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- PDB-5zst: NifS from Hydrogenimonas thermopile in a persulfurated form -

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Basic information

Entry
Database: PDB / ID: 5zst
TitleNifS from Hydrogenimonas thermopile in a persulfurated form
ComponentsCysteine desulfurase
KeywordsBIOSYNTHETIC PROTEIN / Cysteine desulfurase
Function / homology
Function and homology information


cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / 2 iron, 2 sulfur cluster binding / metal ion binding
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: 3.1 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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)92,6422
Polymers92,6422
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-31 kcal/mol
Surface area28620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.940, 136.940, 98.820
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 0 through 310 or resid 312 through 384))
21(chain B and (resid 0 through 310 or resid 312 through 384))

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
11HISHISLEULEU(chain A and (resid 0 through 310 or resid 312 through 384))AA0 - 3103 - 313
12ASPASPSERSER(chain A and (resid 0 through 310 or resid 312 through 384))AA312 - 384315 - 387
21HISHISLEULEU(chain B and (resid 0 through 310 or resid 312 through 384))BB0 - 3103 - 313
22ASPASPSERSER(chain B and (resid 0 through 310 or resid 312 through 384))BB312 - 384315 - 387

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Components

#1: Protein Cysteine desulfurase / NifS


Mass: 46321.098 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) / References: UniProt: A0A1I5NEH3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.11 Å3/Da / Density % sol: 60.42 %
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, 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 double crystal Si(111) monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→45.61 Å / Num. obs: 37536 / % possible obs: 99.9 % / Redundancy: 5.799 % / Biso Wilson estimate: 55.89 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.185 / Rrim(I) all: 0.204 / Χ2: 1.008 / Net I/σ(I): 11.49 / Num. measured all: 217677 / Scaling rejects: 30
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
3.1-3.25.8710.9752.0519938340233960.7461.0799.8
3.2-3.35.8790.6922.8517648301130020.8720.75999.7
3.3-3.45.8760.6233.1715577265126510.8850.684100
3.4-3.55.3940.4824.3312832238623790.9130.53699.7
3.5-3.65.8740.3615.3312558214121380.9520.39699.9
3.6-3.75.5220.3136.4410287186718630.9590.34699.8
3.7-3.85.8910.2577.3210120171917180.9720.28399.9
3.8-3.95.3090.2298.778150154215350.9680.25599.5
3.9-45.6920.2218.837827137713750.980.24399.9
4-65.8910.12314.487247512306123020.9930.135100
6-105.8820.05726.3323922406740670.9980.063100
10-45.615.7140.03145.336343111911100.9990.03499.2

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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: 3.1→45.61 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.09 / Stereochemistry target values: ML
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2358 1882 5.02 %
Rwork0.2019 35631 -
obs0.2036 37513 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.77 Å2 / Biso mean: 59.2349 Å2 / Biso min: 16.05 Å2
Refinement stepCycle: final / Resolution: 3.1→45.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6012 0 0 23 6035
Biso mean---28.72 -
Num. residues----773
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2332X-RAY DIFFRACTION6.56TORSIONAL
12B2332X-RAY DIFFRACTION6.56TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1003-3.18410.36441470.319527522899100
3.1841-3.27780.31121400.289127032843100
3.2778-3.38350.26071490.257827882937100
3.3835-3.50440.33121440.29492701284599
3.5044-3.64470.27571440.23327342878100
3.6447-3.81050.27471480.225127492897100
3.8105-4.01130.27161430.228227412884100
4.0113-4.26240.20591460.182127392885100
4.2624-4.59120.2231430.163927392882100
4.5912-5.05270.16741470.161427372884100
5.0527-5.78260.17991480.167527622910100
5.7826-7.28070.21661420.179527242866100
7.2807-45.61470.1891410.145127622903100
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)
12.2587-1.95511.22123.1666-0.69751.342-0.2705-0.09390.00890.24590.1686-0.2253-0.0918-0.2780.09180.38320.00590.06510.45010.02650.2548-60.288317.576312.6863
22.7153-0.56781.88882.57880.36252.97360.1512-0.0019-0.197-0.33950.01730.05980.3726-0.0451-0.1920.4251-0.06760.05670.42850.02090.336-77.47178.4341-7.3301
30.80630.04811.31342.5650.97462.46320.0157-0.162-0.204-0.10760.03850.36620.123-0.4531-0.05870.3297-0.04220.07040.38970.04110.3948-81.701214.9953-0.5495
42.01522.2861.5453.73311.43412.81880.111-0.5454-1.2246-0.2499-0.0286-0.17490.71940.0842-0.12150.64050.08150.04180.41190.08230.4565-68.75732.24354.7654
50.7972-1.94540.78126.0117-3.54532.6618-0.06760.007-0.18230.64140.14220.5971-0.275-0.2636-0.07740.29810.0440.03430.5805-0.03350.282-73.737330.72258.8224
63.52940.8334-0.28263.691-0.90233.3833-0.09210.22230.0799-0.38790.07120.30950.2228-0.20840.01770.41630.05310.05130.4414-0.04790.3219-77.11735.6496-10.2874
74.4897-0.1242-0.50175.8629-2.9675.7985-0.20850.28860.5534-0.0744-0.12730.2447-0.8213-0.32190.31640.29560.0671-0.04390.3712-0.02560.3535-70.582147.4373-10.3646
81.2388-0.84060.26542.4375-0.11351.22550.11360.301-0.2109-0.6411-0.1786-0.38530.40260.33850.05290.54240.09220.16020.4997-0.00130.4185-49.78351.7388-5.0992
92.007-2.2082-2.81454.88473.89086.75420.9181.15530.5063-0.8514-0.5248-0.4823-1.03570.1555-0.38480.6786-0.00480.0610.6835-0.00490.487-56.57497.592-13.6243
102.1597-1.17850.70272.9736-1.53362.0577-0.0320.1829-0.2875-0.1976-0.2077-0.57070.38240.44290.22630.41120.09120.12430.50420.00030.525-40.1062-5.119713.0163
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 131 )A58 - 131
3X-RAY DIFFRACTION3chain 'A' and (resid 132 through 211 )A132 - 211
4X-RAY DIFFRACTION4chain 'A' and (resid 212 through 241 )A212 - 241
5X-RAY DIFFRACTION5chain 'A' and (resid 242 through 278 )A242 - 278
6X-RAY DIFFRACTION6chain 'A' and (resid 279 through 360 )A279 - 360
7X-RAY DIFFRACTION7chain 'A' and (resid 361 through 386 )A361 - 386
8X-RAY DIFFRACTION8chain 'B' and (resid 0 through 211 )B0 - 211
9X-RAY DIFFRACTION9chain 'B' and (resid 212 through 231 )B212 - 231
10X-RAY DIFFRACTION10chain 'B' and (resid 232 through 384 )B232 - 384

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