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- PDB-6jzv: Crystal structure of SufU from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 6jzv
TitleCrystal structure of SufU from Bacillus subtilis
ComponentsZinc-dependent sulfurtransferase SufU
KeywordsBIOSYNTHETIC PROTEIN / Iron-sulfur cluster biosynthesis / Sulfur mobilization
Function / homology
Function and homology information


Transferases / iron-sulfur cluster assembly / ferrous iron binding / 2 iron, 2 sulfur cluster 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Zinc-dependent sulfurtransferase SufU
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFujishiro, T. / Takahashi, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science17K14510 Japan
CitationJournal: Inorg.Chem. / Year: 2024
Title: Cysteine-Persulfide Sulfane Sulfur-Ligated Zn Complex of Sulfur-Carrying SufU in the SufCDSUB System for Fe-S Cluster Biosynthesis.
Authors: Terahata, T. / Shimada, Y. / Maki, C. / Muroga, S. / Sakurai, R. / Kunichika, K. / Fujishiro, T.
History
DepositionMay 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.2Oct 16, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)69,2888
Polymers69,0274
Non-polymers2624
Water95553
1
A: Zinc-dependent sulfurtransferase SufU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3222
Polymers17,2571
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Zinc-dependent sulfurtransferase SufU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3222
Polymers17,2571
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Zinc-dependent sulfurtransferase SufU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3222
Polymers17,2571
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Zinc-dependent sulfurtransferase SufU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3222
Polymers17,2571
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.320, 54.450, 70.380
Angle α, β, γ (deg.)68.990, 75.860, 72.540
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 101 or resid 107 through 140))
21(chain B and (resid 4 through 101 or resid 107 through 140))
31(chain C and (resid 4 through 101 or resid 107 through 140))
41(chain D and resid 4 through 140)

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNGLYGLY(chain A and (resid 4 through 101 or resid 107 through 140))AA4 - 1014 - 101
12SERSERVALVAL(chain A and (resid 4 through 101 or resid 107 through 140))AA107 - 140107 - 140
21ASNASNGLYGLY(chain B and (resid 4 through 101 or resid 107 through 140))BB4 - 1014 - 101
22SERSERVALVAL(chain B and (resid 4 through 101 or resid 107 through 140))BB107 - 140107 - 140
31ASNASNGLYGLY(chain C and (resid 4 through 101 or resid 107 through 140))CC4 - 1014 - 101
32SERSERVALVAL(chain C and (resid 4 through 101 or resid 107 through 140))CC107 - 140107 - 140
41ASNASNVALVAL(chain D and resid 4 through 140)DD4 - 1404 - 140

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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.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: sufU, iscU, nifU, yurV, BSU32680 / Variant: 168 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: O32163, Transferases
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 1.73 Å3/Da / Density % sol: 28.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 0.15 M potassium thiocyanate, 0.1M MES, 20% w/v PEG1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.25865 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 8, 2018
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.25865 Å / Relative weight: 1
ReflectionResolution: 2→49.409 Å / Num. obs: 31156 / % possible obs: 99.5 % / Redundancy: 8.033 % / Biso Wilson estimate: 38.279 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.187 / Rrim(I) all: 0.201 / Χ2: 0.889 / Net I/σ(I): 8.64 / Num. measured all: 499479 / Scaling rejects: 1252
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2-2.18.1050.9312.6568838851884930.7120.99999.7
2.1-2.28.220.6493.8357904704270440.8660.695100
2.2-2.37.8670.5444.5645746583458150.8970.58499.7
2.3-2.47.7940.4515.6138010490648770.9250.48499.4
2.4-2.58.2260.3766.7934302416641700.9530.403100.1
2.5-2.68.3690.337.9129818358835630.9520.35399.3
2.6-2.78.20.38.5624861302830320.960.321100.1
2.7-2.88.1660.2729.0821003259625720.9720.29199.1
2.8-2.97.7580.2419.9117898231823070.9730.25999.5
2.9-37.6760.21310.7314830193619320.9740.22999.8
3-3.58.0820.16713.2955318689468450.9860.17999.3
3.5-47.9370.14215.9330083383437900.9890.15398.9
4-67.8570.13117.0242866550654560.9910.1499.1
6-107.6860.14817.3913711180017840.9920.15999.1
10-49.4098.6510.14619.1742915104960.9950.15497.3

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XT5

5xt5


Resolution: 2→49.409 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 24.16
RfactorNum. reflection% reflection
Rfree0.2417 1557 5 %
Rwork0.2115 --
obs0.213 31147 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 124.2 Å2 / Biso mean: 43.9021 Å2 / Biso min: 15.32 Å2
Refinement stepCycle: final / Resolution: 2→49.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4261 0 4 53 4318
Biso mean--33.13 45.36 -
Num. residues----557
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2525X-RAY DIFFRACTION16.538TORSIONAL
12B2525X-RAY DIFFRACTION16.538TORSIONAL
13C2525X-RAY DIFFRACTION16.538TORSIONAL
14D2525X-RAY DIFFRACTION16.538TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.06460.31361420.269127072849
2.0646-2.13840.29271410.235826732814
2.1384-2.2240.25641430.224627142857
2.224-2.32520.23461390.222426522791
2.3252-2.44780.24461420.219426912833
2.4478-2.60110.26231440.215727312875
2.6011-2.8020.25831400.227926672807
2.802-3.08390.26721420.209626982840
3.0839-3.530.22541420.201426862828
3.53-4.4470.22561410.187526872828
4.447-49.42360.22421410.214826842825
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)
10.20720.18710.02140.1268-0.05630.0244-0.19330.005-0.5786-0.0799-0.0042-0.4795-0.1295-0.532200.17990.0546-0.00430.421-0.1456-0.0283-10.6623-1.8859-23.8383
20.0213-0.013-0.06630.1067-0.09960.08890.07940.0868-0.4677-0.0140.1911-0.06150.13090.4276-00.1652-0.0187-0.00660.1708-0.0170.16944.679-3.8192-7.5677
30.03640.0618-0.03010.08120.0220.0502-0.08170.31570.01710.06150.13540.1174-0.5060.0792-00.23550.0338-0.0320.303-0.05520.3191-1.199311.0919-6.0874
40.05160.07270.03180.06320.04620.30090.05270.20890.07760.0932-0.04860.0157-0.16480.0512-00.1791-0.0281-0.01720.24140.03530.216.42223.8514-6.6138
50.19450.03410.04950.38430.31550.0007-0.0569-0.0360.1083-0.01020.0127-0.09280.0507-0.0107-00.15740.0019-0.01450.17830.00080.16324.86191.1527-13.4695
60.0344-0.0622-0.1090.0515-0.01720.1426-0.15150.04640.148-0.21320.1226-0.2483-0.0904-0.168800.33330.0162-0.00390.35040.10780.24537.600910.8996-22.0405
70.0149-0.00870.0444-0.0312-0.02870.00390.06990.587-0.4419-0.07750.5274-0.39340.152-0.2654-00.62930.01060.06190.78180.20480.42575.41858.6175-29.9818
8-0.0572-0.06930.0235-0.00090.0140.0343-0.88940.3475-0.5873-0.6315-0.1557-0.7206-0.61640.0634-00.48160.1745-0.23180.3747-0.0064-0.0747-4.84686.8262-25.1797
9-0.02120.0180.08210.03280.03170.1234-0.05480.19470.6675-0.2424-0.05290.0243-0.29710.2068-00.1892-0.0061-0.06910.14050.05190.36593.975511.5906-12.9091
100.18070.1099-0.14550.0472-0.14840.1132-0.1488-0.0707-0.1667-0.12190.09420.0568-0.01670.298900.25530.00790.03810.3036-0.02180.145411.6053-16.4393-23.432
110.0974-0.14740.07480.2266-0.12010.00050.232-0.06090.03930.0512-0.18850.1551-0.33580.0608-00.1520.00550.02440.1359-0.00590.1572-3.9999-9.8657-6.3996
120.0189-0.06130.013-0.0857-0.16310.1003-0.06490.13160.43960.2250.0114-0.03840.33370.0593-00.24070.07650.01320.19880.07580.3551.7184-23.6988-1.6883
130.0034-0.0294-0.0073-0.0707-0.02950.18520.26250.0828-0.2976-0.1275-0.09580.01340.1379-0.006100.2023-0.02790.02170.19970.04120.2537-6.0643-16.9009-3.7003
140.02280.0411-0.1768-0.0039-0.2820.17440.0654-0.14320.2827-0.0155-0.02730.006-0.1011-0.059700.15060.02280.0290.31180.01470.2635-5.8116-14.4054-7.5114
150.2111-0.2281-0.28280.0203-0.07070.1927-0.05230.1626-0.2193-0.1418-0.03470.02850.15320.0092-00.1784-0.02730.00910.1333-0.05590.1624-5.3053-21.6484-15.4236
16-0.01010.0309-0.01660.0150.01960.0039-0.3858-0.091-0.143-0.1412-0.35470.09470.13580.1702-00.5814-0.00270.12830.2351-0.09760.4556-4.732-28.3168-24.7408
170.0109-0.02230.0006-0.0246-0.00290.0366-0.13840.83120.8944-0.32020.73360.39660.5082-0.6705-00.42030.12960.02530.1159-0.25770.05015.5764-24.6068-20.9886
180.0089-0.0301-0.01190.0505-0.01670.18220.21710.0897-0.71520.0469-0.21060.049-0.0472-0.033-00.21550.01950.01020.1483-0.00380.3776-1.6269-26.4811-9.142
190.1115-0.12420.03750.04950.01520.091-0.17060.0333-0.03270.11170.0754-0.01720.02670.2206-00.22890.0115-0.03850.26680.01560.135810.994616.85524.1023
20-0.00740.00440.09060.35220.1297-0.01020.3554-0.02810.0331-0.0373-0.2540.52930.08380.276900.1960.0226-0.03830.0986-0.02330.2331-4.806910.41737.0856
210.1952-0.10350.35840.4648-0.24020.48590.00880.03970.0542-0.0837-0.01020.06960.00930.014700.14280.00030.00470.13910.00810.1768-4.242718.28618.3663
220.06-0.01520.0231-0.0229-0.05960.08260.0344-0.55440.69660.1711-0.23220.3191-0.1583-0.152500.3229-0.00950.02910.2859-0.12450.4275-7.862527.845617.9565
23-0.03130.0374-0.0356-0.0069-0.0092-0.0051-0.133-0.2184-0.48450.28710.26560.2903-0.09940.066600.4502-0.01580.04710.542-0.12430.6367-6.445128.354626.1978
240.0385-0.05950.047-0.002-0.10590.0571-0.2793-0.24810.22020.16640.2732-0.2897-0.1368-0.4278-00.3124-0.0316-0.0330.2207-0.08970.24464.839724.770622.0317
25-0.06030.0429-0.02140.1397-0.00550.19930.0656-0.1270.70790.0441-0.12290.2203-0.0167-0.029200.24930.00710.01870.1574-0.00040.429-0.891226.834510.6305
260.2043-0.0853-0.06650.24380.01490.0477-0.17340.10810.21470.16860.1198-0.05270.3712-0.2895-00.2217-0.0430.01830.2841-0.06680.1634-11.95272.187525.9062
27-0.00340.04750.0517-0.02140.07040.0837-0.0244-0.01310.23920.06710.10360.01180.05110.146700.1487-0.006-0.01450.1991-0.01280.13634.11734.47538.2135
28-0.02030.088-0.0250.03270.14760.0369-0.00990.05110.31130.11680.07050.20890.96710.092800.4336-0.09350.02550.2903-0.08780.2803-1.6398-10.34876.4371
290.0405-0.1453-0.06010.26220.04530.19850.0346-0.5504-0.4661-0.0853-0.2065-0.0904-0.1044-0.0917-00.18280.0220.02590.23550.020.23265.6218-3.2837.1594
300.1689-0.1913-0.37730.22410.18770.3066-0.04290.1211-0.08140.05970.0020.0147-0.06290.038900.190.0058-0.00420.17820.00920.11284.1071-0.557313.9693
310.0080.0095-0.0032-0.0564-0.1309-0.0225-0.2196-0.5815-0.69930.07520.0546-0.1066-0.25460.2953-00.3395-0.0093-0.02460.45290.16820.33677.3029-10.019722.1803
320.0209-0.0134-0.01570.0004-0.00460.0047-0.168-0.27990.01780.30980.48960.0837-0.3897-0.3148-00.5264-0.0496-0.10780.45240.01060.57433.6025-7.408428.2747
330.0384-0.0794-0.00210.0459-0.01430.0285-0.2674-0.62410.07810.360.0043-0.2728-0.0146-0.6248-00.432-0.13120.05620.38240.03480.2615-5.6498-6.530525.6875
34-0.0299-0.04970.01010.0182-0.26050.11330.2285-0.1731-0.68190.0379-0.2839-0.0999-0.03850.04-00.23630.02620.01190.18820.0430.30481.3661-11.102313.8884
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 20 )A4 - 20
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 31 )A21 - 31
3X-RAY DIFFRACTION3chain 'A' and (resid 32 through 42 )A32 - 42
4X-RAY DIFFRACTION4chain 'A' and (resid 43 through 52 )A43 - 52
5X-RAY DIFFRACTION5chain 'A' and (resid 53 through 84 )A53 - 84
6X-RAY DIFFRACTION6chain 'A' and (resid 85 through 100 )A85 - 100
7X-RAY DIFFRACTION7chain 'A' and (resid 101 through 110 )A101 - 110
8X-RAY DIFFRACTION8chain 'A' and (resid 111 through 122 )A111 - 122
9X-RAY DIFFRACTION9chain 'A' and (resid 123 through 144 )A123 - 144
10X-RAY DIFFRACTION10chain 'B' and (resid 2 through 20 )B2 - 20
11X-RAY DIFFRACTION11chain 'B' and (resid 21 through 31 )B21 - 31
12X-RAY DIFFRACTION12chain 'B' and (resid 32 through 42 )B32 - 42
13X-RAY DIFFRACTION13chain 'B' and (resid 43 through 52 )B43 - 52
14X-RAY DIFFRACTION14chain 'B' and (resid 53 through 66 )B53 - 66
15X-RAY DIFFRACTION15chain 'B' and (resid 67 through 99 )B67 - 99
16X-RAY DIFFRACTION16chain 'B' and (resid 100 through 110 )B100 - 110
17X-RAY DIFFRACTION17chain 'B' and (resid 111 through 122 )B111 - 122
18X-RAY DIFFRACTION18chain 'B' and (resid 123 through 142 )B123 - 142
19X-RAY DIFFRACTION19chain 'C' and (resid 2 through 20 )C2 - 20
20X-RAY DIFFRACTION20chain 'C' and (resid 21 through 31 )C21 - 31
21X-RAY DIFFRACTION21chain 'C' and (resid 32 through 84 )C32 - 84
22X-RAY DIFFRACTION22chain 'C' and (resid 85 through 100 )C85 - 100
23X-RAY DIFFRACTION23chain 'C' and (resid 101 through 110 )C101 - 110
24X-RAY DIFFRACTION24chain 'C' and (resid 111 through 122 )C111 - 122
25X-RAY DIFFRACTION25chain 'C' and (resid 123 through 140 )C123 - 140
26X-RAY DIFFRACTION26chain 'D' and (resid 2 through 20 )D2 - 20
27X-RAY DIFFRACTION27chain 'D' and (resid 21 through 31 )D21 - 31
28X-RAY DIFFRACTION28chain 'D' and (resid 32 through 42 )D32 - 42
29X-RAY DIFFRACTION29chain 'D' and (resid 43 through 52 )D43 - 52
30X-RAY DIFFRACTION30chain 'D' and (resid 53 through 84 )D53 - 84
31X-RAY DIFFRACTION31chain 'D' and (resid 85 through 99 )D85 - 99
32X-RAY DIFFRACTION32chain 'D' and (resid 100 through 110 )D100 - 110
33X-RAY DIFFRACTION33chain 'D' and (resid 111 through 122 )D111 - 122
34X-RAY DIFFRACTION34chain 'D' and (resid 123 through 142 )D123 - 142

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