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- PDB-5zsk: SufS from Bacillus subtilis soaked with L-cysteine for 63 sec -

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Basic information

Entry
Database: PDB / ID: 5zsk
TitleSufS from Bacillus subtilis soaked with L-cysteine for 63 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-PDA / Cysteine desulfurase SufS
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.24 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 28, 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 1.5Nov 6, 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)46,9392
Polymers46,6191
Non-polymers3201
Water19811
1
A: Cysteine desulfurase SufS
hetero molecules

A: Cysteine desulfurase SufS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8784
Polymers93,2372
Non-polymers6402
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area7020 Å2
ΔGint-40 kcal/mol
Surface area27870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.800, 91.800, 127.500
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-PDA / 2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-PROPIONIC ACID / PYRIDOXYL-ALANINE-5-PHOSPHATE


Mass: 320.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17N2O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.41 Å3/Da / Density % sol: 63.94 %
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: 3.24→45.9 Å / Num. obs: 10298 / % possible obs: 99.9 % / Redundancy: 5.818 % / Biso Wilson estimate: 72.42 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.185 / Rrim(I) all: 0.204 / Χ2: 0.961 / Net I/σ(I): 10.67
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.24-3.345.8450.8982.1917140.740.986100
3.34-3.65.8010.6423.0934580.8460.70699.9
3.6-45.7610.3266.0537940.950.359100
4-65.8570.1511271220.9890.166100
6-105.8360.06423.1123690.9980.071100
10-45.95.6750.03340.396500.9990.03698.9

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Processing

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

5j8q


Resolution: 3.24→45.9 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.53
RfactorNum. reflection% reflection
Rfree0.2441 515 5 %
Rwork0.206 --
obs0.2081 10295 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 123.63 Å2 / Biso mean: 61.3762 Å2 / Biso min: 14.85 Å2
Refinement stepCycle: final / Resolution: 3.24→45.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3196 0 21 11 3228
Biso mean--56.41 28.92 -
Num. residues----410
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.2402-3.56620.32111260.254524042530
3.5662-4.0820.26251270.21724002527
4.082-5.14170.20781270.180224262553
5.1417-45.90460.23381350.202125502685
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)
13.72541.072-0.55512.88580.14892.45230.0624-0.30860.4536-0.0109-0.07310.3267-0.2897-0.244-0.03240.40570.0784-0.03650.40590.01390.2711-37.008652.0376-37.1417
21.02430.4831-0.19092.23040.04121.7541-0.0712-0.0461-0.29810.20430.067-0.09270.30820.17780.00910.3586-0.0012-0.00220.48570.06710.4822-25.790527.3418-28.3042
32.0784-0.66830.29472.0753-0.83112.9651-0.0648-0.1667-0.24390.2764-0.0824-0.22760.20810.11980.15820.41150.0462-0.0070.40260.0730.421-23.68636.2544-28.8187
42.16650.7943-0.24551.28470.18481.58390.1148-0.3389-0.2350.1756-0.1635-0.0928-0.0729-0.03650.03060.33990.0008-0.00090.37580.09110.3114-32.46138.9805-29.8002
51.7667-0.76240.06872.38380.34290.6178-0.10190.244-0.0731-0.0160.00360.29130.29950.01490.08790.482-0.05980.08930.58830.01530.4529-48.830629.9477-38.6319
64.21681.14431.9783.36720.68212.24780.27050.13260.31890.2145-0.51541.15140.5862-0.30750.14910.4401-0.00340.09110.82960.09890.6922-63.827832.9695-40.5991
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 57 )A1 - 57
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 198 )A58 - 198
3X-RAY DIFFRACTION3chain 'A' and (resid 199 through 253 )A199 - 253
4X-RAY DIFFRACTION4chain 'A' and (resid 254 through 330 )A254 - 330
5X-RAY DIFFRACTION5chain 'A' and (resid 331 through 384 )A331 - 384
6X-RAY DIFFRACTION6chain 'A' and (resid 385 through 410 )A385 - 410

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