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- PDB-5a11: The crystal structure of Ta-TFP, a thiocyanate-forming protein in... -

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Basic information

Entry
Database: PDB / ID: 5a11
TitleThe crystal structure of Ta-TFP, a thiocyanate-forming protein involved in glucosinolate breakdown (space group P21)
ComponentsTHIOCYANATE FORMING PROTEIN
KeywordsIMMUNE SYSTEM / SPECIFIER PROTEIN / KELCH PROTEIN / FIELD-PENNY CRESS / FE(II) DEPENDENT
Function / homology
Function and homology information


N-(sulfonatooxy)prop-2-enimidothioate sulfolyase / nitrile biosynthetic process / glucosinolate metabolic process / enzyme regulator activity / lyase activity / protein homodimerization activity / metal ion binding / identical protein binding / nucleus / cytosol
Similarity search - Function
KLHDC2/KLHL20/DRC7 Kelch-repeats domain / Kelch motif / Kelch-type beta propeller
Similarity search - Domain/homology
IODIDE ION / N-(sulfonatooxy)prop-2-enimidothioate sulfolyase
Similarity search - Component
Biological speciesTHLASPI ARVENSE (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsKrausze, J. / Gumz, F. / Wittstock, U.
CitationJournal: Plant Mol.Biol. / Year: 2015
Title: The Crystal Structure of the Thiocyanate-Forming Protein from Thlaspi Arvense, a Kelch Protein Involved in Glucosinolate Breakdown.
Authors: Gumz, F. / Krausze, J. / Eisenschmidt, D. / Backenkohler, A. / Barleben, L. / Brandt, W. / Wittstock, U.
History
DepositionApr 27, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: THIOCYANATE FORMING PROTEIN
B: THIOCYANATE FORMING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3899
Polymers79,5012
Non-polymers8887
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-9 kcal/mol
Surface area25730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.367, 89.613, 83.842
Angle α, β, γ (deg.)90.00, 101.08, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: generate
Matrix: (-0.99998, 0.00667, 5.0E-5), (0.00626, 0.94176, -0.33622), (-0.00229, -0.33621, -0.94178)
Vector: 13.74419, 35.56956, 205.34927)

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Components

#1: Protein THIOCYANATE FORMING PROTEIN


Mass: 39750.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THLASPI ARVENSE (plant) / Plasmid: PGEX6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: G1FNI6
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.25 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 5.6
Details: 0.1 M SODIUM CITRATE PH 5.6, 20% (W/V) PEG 3350, 0.2 M KI

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 23, 2014 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2.47→45.03 Å / Num. obs: 24907 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 24.55 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 6.94
Reflection shellResolution: 2.47→2.56 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.02 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5A10

5a10


Resolution: 2.47→45.031 Å / SU ML: 0.34 / σ(F): 1.37 / Phase error: 28.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2876 1246 5 %
Rwork0.2601 --
obs0.2615 24904 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.7 Å2
Refinement stepCycle: LAST / Resolution: 2.47→45.031 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5411 0 7 30 5448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045565
X-RAY DIFFRACTIONf_angle_d1.0787554
X-RAY DIFFRACTIONf_dihedral_angle_d13.5031984
X-RAY DIFFRACTIONf_chiral_restr0.042778
X-RAY DIFFRACTIONf_plane_restr0.006995
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4701-2.5690.32211360.29842587X-RAY DIFFRACTION98
2.569-2.68590.31531400.30012652X-RAY DIFFRACTION99
2.6859-2.82740.29181370.28122608X-RAY DIFFRACTION99
2.8274-3.00460.33741400.29392650X-RAY DIFFRACTION99
3.0046-3.23650.32721370.29042612X-RAY DIFFRACTION99
3.2365-3.56210.26961370.2622609X-RAY DIFFRACTION99
3.5621-4.07720.25381390.25072638X-RAY DIFFRACTION98
4.0772-5.13570.28981380.21432614X-RAY DIFFRACTION98
5.1357-45.03880.25271420.23992688X-RAY DIFFRACTION98
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)
10.0084-0.00490.02150.0906-0.10170.16710.05850.0024-0.0020.00630.06020.01850.10.01310.17870.0837-0.0247-0.00760.0785-0.03860.3477-7.3717-28.059796.0878
20.1837-0.02810.03470.0722-0.07770.142-0.1203-0.0638-0.0264-0.14330.0983-0.0738-0.0219-0.13940.01520.0702-0.0230.01080.0618-0.02310.1569-0.6485-32.640185.0029
30.29480.0589-0.14560.391-0.04720.0781-0.1579-0.08840.0637-0.16280.0562-0.18360.07270.0077-0.07530.1907-0.080.00080.1553-0.02530.14155.9429-25.26776.8977
40.02610.03960.03420.0989-0.04960.3258-0.01830.0159-0.0269-0.0364-0.12060.01910.0247-0.0387-0.17730.2017-0.086-0.10320.1509-0.01650.09913.9725-14.935480.2139
50.03620.0142-0.02050.2016-0.08140.0365-0.0113-0.0069-0.0256-0.13190.00350.09270.076-0.0798-0.08440.0534-0.0769-0.05520.1198-0.13650.145911.9333-15.2177.9795
60.0338-0.03780.00110.0998-0.00070.05010.0685-0.0044-0.0145-0.16620.0982-0.0278-0.0967-0.10830.36750.1287-0.0021-0.0154-0.21720.20420.08859.2969-6.457789.6496
70.14780.1476-0.0470.1595-0.08070.0551-0.03080.0835-0.0572-0.09750.0733-0.01320.0898-0.06580.04040.05190.00370.00010.08750.01140.0534-1.9277-16.83199.0787
80.01440.01230.04880.01370.03620.1439-0.02980.02360.08330.10470.0751-0.13430.0780.02760.02330.13370.07950.00310.17830.01620.13720.9943-23.2102124.224
90.00090.0027-0.00510.0294-0.03350.0409-0.0401-0.0319-0.1450.008-0.06210.07410.001-0.0114-0.17670.2003-0.21590.1028-0.03380.07850.094512.0034-23.0418133.7926
100.2068-0.01410.00930.1395-0.10060.2019-0.1401-0.0423-0.1339-0.16210.12540.14160.0218-0.0689-0.0110.1944-0.0494-0.02880.16390.04680.17411.8674-20.4313138.4732
110.0079-0.00040.03210.1190.05630.21220.1458-0.200400.1281-0.1306-0.0387-0.0271-0.07090.04020.1157-0.01560.0860.13870.10140.03669.3914-11.2511142.1321
120.0424-0.11750.0870.302-0.22280.15780.15250.07-0.101-0.03280.03950.1653-0.0631-0.06020.11270.15270.03780.02470.2585-0.05220.19752.9534-5.0947136.2718
130.0008-0.00590.00270.1814-0.14660.11850.0293-0.01310.0676-0.02350.14210.1676-0.18790.0550.02650.1340.0110.02410.1528-0.02320.19287.7873-1.1075125.4566
140.2437-0.22360.0330.2205-0.08040.24780.11430.0841-0.0209-0.02330.0740.1017-0.05980.02460.62170.15220.03440.07510.0828-0.02110.12621.6143-0.1251120.9077
150.19260.0101-0.13830.3199-0.0710.10630.002-0.17250.02160.09970.06690.0958-0.01820.07420.07570.07330.0096-0.010.10420.0040.075513.2231-11.129115.2581
160.1094-0.1118-0.0250.37130.08910.1943-0.0141-0.03050.0184-0.0538-0.0183-0.10060.1504-0.1396-0.1130.10910.00570.00120.10730.01160.031620.1828-18.5062122.596
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 4 THROUGH 26 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 27 THROUGH 79 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 80 THROUGH 131 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 132 THROUGH 148 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 149 THROUGH 173 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 174 THROUGH 236 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 237 THROUGH 348 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 4 THROUGH 26 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 27 THROUGH 52 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 53 THROUGH 102 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 103 THROUGH 138 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 139 THROUGH 173 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 174 THROUGH 203 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 204 THROUGH 236 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 237 THROUGH 310 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 311 THROUGH 348 )

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