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- PDB-5zso: SufS from Bacillus subtilis, soaked with L-cysteine for 90 sec -

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Basic information

Entry
Database: PDB / ID: 5zso
TitleSufS from Bacillus subtilis, soaked with L-cysteine for 90 sec
ComponentsCysteine desulfurase SufS
KeywordsBIOSYNTHETIC PROTEIN / Cysteine desulfurase
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: 2.7 Å
AuthorsNakamura, R. / Fujishiro, T. / Takahashi, Y.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science17K14510 Japan
Japan Society for the Promotion of Science15H04472 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
DepositionApr 29, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
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.title / _citation.year
Revision 1.2Oct 23, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Apr 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 1.4Nov 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 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)47,0773
Polymers46,6191
Non-polymers4582
Water1,22568
1
A: Cysteine desulfurase SufS
hetero molecules

A: Cysteine desulfurase SufS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1546
Polymers93,2372
Non-polymers9174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area7630 Å2
ΔGint-32 kcal/mol
Surface area26340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.800, 91.800, 127.000
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: 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 (E. coli) / Strain (production host): C41(DE3) / References: UniProt: O32164, cysteine desulfurase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 3.44 Å3/Da / Density % sol: 64.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.05M Lithium sulfate, 0.1M Tris-HCl, 50% (v/v) PEG 200, 5mM L-cysteine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 24, 2017
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→45.9 Å / Num. obs: 17487 / % possible obs: 100 % / Redundancy: 6.107 % / Biso Wilson estimate: 49.56 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.148 / Rrim(I) all: 0.162 / Χ2: 0.978 / Net I/σ(I): 10.18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.7-2.86.4820.8162.0333630.7620.887100
2.8-36.4850.5653.0155050.8380.615100
3-46.1060.2128.2138740.980.232100
4-65.7670.08717.7371020.9940.095100
6-105.8370.05422.6923500.9980.06100
10-45.95.6480.04227.926450.9980.04699.1

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J8Q

5j8q


Resolution: 2.7→45.9 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.52
RfactorNum. reflection% reflection
Rfree0.2511 875 5 %
Rwork0.2009 --
obs0.2034 17485 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.73 Å2 / Biso mean: 49.6693 Å2 / Biso min: 14.92 Å2
Refinement stepCycle: final / Resolution: 2.7→45.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3153 0 29 68 3250
Biso mean--55.14 44.19 -
Num. residues----405
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7002-2.86940.32931420.265726982840
2.8694-3.09090.2881440.240527342878
3.0909-3.40180.2471440.230227352879
3.4018-3.89390.26871450.193727532898
3.8939-4.9050.23821460.169227812927
4.905-45.90660.221540.193129093063
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)
15.83070.92740.71035.0769-1.21333.90250.33480.0896-0.49610.11720.0320.60370.4252-0.5222-0.29460.3825-0.0694-0.01820.25470.02850.337525.8705-16.6855-14.8682
22.4864-0.59430.2722.2926-0.11352.00270.175-0.15970.21740.0396-0.1467-0.3654-0.19280.0418-0.040.3871-0.036-0.03610.23740.05640.290342.94674.3589-11.8043
31.68010.3098-0.76822.95440.4561.61090.1602-0.4947-0.38190.586-0.1435-0.84990.39110.63690.02350.46450.0146-0.17590.47780.12910.583459.0437-16.1784-5.5863
43.0539-0.30020.30684.142-0.72014.89460.2416-0.4929-0.15810.2955-0.1594-0.03060.4316-0.0356-0.02210.3377-0.0563-0.04260.33160.08760.312145.5138-8.2179-3.7543
50.28360.2153-0.53822.0229-0.04381.1841-0.0361-0.1350.13740.2849-0.0019-0.5466-0.3730.38540.0250.3422-0.0691-0.13270.40510.03440.469753.53837.5326-13.531
64.8293-0.12380.35163.9234-0.84971.09320.339-0.27460.37770.6311-0.2173-0.253-0.403-0.0138-0.18840.4367-0.0632-0.03430.2521-0.01860.211441.37444.1261-10.377
72.0595-0.5735-0.35033.6445-1.77591.3329-0.1773-0.2297-0.24620.5007-0.0186-0.06060.62310.01520.180.6131-0.0619-0.02920.46080.11190.370136.5375-27.5806-3.862
84.0227-0.2014-0.32573.6190.08211.2445-0.1680.1539-0.6209-0.43830.16680.14130.4684-0.1084-0.04920.6078-0.0464-0.01320.3490.11260.432337.9896-30.0083-17.3368
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 34 )A1 - 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 224 )A199 - 224
5X-RAY DIFFRACTION5chain 'A' and (resid 225 through 263 )A225 - 263
6X-RAY DIFFRACTION6chain 'A' and (resid 264 through 295 )A264 - 295
7X-RAY DIFFRACTION7chain 'A' and (resid 296 through 330 )A296 - 330
8X-RAY DIFFRACTION8chain 'A' and (resid 331 through 405 )A331 - 405

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