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- PDB-6jzw: Crystal structure of SufU from Bacillus subtilis with Cys persulf... -

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Basic information

Entry
Database: PDB / ID: 6jzw
TitleCrystal structure of SufU from Bacillus subtilis with Cys persulfurated
Components(Zinc-dependent sulfurtransferase SufU) x 2
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: 2.64 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 ...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
Revision 1.2Oct 16, 2024Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
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)69,3528
Polymers69,0914
Non-polymers2624
Water46826
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)17,3542
Polymers17,2891
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)17,3542
Polymers17,2891
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.690, 35.520, 105.220
Angle α, β, γ (deg.)90.000, 96.410, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 40 or resid 42 through 103 or resid 110 through 141))
21(chain B and (resid 4 through 40 or resid 42 through 103 or resid 110 through 141))
31(chain C and (resid 4 through 40 or resid 42 through 103 or resid 110 through 141))
41(chain D and (resid 4 through 40 or resid 42 through 141))

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
11ASNASNTHRTHR(chain A and (resid 4 through 40 or resid 42 through 103 or resid 110 through 141))AA4 - 404 - 40
12GLYGLYGLUGLU(chain A and (resid 4 through 40 or resid 42 through 103 or resid 110 through 141))AA42 - 10342 - 103
13LEULEUALAALA(chain A and (resid 4 through 40 or resid 42 through 103 or resid 110 through 141))AA110 - 141110 - 141
21ASNASNTHRTHR(chain B and (resid 4 through 40 or resid 42 through 103 or resid 110 through 141))BB4 - 404 - 40
22GLYGLYGLUGLU(chain B and (resid 4 through 40 or resid 42 through 103 or resid 110 through 141))BB42 - 10342 - 103
23LEULEUALAALA(chain B and (resid 4 through 40 or resid 42 through 103 or resid 110 through 141))BB110 - 141110 - 141
31ASNASNTHRTHR(chain C and (resid 4 through 40 or resid 42 through 103 or resid 110 through 141))CC4 - 404 - 40
32GLYGLYGLUGLU(chain C and (resid 4 through 40 or resid 42 through 103 or resid 110 through 141))CC42 - 10342 - 103
33LEULEUALAALA(chain C and (resid 4 through 40 or resid 42 through 103 or resid 110 through 141))CC110 - 141110 - 141
41ASNASNTHRTHR(chain D and (resid 4 through 40 or resid 42 through 141))DD4 - 404 - 40
42GLYGLYALAALA(chain D and (resid 4 through 40 or resid 42 through 141))DD42 - 14142 - 141

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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 / Variant: 168 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: O32163, Transferases
#2: Protein Zinc-dependent sulfurtransferase SufU / Putative iron-sulfur cluster assembly scaffold protein SufU / Sulfur acceptor protein SufU


Mass: 17288.697 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 / Variant: 168 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: O32163, Transferases
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.97 Å3/Da / Density % sol: 37.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Potassium thiocyanate, 0.1M Tris, 10% w/v PEG 8000, 10% w/v PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1.9 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Jun 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.9 Å / Relative weight: 1
ReflectionResolution: 2.64→44.924 Å / Num. obs: 16349 / % possible obs: 99.7 % / Redundancy: 23.28 % / Biso Wilson estimate: 52.089 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.126 / Rrim(I) all: 0.129 / Χ2: 1.069 / Net I/σ(I): 20.44 / Num. measured all: 720551 / Scaling rejects: 998
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
2.64-2.7422.9510.974.0275003329832680.9720.99299.1
2.74-2.8422.0980.7934.5362051281928080.980.81299.6
2.84-323.3690.5586.488872380638030.9910.5799.9
3-3.223.7570.3299.4787949371137020.9970.33699.8
3.2-3.422.7380.23313.1365576288828840.9980.23899.9
3.4-3.723.0670.16119.5474228322432180.9990.16599.8
3.7-423.3320.10827.3255483238423780.9990.11199.7
4-4.522.9240.07736.8160428263926360.9990.07999.9
4.5-624.0830.0741.16873743630362810.07199.9
6-1024.2990.04849.55499112061205410.04999.7
10-44.92423.8670.03858.81367657857310.03999.1

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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: 2.64→44.924 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.49
RfactorNum. reflection% reflection
Rfree0.2566 816 5 %
Rwork0.2422 --
obs0.243 16311 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 143.47 Å2 / Biso mean: 66.95 Å2 / Biso min: 25.06 Å2
Refinement stepCycle: final / Resolution: 2.64→44.924 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4238 0 4 26 4268
Biso mean--59.61 48.94 -
Num. residues----554
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2543X-RAY DIFFRACTION11.495TORSIONAL
12B2543X-RAY DIFFRACTION11.495TORSIONAL
13C2543X-RAY DIFFRACTION11.495TORSIONAL
14D2543X-RAY DIFFRACTION11.495TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.64-2.80530.34791320.32882520265299
2.8053-3.02190.33121360.305425732709100
3.0219-3.32590.2751340.271525452679100
3.3259-3.8070.27431350.240925712706100
3.807-4.79550.23021370.20525902727100
4.7955-44.93060.22431420.230826962838100
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)
12.8799-3.50840.77164.607-0.02926.07120.5658-0.1546-0.6342-0.3237-0.2678-1.75680.75890.7344-0.3090.52440.0409-0.00990.5392-0.02390.96829.2147-11.3974-8.2082
27.50230.20121.98117.0129-1.18766.83530.12470.314-0.0659-1.05410.05460.64740.2464-0.3916-0.25850.5460.019-0.01460.4274-0.01980.502810.520.635-15.5105
35.9745-2.14120.4519.98992.07672.1067-0.42090.72980.3240.25330.07420.9294-0.48160.13540.48350.5211-0.1023-0.04950.4180.07030.476210.12065.1332-15.7658
41.0465-0.68090.39072.61231.28373.5380.2428-0.44750.0423-0.1539-0.5254-0.0958-0.0075-0.22340.01730.2873-0.0787-0.04230.4659-0.03670.515116.73193.6214-12.3314
52.8028-4.45420.08648.72082.82216.65760.81011.2475-0.3769-2.7435-0.6667-1.0257-0.5724-0.1211-0.69280.7926-0.07290.29980.5782-0.06850.837326.83256.3996-20.7948
65.7536-1.041-2.18764.7631-2.34618.7475-0.044-0.3410.2297-0.95760.0089-1.4598-0.30780.35020.21230.3144-0.01590.11170.44490.05820.875624.98530.8635-19.6053
73.8013-0.44571.46375.1622-0.90511.5867-0.00610.19450.9137-0.409-0.1688-1.02280.11320.2930.09990.43510.0070.13110.37330.05410.339752.57254.588446.6746
85.15050.6898-0.01922.431-2.33373.9413-0.74060.3583-0.2133-1.07720.60730.08330.87950.35670.04090.57540.05750.12080.469-0.0170.566261.6471-5.203246.8407
94.0507-0.83911.02726.3055-0.50492.720.0028-0.61710.19370.32470.4275-0.8678-0.1550.69750.07850.4603-0.0010.13620.5286-0.06210.707357.8317-5.314948.9771
103.522-0.40921.04598.9952-2.08331.6384-0.00420.00860.1491-1.5186-0.2173-0.2242-0.001-0.1411-0.0080.5153-0.05060.13630.4807-0.05240.445651.5199-2.526946.2219
115.5657-0.61331.70034.395-2.70134.76620.4442-0.4544-0.0878-2.09930.025-0.0180.08540.1645-0.03470.72390.01480.110.42770.06980.417648.9902-6.474735.402
124.7039-1.741.67415.87261.97498.77680.44850.5946-0.3356-0.0177-0.74340.34590.4639-1.33910.24310.9072-0.33190.03281.19140.12250.772339.9415-4.813434.3416
134.1761-2.30750.56366.41791.2977.4455-0.25210.1127-0.2606-0.69350.3045-0.1079-0.1694-0.65170.040.566-0.06480.0860.64360.10660.399651.76431.913337.7173
145.77633.9955-3.01455.2695-1.60343.8414-0.48062.3765-1.0652-0.47230.5921-0.61550.9577-1.3046-0.10680.6074-0.0969-0.2070.79590.12290.308738.1229-9.716860.2652
158.8422-3.97382.36615.74322.16893.95270.20170.9970.8456-0.1290.2419-1.1046-0.57540.9142-0.19010.7309-0.03610.12720.58560.0410.379657.30455.077560.6187
163.41573.1147-0.1298.1024-1.50180.30990.8116-1.1523-0.14910.4394-0.89410.72980.29570.6498-0.18550.8607-0.1336-0.10081.28050.09850.609555.9384-0.92275.2968
175.8494-2.66911.47863.71951.55488.6294-0.470.00310.85181.5770.1764-1.1239-1.0450.31590.16390.43330.0646-0.09840.5497-0.24890.552157.01396.835467.9878
187.7606-0.0703-1.67084.6205-0.46243.94570.36720.40710.2198-0.8053-0.1237-1.2262-0.0310.698-0.36520.45880.0628-0.15710.7063-0.16440.593954.35716.874764.6995
194.1211-1.6099-1.68695.5814-0.41153.59130.39470.8055-0.27180.7482-0.97390.6069-0.8328-0.40730.42190.47260.0014-0.14290.4087-0.03990.334247.37124.193264.3625
208.53385.7133-3.10594.7727-3.28077.08010.80420.09311.10832.6355-0.64491.6022-0.1668-0.5273-0.08060.6656-0.06230.15030.71120.02020.408140.44938.710672.2601
215.2026-0.5345-2.08993.933543.7467-0.16760.1337-0.05010.82940.13740.4008-0.18490.11180.05070.5858-0.0514-0.06570.41260.06930.387241.79522.592971.757
223.19583.0217-1.31496.96120.13741.34110.3196-0.62510.29721.02420.0519-0.47540.15320.4703-0.29050.46390.0492-0.10730.5637-0.05630.472914.82622.96385.5721
231.85262.2596-1.03012.8038-1.3061.0857-0.10130.45750.11610.1891-0.0479-0.32550.2023-0.0737-0.06140.32750.0048-0.08880.3673-0.01240.433911.24-5.92444.9376
247.35946.96070.98947.86992.73964.45870.10440.82591.0792.9517-0.1687-0.85730.01750.7257-0.29481.07080.0433-0.37620.62390.0090.823818.5913-8.173916.7395
251.1131-0.0168-2.10784.1637-3.91987.0726-0.9351-0.6706-0.21041.5912-1.9438-0.45981.25981.3640.79440.8574-0.0131-0.40250.79250.00280.884123.75311.754715.5294
263.70143.3165-1.55193.4320.25574.4027-0.1107-0.6585-0.01091.694-0.06790.0321-0.38780.16050.5580.69990.0791-0.13670.5397-0.02350.489211.0693-2.182415.0639
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 20 )A2 - 20
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 42 )A21 - 42
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 52 )A43 - 52
4X-RAY DIFFRACTION4chain 'A' and (resid 53 through 84 )A53 - 84
5X-RAY DIFFRACTION5chain 'A' and (resid 85 through 100 )A85 - 100
6X-RAY DIFFRACTION6chain 'A' and (resid 101 through 143 )A101 - 143
7X-RAY DIFFRACTION7chain 'B' and (resid 4 through 42 )B4 - 42
8X-RAY DIFFRACTION8chain 'B' and (resid 43 through 52 )B43 - 52
9X-RAY DIFFRACTION9chain 'B' and (resid 53 through 66 )B53 - 66
10X-RAY DIFFRACTION10chain 'B' and (resid 67 through 84 )B67 - 84
11X-RAY DIFFRACTION11chain 'B' and (resid 85 through 100 )B85 - 100
12X-RAY DIFFRACTION12chain 'B' and (resid 101 through 110 )B101 - 110
13X-RAY DIFFRACTION13chain 'B' and (resid 111 through 141 )B111 - 141
14X-RAY DIFFRACTION14chain 'C' and (resid 2 through 20 )C2 - 20
15X-RAY DIFFRACTION15chain 'C' and (resid 21 through 31 )C21 - 31
16X-RAY DIFFRACTION16chain 'C' and (resid 32 through 42 )C32 - 42
17X-RAY DIFFRACTION17chain 'C' and (resid 43 through 52 )C43 - 52
18X-RAY DIFFRACTION18chain 'C' and (resid 53 through 66 )C53 - 66
19X-RAY DIFFRACTION19chain 'C' and (resid 67 through 84 )C67 - 84
20X-RAY DIFFRACTION20chain 'C' and (resid 85 through 99 )C85 - 99
21X-RAY DIFFRACTION21chain 'C' and (resid 100 through 143 )C100 - 143
22X-RAY DIFFRACTION22chain 'D' and (resid 4 through 42 )D4 - 42
23X-RAY DIFFRACTION23chain 'D' and (resid 43 through 84 )D43 - 84
24X-RAY DIFFRACTION24chain 'D' and (resid 85 through 100 )D85 - 100
25X-RAY DIFFRACTION25chain 'D' and (resid 101 through 122 )D101 - 122
26X-RAY DIFFRACTION26chain 'D' and (resid 123 through 141 )D123 - 141

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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