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- PDB-6kfz: SufS from Bacillus subtilis, soaked with L-cysteine for 90 sec at... -

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Basic information

Entry
Database: PDB / ID: 6kfz
TitleSufS from Bacillus subtilis, soaked with L-cysteine for 90 sec at 1.96 angstrom resolution
ComponentsCysteine desulfurase SufS
KeywordsBIOSYNTHETIC PROTEIN / iron / sulfur / cysteine desulfurase / reaction intermediate
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 / 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 ...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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-C6P / DI(HYDROXYETHYL)ETHER / Cysteine desulfurase SufS
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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: 2020
Title: Snapshots of PLP-substrate and PLP-product external aldimines as intermediates in two types of cysteine desulfurase enzymes.
Authors: Nakamura, R. / Hikita, M. / Ogawa, S. / Takahashi, Y. / Fujishiro, T.
History
DepositionJul 9, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteine desulfurase SufS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2895
Polymers46,6191
Non-polymers6714
Water3,783210
1
A: Cysteine desulfurase SufS
hetero molecules

A: Cysteine desulfurase SufS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,57910
Polymers93,2372
Non-polymers1,3418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area8510 Å2
ΔGint-13 kcal/mol
Surface area26830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.800, 92.800, 128.600
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-709-

HOH

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Components

#1: Protein Cysteine desulfurase SufS


Mass: 46618.648 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-C6P / N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-CYSTEINE / 4-((1-CARBOXY-2-THIOL-ETHYLAMINO)-METHYL)-3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDINIUM


Mass: 352.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17N2O7PS
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.43 Å3/Da / Density % sol: 64.15 %
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: 1.86→34.077 Å / Num. obs: 46569 / % possible obs: 99.9 % / Redundancy: 5.194 % / Biso Wilson estimate: 40.483 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rrim(I) all: 0.051 / Χ2: 1.168 / Net I/σ(I): 18.77 / Num. measured all: 539893 / 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
1.86-1.965.3610.7272.168060815036150350.7420.806100
1.96-2.25.070.3134.8813241026121261170.9410.35100
2.2-2.65.3650.12812.4513284324771247620.990.142100
2.6-35.030.06223.336665913282132510.9970.0799.8
3-45.0930.03241.617276314314142880.9990.03699.8
4-65.1560.02354.0238051738273800.9990.026100
6-105.4090.02157.81131712436243510.023100
10-34.0775.0640.01959.533886826690.9990.02198.1

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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: 1.96→34.077 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 16.23
RfactorNum. reflection% reflection
Rfree0.1766 2328 5 %
Rwork0.1562 --
obs0.1572 46568 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 97.1 Å2 / Biso mean: 41.1235 Å2 / Biso min: 21.81 Å2
Refinement stepCycle: final / Resolution: 1.96→34.077 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3163 0 43 210 3416
Biso mean--44.17 44.44 -
Num. residues----406
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.96-20.25091350.20612571
2-2.04350.21941350.17382560
2.0435-2.0910.19161350.172574
2.091-2.14330.17241370.15552596
2.1433-2.20130.18011350.15262570
2.2013-2.2660.19261360.1552572
2.266-2.33920.18411350.15542565
2.3392-2.42270.17571360.15622580
2.4227-2.51970.20321350.16252581
2.5197-2.63430.17081370.15512596
2.6343-2.77320.18261360.16572586
2.7732-2.94680.19891360.17192584
2.9468-3.17420.20321380.17162623
3.1742-3.49340.1931370.17332601
3.4934-3.99820.16221380.14792626
3.9982-5.03470.14891410.12842682
5.0347-34.0770.161460.15492773
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)
12.67320.57780.51113.11290.67323.22390.0359-0.2799-0.11630.09880.065-0.46540.08210.7002-0.09350.18180.0264-0.03210.3886-0.03460.285747.3966-49.0316-35.4042
23.75641.1589-0.07092.78170.80033.06820.0087-0.2774-0.05690.0907-0.05080.15890.2868-0.29240.03680.2059-0.0103-0.0140.21690.03640.138721.4185-54.5907-34.8574
31.6260.7862-0.01384.0159-1.04782.2567-0.1165-0.30420.51670.06490.1050.6035-0.3215-0.3016-0.00260.21260.0444-0.03880.3381-0.12420.397419.201-30.7506-31.822
42.379-0.2128-0.03292.07330.16581.8331-0.0663-0.49430.62810.2240.04470.0667-0.41610.01060.03230.30230.0102-0.02330.3426-0.15830.360627.6158-26.9077-27.7325
54.9776-1.18231.25952.4548-0.28952.4937-0.1052-0.60250.17920.08150.07790.331-0.0612-0.36760.02250.1998-0.03480.02290.2855-0.05310.227615.6863-43.7936-34.5138
64.97812.24380.74773.7926-0.21070.48670.1726-0.6180.27810.4368-0.2365-0.1156-0.26550.40330.0960.3326-0.0343-0.0670.53-0.12360.31351.3777-34.4729-24.7956
72.0799-0.65610.10112.9462-0.08751.7923-0.04270.17650.41240.0185-0.0175-0.3521-0.30740.42980.06190.2982-0.0924-0.05040.4411-0.05590.385249.0101-30.1952-38.3885
84.08333.1712-1.66542.0267-6.78019.35860.0823-0.4326-0.16190.058-0.9567-1.4726-0.39091.46960.77030.3503-0.04260.020.6907-0.08970.659862.1554-35.3724-37.9104
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 34 )A0 - 34
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 78 )A35 - 78
3X-RAY DIFFRACTION3chain 'A' and (resid 79 through 112 )A79 - 112
4X-RAY DIFFRACTION4chain 'A' and (resid 113 through 253 )A113 - 253
5X-RAY DIFFRACTION5chain 'A' and (resid 254 through 295 )A254 - 295
6X-RAY DIFFRACTION6chain 'A' and (resid 296 through 330 )A296 - 330
7X-RAY DIFFRACTION7chain 'A' and (resid 331 through 384 )A331 - 384
8X-RAY DIFFRACTION8chain 'A' and (resid 385 through 405 )A385 - 405

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