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- PDB-5xt5: SufS-SufU complex from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 5xt5
TitleSufS-SufU complex from Bacillus subtilis
Components
  • Cysteine desulfurase SufS
  • Zinc-dependent sulfurtransferase SufU
KeywordsBIOSYNTHETIC PROTEIN / Iron-sulfur cluster biosynthesis / SUF machinery / Cysteine desulfurase / Sulfur mobilization / Metalloprotein
Function / homology
Function and homology information


Transferases / cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / iron-sulfur cluster assembly / ferrous iron binding / 2 iron, 2 sulfur cluster binding / pyridoxal phosphate binding / transferase activity / intracellular iron ion homeostasis / cytoplasm
Similarity search - Function
Sufe protein. Chain: A - #10 / Sufe protein. Chain: A / NIF system FeS cluster assembly, NifU, N-terminal / NifU-like N terminal domain / Cysteine desulfurase, SufS / Cysteine desulfurase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V ...Sufe protein. Chain: A - #10 / Sufe protein. Chain: A / NIF system FeS cluster assembly, NifU, N-terminal / NifU-like N terminal domain / Cysteine desulfurase, SufS / Cysteine desulfurase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Zinc-dependent sulfurtransferase SufU / Cysteine desulfurase SufS
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsFujishiro, T. / Takahashi, Y.
Funding support Japan, 3items
OrganizationGrant numberCountry
JSPS15H04472 Japan
JSPS17K14510 Japan
Sumitomo Foundation163037 Japan
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Zinc-Ligand Swapping Mediated Complex Formation and Sulfur Transfer between SufS and SufU for Iron-Sulfur Cluster Biogenesis in Bacillus subtilis
Authors: Fujishiro, T. / Terahata, T. / Kunichika, K. / Yokoyama, N. / Maruyama, C. / Asai, K. / Takahashi, Y.
History
DepositionJun 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed
Revision 1.2Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Zinc-dependent sulfurtransferase SufU
A: Cysteine desulfurase SufS
B: Cysteine desulfurase SufS
C: Zinc-dependent sulfurtransferase SufU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,3128
Polymers127,6864
Non-polymers6254
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, Homologous to (IscS)2-(IscU)2 complex
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11730 Å2
ΔGint-129 kcal/mol
Surface area37670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.980, 74.980, 364.410
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21C
12A
22B

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNGLYGLYDA6 - 1396 - 139
21ASNASNGLYGLYCD6 - 1396 - 139
12METMETTHRTHRAB1 - 4034 - 406
22METMETTHRTHRBC1 - 4034 - 406

NCS ensembles :
ID
1
2

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Components

#1: Protein Zinc-dependent sulfurtransferase SufU / Putative iron-sulfur cluster assembly scaffold protein SufU / Sulfur acceptor protein SufU


Mass: 17256.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: sufU, iscU, nifU, yurV, BSU32680 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: O32163, Transferases
#2: Protein Cysteine desulfurase SufS


Mass: 46586.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: sufS, csd, yurW, BSU32690 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: O32164, cysteine desulfurase
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M Potassium nitrate, 20 % (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1.28229 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 8, 2017 / Details: bending magnet
RadiationMonochromator: A fixed exit Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28229 Å / Relative weight: 1
ReflectionResolution: 2.34→64.93 Å / Num. obs: 95808 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 5.316 % / Biso Wilson estimate: 59.523 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.08 / Χ2: 1.342 / Net I/σ(I): 14.87 / Num. measured all: 509344 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.34-2.445.5770.9791.74111550.6121.07998.6
2.44-2.545.5410.7212.3895820.7690.79598.9
2.54-2.75.4420.5083.53125110.8570.56198.9
2.7-2.95.3980.3145.47120650.9460.34799.2
2.9-3.15.2190.1819.2391880.9780.20299.3
3.1-3.54.8260.09915.57125330.9920.11299.3
3.5-44.870.05924.9694880.9970.06699.3
4-4.55.5030.04435.0457560.9980.04899.8
4.5-55.520.03838.5537130.9990.04299.7
5-5.55.5930.03838.2823940.9990.04299.7
5.5-65.5960.03737.6117220.9990.04199.6
6-105.5640.02843.4544800.9990.03199.5
10-64.934.9590.02248.5212210.9990.02598.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J8Q, 2AZH

5j8q

2azh


Resolution: 2.34→64.93 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 18.385 / SU ML: 0.214 / SU R Cruickshank DPI: 0.4118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.412 / ESU R Free: 0.251 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2426 2414 5 %RANDOM
Rwork0.1985 ---
obs0.2007 45864 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 248.77 Å2 / Biso mean: 70.098 Å2 / Biso min: 31.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å2-0.22 Å20 Å2
2---0.45 Å20 Å2
3---1.46 Å2
Refinement stepCycle: final / Resolution: 2.34→64.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8393 0 32 189 8614
Biso mean--46.68 50.11 -
Num. residues----1082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0198592
X-RAY DIFFRACTIONr_angle_refined_deg2.0021.95811626
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.77751080
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.26425.065383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.35151509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.691538
X-RAY DIFFRACTIONr_chiral_restr0.1380.21318
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216404
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11D71280.23
12C71280.23
21A258420.1
22B258420.1
LS refinement shellResolution: 2.34→2.401 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 176 -
Rwork0.288 3341 -
all-3517 -
obs--98.85 %
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)
13.2723-2.8104-0.30293.73331.55013.972-0.2719-0.1777-0.08430.29950.2559-0.46210.52610.26240.0160.3919-0.08010.04650.340.04420.332219.543-2.454.211
21.7727-0.1449-1.20091.5468-1.40618.2823-0.2265-0.33960.48310.33290.0441-0.3404-0.7408-0.33080.18240.3573-0.0038-0.11030.3219-0.0410.29879.58220.7286.623
32.3477-0.18670.29661.4497-0.24892.1194-0.17120.36420.3935-0.37070.054-0.2712-0.11790.01070.11720.3971-0.1370.03190.32470.0780.13548.1717.92-13.738
42.92710.24370.58032.1752-0.12442.9155-0.14280.4715-0.5346-0.39450.0689-0.5110.53530.23880.0740.565-0.08270.19680.3991-0.04720.319219.235-8.654-14.709
56.1675-1.51371.62461.0228-0.96747.3036-0.3037-0.78030.08660.1640.0771-0.24880.0129-0.51190.22660.44330.0869-0.05590.6777-0.07070.09930.64812.24226.187
64.2372-1.39221.18783.9062-1.35821.042-0.1462-0.1830.1064-0.20220.1365-0.02890.1907-0.39450.00970.3707-0.12260.01250.48540.03410.008-7.4877.4641.257
73.0398-0.020.51421.2517-0.86361.9482-0.2754-0.62260.23560.12580.28790.3411-0.0866-0.7344-0.01250.3542-0.03010.00260.65990.00520.1431-16.08512.9585.968
83.6812-0.33851.29786.1159-1.15362.1554-0.5242-0.9710.9560.55840.16450.4907-0.8461-0.86630.35970.72850.319-0.13570.9884-0.34540.3694-8.19728.16125.021
99.79678.1282.683313.01810.299412.8861-0.09820.1661-1.3453-0.6325-0.0078-1.14820.57590.48420.10590.5612-0.07360.10840.5011-0.11630.51526.185-28.677-12.999
1024.5705-15.159610.921211.0931-5.16526.39320.29790.56840.0143-0.362-0.46590.42150.075-0.02550.1680.8319-0.1242-0.04490.82590.01080.7716-7.757-24.671-27.575
1136.8866-27.1985-9.475220.44717.8364.3691-0.1003-1.60810.58280.24410.4241-0.36440.3707-1.423-0.32380.9323-0.3609-0.5121.92110.52251.5085-5.964-11.771-18.896
123.3007-3.50922.40047.53731.93347.03360.1424-0.2311-0.8683-0.8984-0.20221.5139-0.7506-0.74710.05981.1523-0.5788-0.27731.4760.45170.8342-15.625-20.075-23.374
1313.5131-1.0284-3.37754.61653.2253.2029-0.95331.8347-1.0167-0.85980.50430.9268-0.1497-0.65690.44910.9677-0.6137-0.34711.33370.460.5987-10.885-25.123-18.523
1410.31262.7456-1.15851.7454-1.14094.70950.0951-0.5692-0.3160.37960.27190.3937-0.1584-0.3323-0.36690.706-0.18540.01750.50530.13550.5109-7.044-27.27-4.672
1516.46181.96555.8862.4081-0.71337.67810.0446-0.33010.833-0.1260.53350.744-0.7012-1.0084-0.57820.7375-0.2110.13690.5310.21970.5256-6.581-17.435-11.62
160.976-2.0453-1.09619.6556-5.266119.6182-0.2124-0.22550.31980.9109-0.30710.38690.04260.55890.51951.16130.0233-0.18151.0124-0.28281.20418.47339.43330.189
171.77772.2369-0.59913.3051-1.00470.41770.10690.05720.69980.31080.0220.5914-0.3241-0.1696-0.12891.7860.4537-0.66050.6584-0.22721.0768-0.63649.82613.74
184.34932.4921-6.586910.378-9.351913.56840.33190.78080.92251.49470.96610.2747-1.316-1.2472-1.2981.34280.0652-0.51540.7430.00670.76621.50348.3916.155
193.44975.2232-8.59978.2869-12.825822.0380.49250.02990.1070.3875-0.0630.0743-1.02130.4192-0.42951.33390.3876-0.45290.6759-0.03351.04692.23149.75613.802
208.96525.3317-7.64593.2248-4.55556.5240.0362-0.3941-0.1827-0.249-0.2133-0.23730.00340.3690.17712.0542-0.4671-0.27990.75140.27571.584815.53448.1978.261
215.6797-3.1415-4.15831.98551.70855.29620.0374-0.79191.216-0.076-0.1266-0.9191-1.04712.15650.08921.7525-0.1684-0.85971.46240.43621.600616.70642.4318.333
222.69614.1525-4.47320.6089-20.909821.3817-0.62170.53370.24680.7471-0.7291-1.3702-0.97410.47431.35081.16270.0891-0.28650.5971-0.05340.87287.14741.8677.536
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 43
2X-RAY DIFFRACTION2A44 - 93
3X-RAY DIFFRACTION3A94 - 296
4X-RAY DIFFRACTION4A297 - 404
5X-RAY DIFFRACTION5B1 - 34
6X-RAY DIFFRACTION6B35 - 130
7X-RAY DIFFRACTION7B131 - 322
8X-RAY DIFFRACTION8B323 - 405
9X-RAY DIFFRACTION9C6 - 19
10X-RAY DIFFRACTION10C20 - 31
11X-RAY DIFFRACTION11C32 - 43
12X-RAY DIFFRACTION12C44 - 54
13X-RAY DIFFRACTION13C55 - 91
14X-RAY DIFFRACTION14C92 - 121
15X-RAY DIFFRACTION15C122 - 140
16X-RAY DIFFRACTION16D6 - 13
17X-RAY DIFFRACTION17D14 - 38
18X-RAY DIFFRACTION18D39 - 55
19X-RAY DIFFRACTION19D56 - 80
20X-RAY DIFFRACTION20D81 - 98
21X-RAY DIFFRACTION21D99 - 124
22X-RAY DIFFRACTION22D125 - 142

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