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- PDB-3p3a: Crystal structure of a putative thiosulfate sulfurtransferase fro... -

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Basic information

Entry
Database: PDB / ID: 3p3a
TitleCrystal structure of a putative thiosulfate sulfurtransferase from Mycobacterium thermoresistible
ComponentsThiosulfate sulfurtransferase
KeywordsTRANSFERASE / Seattle Structural Genomics Center for Infectious Disease / SSGCID / tuberculosis / paratuberculosis / thermostable / Rhodanese / Thiosulfate cyanide transsulfurase / Thiosulfate thiotransferase
Function / homology
Function and homology information


thiosulfate sulfurtransferase activity
Similarity search - Function
Rhodanese signature 1. / Rhodanese C-terminal signature. / Thiosulphate sulfurtransferase, conserved site / Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain ...Rhodanese signature 1. / Rhodanese C-terminal signature. / Thiosulphate sulfurtransferase, conserved site / 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
Biological speciesMycobacterium thermoresistibile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Citation
Journal: Protein Sci. / Year: 2012
Title: Mycobacterium thermoresistibile as a source of thermostable orthologs of Mycobacterium tuberculosis proteins.
Authors: Edwards, T.E. / Liao, R. / Phan, I. / Myler, P.J. / Grundner, C.
#1: Journal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionOct 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 27, 2012Group: Database references
Revision 1.3Apr 22, 2015Group: Database references
Revision 1.4Sep 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

Downloads & links

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Assembly

Deposited unit
A: Thiosulfate sulfurtransferase
B: Thiosulfate sulfurtransferase


Theoretical massNumber of molelcules
Total (without water)71,7582
Polymers71,7582
Non-polymers00
Water7,945441
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-8 kcal/mol
Surface area24310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.220, 83.370, 146.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Thiosulfate sulfurtransferase


Mass: 35879.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium thermoresistibile (bacteria)
Strain: ATCC 19527 / NCTC 10409 / Gene: NODE_3859_LENGTH_3444_COV_7.617015_22 / Production host: Escherichia coli (E. coli)
References: UniProt: E2QRA0*PLUS, thiosulfate sulfurtransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 48.2 mg/mL MythA.01241.a.A1 peak2 PS00652 against Emerald BioSystems Wizard III screen condition 13 B1 8% PEG 4000, 0.1 M NaOAc pH 4.6, with 20% ethylene glycol as cryo-protectant, crystal ...Details: 48.2 mg/mL MythA.01241.a.A1 peak2 PS00652 against Emerald BioSystems Wizard III screen condition 13 B1 8% PEG 4000, 0.1 M NaOAc pH 4.6, with 20% ethylene glycol as cryo-protectant, crystal tracking ID 216651b1, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 41111 / Num. obs: 40671 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 25.362 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 14.82
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.1-2.150.5364.116229298799.8
2.15-2.210.474.516044290599.9
2.21-2.280.3845.315704282999.6
2.28-2.350.3466.314713274699
2.35-2.420.3026.614730265899.8
2.42-2.510.2587.714456260299.7
2.51-2.60.2238.813768249299.5
2.6-2.710.1929.913343241499.3
2.71-2.830.16611.212499228299.2
2.83-2.970.1261412338223699.3
2.97-3.130.1081611556210199
3.13-3.320.08918.610995199798.9
3.32-3.550.06823.19998184198.4
3.55-3.830.05428.49401175298.5
3.83-4.20.04731.68574161398.1
4.2-4.70.0435.27570144896.8
4.7-5.420.03636.26954129598
5.42-6.640.03833.56021109996.7
6.64-9.390.03137.2461087695.5
9.390.02346.7247549893.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 49.69 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å39.35 Å
Translation3 Å39.35 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3hzu

3hzu


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.1837 / WRfactor Rwork: 0.1595 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8535 / SU B: 10.177 / SU ML: 0.119 / SU R Cruickshank DPI: 0.2035 / SU Rfree: 0.1664 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2151 2000 4.9 %RANDOM
Rwork0.1823 ---
obs0.1839 40509 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 58.65 Å2 / Biso mean: 21.7541 Å2 / Biso min: 7.51 Å2
Baniso -1Baniso -2Baniso -3
1--2.26 Å20 Å20 Å2
2--2.72 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4531 0 0 441 4972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0224704
X-RAY DIFFRACTIONr_angle_refined_deg1.461.9466448
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5785583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.99523.026228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35415692
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3151542
X-RAY DIFFRACTIONr_chiral_restr0.0960.2689
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213730
X-RAY DIFFRACTIONr_mcbond_it0.7181.52881
X-RAY DIFFRACTIONr_mcangle_it1.30324665
X-RAY DIFFRACTIONr_scbond_it1.931823
X-RAY DIFFRACTIONr_scangle_it3.1374.51776
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 138 -
Rwork0.231 2831 -
all-2969 -
obs--99.46 %
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)
10.7078-0.2373-0.74220.13360.00872.00640.07670.0140.0967-0.01270.0313-0.0247-0.0588-0.0648-0.10790.06160.02690.0150.06370.03020.09139.469851.4494-2.3317
20.8104-0.39960.05380.4303-0.11650.12120.0448-0.103-0.0266-0.03380.0244-0.0192-0.0204-0.0298-0.06920.05810.00390.01820.09040.03030.080741.286441.20974.2166
30.6585-0.56830.52210.6356-0.6950.8583-0.02980.02730.02330.0323-0.0541-0.0291-0.05230.09590.0840.057-0.0065-0.00930.090.03790.082361.89942.8045-1.6704
40.2183-0.29980.34010.7389-0.63520.86490.0188-0.0324-0.0231-0.0468-0.12450.02660.0820.07420.10570.05980.01610.00730.10340.02820.084365.840734.44822.7342
50.65950.39130.02850.5547-0.38251.34560.0154-0.04870.0735-0.02580.01090.04170.04160.0445-0.02630.06280.0196-0.00920.0654-0.00860.057184.863428.628541.1623
60.5347-0.06060.2050.05890.08711.0138-0.03750.09160.06140.05180.0160.01820.01460.03310.02150.07160.0131-0.00160.07280.01420.079884.171529.619632.3009
73.7497-0.45890.82010.0679-0.15450.76150.1463-0.258-0.0256-0.03410.0180.00140.1012-0.1539-0.16430.0292-0.0210.00370.0990.0460.073866.439323.944626.578
81.5093-0.16011.20480.0232-0.1280.98050.0769-0.2832-0.0406-0.02680.00740.00110.083-0.2535-0.08430.057-0.0143-0.01020.1790.0510.077164.013121.997933.0811
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 61
2X-RAY DIFFRACTION2A62 - 165
3X-RAY DIFFRACTION3A166 - 261
4X-RAY DIFFRACTION4A262 - 296
5X-RAY DIFFRACTION5B4 - 63
6X-RAY DIFFRACTION6B64 - 143
7X-RAY DIFFRACTION7B144 - 216
8X-RAY DIFFRACTION8B217 - 296

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