophilic)
Species: Thermoplasma acidophilum / Strain: DSM1728 / Gene: Ta0289 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HLD9
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 2.14 Å3/Da / Density % sol: 42.61 % / Description: Friedel pairs were used.
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 0.1M tris, 0.2M ammonium formate, 8% Glycerol, 24%PEG3350, 1.6M Mercury sulphate in protein,, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 MTris-HCl1reservoirpH7.8
20.2 Mammonium formate1reservoir
320 %PEG33501reservoir
48 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.013 Å
DetectorType: SBC-2 / Detector: CCD / Date: Jun 17, 2003 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.013 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 105550 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 10.5 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 44.06
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 5.04 / Num. unique all: 5748 / % possible all: 82.5
Reflection
*PLUS
Highest resolution: 1.5 Å
Reflection shell
*PLUS
Mean I/σ(I) obs: 5

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Processing

Software
NameVersionClassification
CNS1.1refinement
d*TREKdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→37.46 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: friedel pairs were used.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 4830 4.6 %RANDOM
Rwork0.194 ---
obs0.194 105550 94.6 %-
all-111575 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.239 Å2 / ksol: 0.38879 e/Å3
Displacement parametersBiso mean: 17.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.54 Å20 Å20 Å2
2---1.29 Å20 Å2
3---2.82 Å2
Refine analyzeLuzzati coordinate error free: 0.19 Å / Luzzati sigma a free: 0.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→37.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2887 0 2 502 3391
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.263 410 2.8 %
Rwork0.272 14293 -
obs--79.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82

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