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- PDB-5zsp: NifS from Hydrogenimonas thermophila -

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Basic information

Entry
Database: PDB / ID: 5zsp
TitleNifS from Hydrogenimonas thermophila
ComponentsCysteine desulfurase
KeywordsBIOSYNTHETIC PROTEIN / Cysteine desulfurase
Function / homology
Function and homology information


cysteine desulfurase activity / cysteine metabolic process / iron-sulfur cluster assembly / iron-sulfur cluster binding / metal ion binding / cytosol
Similarity search - Function
Cysteine desulfurase NifS, proteobacteria / 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 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) ...Cysteine desulfurase NifS, proteobacteria / 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 1 / Aspartate Aminotransferase, domain 1 / 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 / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cysteine desulfurase
Similarity search - Component
Biological speciesHydrogenimonas thermophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine desulfurase
B: Cysteine desulfurase


Theoretical massNumber of molelcules
Total (without water)92,5782
Polymers92,5782
Non-polymers00
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-33 kcal/mol
Surface area29360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.940, 134.940, 98.760
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid -1 through 330 or resid 335 through 384))
21chain B

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
11ALAALAASPASP(chain A and (resid -1 through 330 or resid 335 through 384))AA-1 - 3302 - 333
12PROPROSERSER(chain A and (resid -1 through 330 or resid 335 through 384))AA335 - 384338 - 387
21ALAALASERSERchain BBB-1 - 3842 - 387

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Components

#1: Protein Cysteine desulfurase / NifS


Mass: 46289.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hydrogenimonas thermophila (bacteria) / Gene: SAMN05216234_11013 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: A0A1I5NEH3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

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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: 3.02 Å3/Da / Density % sol: 59.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Magnesium chloride, 0.1M Tris-HCl, 20% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 23, 2017
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator,A
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.57→45.486 Å / Num. obs: 32592 / % possible obs: 99.8 % / Redundancy: 20.221 % / Biso Wilson estimate: 56.07 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.092 / Χ2: 1.062 / Net I/σ(I): 26.59 / Num. measured all: 659039 / Scaling rejects: 1186
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
2.57-2.6719.3070.9514.1967477350234950.9450.97799.8
2.67-2.7720.8180.7665.462350300529950.9650.78599.7
2.77-2.8721.6440.5736.8957228264926440.9820.58799.8
2.87-321.4660.3929.5162831293129270.9920.40199.9
3-3.520.6830.20116.57155849754875350.9980.20699.8
3.5-417.9920.09432.0476410425942470.9990.09799.7
4-620.670.05454.52126582612961240.9990.05699.9
6-1018.8590.03470.35385852046204610.035100
10-45.48620.2540.02687.74117275855790.9990.02699

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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: 1EG5

1eg5


Resolution: 2.57→45.486 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2378 1629 5 %
Rwork0.2143 30927 -
obs0.2155 32556 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 176.91 Å2 / Biso mean: 80.7119 Å2 / Biso min: 33.59 Å2
Refinement stepCycle: final / Resolution: 2.57→45.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5985 0 0 43 6028
Biso mean---64.44 -
Num. residues----770
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3460X-RAY DIFFRACTION10.973TORSIONAL
12B3460X-RAY DIFFRACTION10.973TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.57-2.64560.38381350.3425652700100
2.6456-2.7310.34221350.31952547268299
2.731-2.82860.34791350.304625702705100
2.8286-2.94180.32521350.306525642699100
2.9418-3.07570.35481350.301825562691100
3.0757-3.23780.27061350.282825582693100
3.2378-3.44060.29021340.24952573270799
3.4406-3.70620.2711360.239725832719100
3.7062-4.07890.22761360.197825812717100
4.0789-4.66860.16471360.165825812717100
4.6686-5.880.22411370.170426072744100
5.88-45.4930.17281400.165826422782100
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)
13.14821.85531.5371.86820.72112.7605-0.00680.3921-0.2795-0.04610.00020.04990.46620.28780.01720.5670.18660.00270.5219-0.05940.342959.098217.1462-12.4656
21.75180.03331.06622.4982-0.64933.20030.11150.0537-0.3810.2920.01-0.47970.70750.8242-0.15750.75490.2938-0.04590.7955-0.03550.458678.550511.17933.4524
31.59340.79730.08871.74251.3182.86630.02670.1509-0.2655-0.11670.1603-0.42220.29520.8084-0.13970.45230.1925-0.01060.6905-0.03380.373372.776924.4322-3.2659
47.0559-2.85831.83964.80450.09486.4127-0.3722-0.52650.35510.74170.2448-0.73690.1551.20440.03120.539-0.00370.00230.6885-0.03240.414774.443834.632112.0479
56.6586-0.2765-2.60642.57256.2677.372-0.0421-0.50560.49010.01870.2365-0.3648-1.32610.6838-0.36490.5794-0.1268-0.01490.40430.00060.419469.727447.028210.5324
62.04342.05951.16284.15752.37262.36980.07580.07880.13520.4368-0.40590.84790.5571-0.10690.34810.63980.1290.04430.4931-0.13970.61847.712218.5696-2.736
72.96520.86430.4092.6925-0.81721.76880.3627-0.3542-0.71660.8413-0.34230.14841.1211-0.2476-0.0211.31-0.07610.07030.5199-0.0550.673149.8517-2.93548.8894
85.67473.63541.44493.16651.82813.37040.11070.2074-0.01530.4475-0.48771.01020.7098-0.79790.53920.8741-0.0520.11290.7177-0.25680.812734.3518-1.6365-9.1581
94.72570.5226-0.72276.67191.05355.20960.03720.1705-1.0876-0.395-0.17420.3151.3493-0.03250.25580.87080.1233-0.05310.7068-0.24420.842740.4152-9.8938-19.0212
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 57 )A-1 - 57
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 219 )A58 - 219
3X-RAY DIFFRACTION3chain 'A' and (resid 220 through 301 )A220 - 301
4X-RAY DIFFRACTION4chain 'A' and (resid 302 through 360 )A302 - 360
5X-RAY DIFFRACTION5chain 'A' and (resid 361 through 386 )A361 - 386
6X-RAY DIFFRACTION6chain 'B' and (resid -1 through 57 )B-1 - 57
7X-RAY DIFFRACTION7chain 'B' and (resid 58 through 241 )B58 - 241
8X-RAY DIFFRACTION8chain 'B' and (resid 242 through 305 )B242 - 305
9X-RAY DIFFRACTION9chain 'B' and (resid 306 through 384 )B306 - 384

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