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- PDB-6kfy: SufS from Bacillus subtilis in a resting state at 1.96 angstrom r... -

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Basic information

Entry
Database: PDB / ID: 6kfy
TitleSufS from Bacillus subtilis in a resting state at 1.96 angstrom resolution
ComponentsCysteine desulfurase SufS
KeywordsBIOSYNTHETIC PROTEIN / Iron / sulfur / cysteine desulfurase / resting state
Function / homology
Function and homology information


cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / pyridoxal phosphate binding
Similarity search - Function
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 / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Cysteine desulfurase SufS
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsNakamura, R. / Takahashi, Y. / Fujishiro, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science17K14510 Japan
CitationJournal: Febs J. / Year: 2022
Title: Cycloserine enantiomers inhibit PLP-dependent cysteine desulfurase SufS via distinct mechanisms.
Authors: Nakamura, R. / Ogawa, S. / Takahashi, Y. / Fujishiro, T.
History
DepositionJul 9, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Apr 27, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine desulfurase SufS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5928
Polymers46,8151
Non-polymers7777
Water4,035224
1
A: Cysteine desulfurase SufS
hetero molecules

A: Cysteine desulfurase SufS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,18316
Polymers93,6292
Non-polymers1,55414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area11110 Å2
ΔGint-30 kcal/mol
Surface area26750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.900, 92.900, 129.200
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Cysteine desulfurase SufS


Mass: 46814.699 Da / Num. of mol.: 1
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 BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: O32164, cysteine desulfurase
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.45 Å3/Da / Density % sol: 64.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Tris-HCl, 50mM lithium sulfate, 50 % (v/v) PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 10, 2019 / Details: Si(111) double crystal monochromator
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.97→43.067 Å / Num. obs: 46158 / % possible obs: 99.9 % / Redundancy: 5.062 % / Biso Wilson estimate: 43.543 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.103 / Χ2: 1.163 / Net I/σ(I): 9.23 / Num. measured all: 445987 / Scaling rejects: 5
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
1.97-2.075.1860.7572.076296312145121400.7440.843100
2.07-2.24.8650.4653.356164912679126730.8880.522100
2.2-2.55.3830.2835.9810872520198201970.9640.314100
2.5-35.0380.13610.539156818185181760.9880.153100
3-44.7980.08216.166905914420143930.9930.09299.8
4-64.7960.06918.6835545741674110.9950.07799.9
6-105.2970.05120.1212983245224510.9980.057100
10-43.0675.2090.0420.2434956826710.9980.04598.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZS9

5zs9


Resolution: 1.97→43.067 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 16.14
RfactorNum. reflection% reflection
Rfree0.1825 2307 5 %
Rwork0.1564 --
obs0.1577 46150 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.05 Å2 / Biso mean: 45.998 Å2 / Biso min: 23.92 Å2
Refinement stepCycle: final / Resolution: 1.97→43.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3192 0 50 224 3466
Biso mean--74 49.7 -
Num. residues----408
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.97-2.01280.25141410.20272694
2.0128-2.05970.19591430.1832709
2.0597-2.11120.21621420.17942690
2.1112-2.16830.20141420.16152708
2.1683-2.2320.18251420.15342704
2.232-2.30410.19021440.16272719
2.3041-2.38640.17291430.14952717
2.3864-2.4820.18221430.15462727
2.482-2.59490.17611440.14972727
2.5949-2.73170.19721430.16482725
2.7317-2.90280.20171440.17312735
2.9028-3.12690.21771450.16982750
3.1269-3.44140.18541450.17292752
3.4414-3.93910.17971450.1482756
3.9391-4.96170.16121480.12742810
4.9617-43.0670.16541530.16122920
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)
15.27190.00720.08745.0205-0.05633.33410.167-0.21250.27860.2824-0.0647-0.5358-0.50270.4256-0.10020.3288-0.09840.02490.2456-0.06940.3103-26.703416.3342-13.6661
22.9842-1.3959-0.99742.59720.36362.2470.1246-0.0381-0.30270.2127-0.17380.41170.2323-0.07230.04950.2668-0.06140.00080.1827-0.03610.2281-43.9141-4.7408-12.2402
32.6470.27260.01722.6514-0.05112.60350.1755-0.35550.39760.5104-0.18160.7074-0.3853-0.5190.00710.4010.02880.16260.3815-0.11630.5018-59.946315.6925-5.3905
42.03050.49780.15012.26720.7532.25110.1564-0.2511-0.01680.3689-0.21640.3830.1445-0.23410.05850.2968-0.03430.05270.2406-0.00330.2659-48.3547-2.1028-10.3231
51.8225-0.25540.48355.09570.75440.6088-0.0931-0.22610.24520.5704-0.00410.0544-0.3726-0.05850.07710.556-0.07630.0710.3885-0.10460.3654-37.368727.1248-3.2698
62.52090.06340.14351.711-0.00561.4568-0.08060.08790.4048-0.14180.04840.1606-0.5405-0.07190.04260.4966-0.02210.03510.2525-0.06040.3712-42.004527.3333-16.8681
75.2089-2.08252.9056.5309-3.63818.4993-0.32320.20421.07150.5171-0.2358-0.4957-1.38780.14270.5380.6919-0.13730.04860.3643-0.08640.608-31.513236.7672-16.8011
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 34 )A-1 - 34
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 112 )A35 - 112
3X-RAY DIFFRACTION3chain 'A' and (resid 113 through 198 )A113 - 198
4X-RAY DIFFRACTION4chain 'A' and (resid 199 through 295 )A199 - 295
5X-RAY DIFFRACTION5chain 'A' and (resid 296 through 330 )A296 - 330
6X-RAY DIFFRACTION6chain 'A' and (resid 331 through 384 )A331 - 384
7X-RAY DIFFRACTION7chain 'A' and (resid 385 through 406 )A385 - 406

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