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- PDB-2fsx: Crystal structure of Rv0390 from M. tuberculosis -

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Basic information

Entry
Database: PDB / ID: 2fsx
TitleCrystal structure of Rv0390 from M. tuberculosis
ComponentsCOG0607: Rhodanese-related sulfurtransferase
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Rv0390 Br SAD data with Fbar / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


Rhodanese-like domain-containing protein STR4-like / 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
BROMIDE ION / : / Conserved protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsBursey, E.H. / Radhakannan, T. / Yu, M. / Segelke, B.W. / Lekin, T. / Toppani, D. / Chang, Y.-B. / Kaviratne, T. / Woodruff, T. / Terwilliger, T.C. ...Bursey, E.H. / Radhakannan, T. / Yu, M. / Segelke, B.W. / Lekin, T. / Toppani, D. / Chang, Y.-B. / Kaviratne, T. / Woodruff, T. / Terwilliger, T.C. / Hung, L.-W. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: To be Published
Title: Crystal Structure of Rv0390 from Mycobacterium tuberculosis
Authors: Bursey, E.H. / Radhakannan, T. / Yu, M. / Segelke, B.W. / Lekin, T. / Toppani, D. / Chang, Y.-B. / Kaviratne, T. / Woodruff, T. / Terwilliger, T.C. / Hung, L.-W.
History
DepositionJan 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
Remark 999SEQUENCE THE PROTEIN USED TO SOLVE THIS STRUCTURE WAS OBTAINED FROM A DIFFERENT STRAIN H37Rv OF THE ...SEQUENCE THE PROTEIN USED TO SOLVE THIS STRUCTURE WAS OBTAINED FROM A DIFFERENT STRAIN H37Rv OF THE SAME ORGANISM

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COG0607: Rhodanese-related sulfurtransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,34412
Polymers16,4491
Non-polymers89511
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.814, 50.814, 119.184
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsIt appeared to be a monomer judged by the crystal structure

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Components

#1: Protein COG0607: Rhodanese-related sulfurtransferase / Rv0390


Mass: 16449.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: F11 / Gene: Rv0390 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 76785673, UniProt: P95198*PLUS
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Sodium Citrate 1.0176M, MES 0.1M, Ammonium Sulfate 0.31752M , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2005
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 15254 / Num. obs: 15238 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 5
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 8 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.5 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→30.4 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.248 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21767 767 5.1 %RANDOM
Rwork0.17415 ---
obs0.1763 14404 99.89 %-
all-14420 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.596 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1023 0 15 123 1161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211058
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.9381446
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5265134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08622.552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.97115152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5311512
X-RAY DIFFRACTIONr_chiral_restr0.1160.2154
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02840
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.2508
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2709
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2100
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2950.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4020.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9081.5679
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.39221052
X-RAY DIFFRACTIONr_scbond_it2.3143448
X-RAY DIFFRACTIONr_scangle_it3.6334.5392
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 46 -
Rwork0.213 1016 -
obs--98.61 %
Refinement TLS params.Method: refined / Origin x: 7.079 Å / Origin y: 10.435 Å / Origin z: 43.991 Å
111213212223313233
T-0.0208 Å20.0052 Å2-0.0083 Å2--0.0511 Å20.0059 Å2---0.0456 Å2
L0.8122 °20.1518 °2-0.039 °2-1.4522 °20.1638 °2--1.2811 °2
S-0.0274 Å °0.008 Å °0.0164 Å °-0.0979 Å °0.0318 Å °0.1088 Å °-0.0294 Å °0.0021 Å °-0.0044 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 732 - 73
2X-RAY DIFFRACTION1AA81 - 14081 - 140

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