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- PDB-5zss: L-Cysteine-PLP reaction intermediate of NifS from Hydrogenimonas ... -

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Basic information

Entry
Database: PDB / ID: 5zss
TitleL-Cysteine-PLP reaction intermediate of NifS from Hydrogenimonas thermophila
Components(Cysteine desulfurase) x 2
KeywordsBIOSYNTHETIC PROTEIN / Cysteine desulfurase
Function / homology
Function and homology information


cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / iron-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
Chem-C6P / cysteine desulfurase
Similarity search - Component
Biological speciesHydrogenimonas thermophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.17 Å
AuthorsNakamura, T. / 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: to be published
Title: X-ray snapshots of two classes of cysteine desulfurase enzymes NifS and SufS
Authors: Nakamura, R. / Fujishiro, T. / Takahashi, Y.
History
DepositionApr 29, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7023
Polymers92,3502
Non-polymers3521
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-34 kcal/mol
Surface area28630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.200, 138.200, 99.100
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 203 or resid 205 through 384))
21(chain B and (resid 0 through 203 or resid 205 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
11HISHISHISHIS(chain A and (resid 0 through 203 or resid 205 through 384))AA0 - 2033 - 206
12PHEPHESERSER(chain A and (resid 0 through 203 or resid 205 through 384))AA205 - 384208 - 387
21HISHISHISHIS(chain B and (resid 0 through 203 or resid 205 through 384))BB0 - 2033 - 206
22PHEPHESERSER(chain B and (resid 0 through 203 or resid 205 through 384))BB205 - 384208 - 387

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Components

#1: Protein Cysteine desulfurase / NifS


Mass: 46060.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: This chain A is an reaction intermediate of L-Cysteine-PLP form of NifS.
Source: (gene. exp.) Hydrogenimonas thermophila (bacteria) / Gene: SAMN05216234_11013 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: A0A1I5NEH3
#2: Protein Cysteine desulfurase / NifS


Mass: 46289.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: This chain B is the resting state of NifS molecule.
Source: (gene. exp.) Hydrogenimonas thermophila (bacteria) / Gene: SAMN05216234_11013 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: A0A1I5NEH3
#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: isolated from a natural source / Formula: C11H17N2O7PS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.19 Å3/Da / Density % sol: 61.48 %
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-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 24, 2017
RadiationMonochromator: Numerical link type double Si(111) crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.17→45.782 Å / Num. obs: 18389 / % possible obs: 100 % / Redundancy: 5.873 % / Biso Wilson estimate: 73.4 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.176 / Rrim(I) all: 0.193 / Χ2: 0.967 / Net I/σ(I): 11.86 / Num. measured all: 210918 / Scaling rejects: 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.17-3.275.8740.9772.2131940.8081.07399.8
3.27-3.55.8680.6543.2460530.8760.718100
3.5-45.870.3086.5387790.9670.338100
4-65.8920.12814125960.9930.141100
6-105.8710.05427.1141710.9990.06100
10-45.7825.70.03146.7811220.9990.03499.2

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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: 3.17→45.782 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 23.7
RfactorNum. reflection% reflection
Rfree0.2379 920 5 %
Rwork0.1878 --
obs0.1904 18385 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 143.28 Å2 / Biso mean: 71.8332 Å2 / Biso min: 19.41 Å2
Refinement stepCycle: final / Resolution: 3.17→45.782 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5995 0 22 12 6029
Biso mean--88.24 33.18 -
Num. residues----773
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2330X-RAY DIFFRACTION9.051TORSIONAL
12B2330X-RAY DIFFRACTION9.051TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.17-3.33710.35861310.28824782609
3.3371-3.54610.29711310.242225032634
3.5461-3.81980.2651300.213524632593
3.8198-4.20390.23241310.177924812612
4.2039-4.81170.1971310.161724942625
4.8117-6.060.22141310.175825022633
6.06-45.78640.21491350.159625442679
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)
11.7969-1.4797-0.23374.20181.87372.0880.05560.0689-0.0918-0.34160.0214-0.0430.01360.2007-0.10850.4923-0.0760.08090.4640.0570.319815.117561.5942-12.7255
21.91771.04153.89492.9270.70597.44230.25280.40180.107-0.1969-0.0039-0.45550.76410.961-0.25210.49330.12960.13870.46030.00210.574931.970566.6928-1.0669
36.1666-2.58842.43128.85290.06083.6420.0032-0.58350.05390.43980.4096-0.50120.20350.4146-0.44490.4381-0.01750.02830.6309-0.04350.352231.216675.186212.79
42.85-0.76471.37332.40872.23184.2138-0.21680.03750.3414-0.42980.1753-0.7043-0.3180.47880.04540.4481-0.00550.09850.44380.10770.58930.193780.71631.3189
59.9231-1.91694.98353.67851.865.57530.28160.0728-0.29360.04790.09210.00840.04070.6895-0.30150.5290.00610.05460.40730.04640.391524.51668.6499-5.2825
67.30165.55073.14695.96196.00449.1704-0.19790.1234-0.8014-0.62740.8297-1.47610.83190.6404-0.8180.82260.10380.14150.41610.06720.604931.476756.846-4.1287
72.1747-3.5099-2.01044.67742.58874.48540.38330.34890.2236-0.7615-0.2417-0.137-0.8592-0.2317-0.26070.5054-0.11-0.01070.39240.03520.43610.457279.813-8.8509
89.2481-0.8582-2.85085.1820.5425.11070.12650.17790.7717-0.1738-0.28330.0976-1.0191-0.33370.09050.40570.0645-0.09280.3657-0.00640.43157.503689.07058.2693
97.34073.13155.19785.35525.20253.85970.3538-0.5484-0.42190.3587-0.3701-0.1727-0.1091-0.5039-0.02750.5278-0.00690.08490.47690.08640.39642.873679.640512.6946
105.13471.46831.9284.6655.00835.4967-0.2336-0.440.4328-0.43480.37270.0561-0.50390.3968-0.28550.5954-0.06350.03560.4720.09690.387611.243485.741310.3086
114.77630.0943-3.91165.50730.7336.04130.0753-0.04480.22720.3483-0.25380.7973-0.7275-0.29780.25670.51830.115-0.0080.40910.00820.5458-5.792385.433610.2903
121.8901-1.5127-1.69753.32181.97842.65440.1535-0.021-0.1198-0.0719-0.2523-0.15070.3202-0.21370.11670.5413-0.08550.05430.45350.04490.45899.949452.0235-8.0519
134.1121-2.78420.45093.8111-0.11972.2059-0.3604-0.5553-0.16480.81730.2001-0.18580.63810.35980.16250.80110.0325-0.00040.5730.11290.487526.428647.32678.2281
142.31650.45910.75052.8399-1.24032.82110.0477-0.544-0.44790.88650.0955-0.2221.40720.3868-0.10861.23880.20290.06210.61830.18440.754627.473136.29379.8077
154.3527-0.6684.2670.87940.93464.87420.0294-0.6173-0.20790.37470.31380.03450.4756-0.2779-0.40880.6559-0.03740.14520.48540.09130.452719.526652.80037.0005
161.6854-1.8367-2.73436.53873.33083.2478-0.4052-0.181-1.00560.3402-0.28170.74940.96250.09430.631.00010.03830.09790.52280.13180.744219.366230.9206-9.4473
174.9859-1.65460.884.19682.15933.1121-0.2911-0.0657-0.83810.37340.2345-0.41720.67120.760.11920.73590.11610.14420.52490.13560.651132.058332.2962-14.3202
184.2809-0.8534-2.68964.6062-0.42776.8802-0.16110.854-1.23250.1858-0.75530.32980.3313-0.24720.88110.8115-0.03050.05470.338-0.11680.83626.148428.9395-26.7509
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 86 )A58 - 86
3X-RAY DIFFRACTION3chain 'A' and (resid 87 through 131 )A87 - 131
4X-RAY DIFFRACTION4chain 'A' and (resid 132 through 201 )A132 - 201
5X-RAY DIFFRACTION5chain 'A' and (resid 202 through 221 )A202 - 221
6X-RAY DIFFRACTION6chain 'A' and (resid 222 through 241 )A222 - 241
7X-RAY DIFFRACTION7chain 'A' and (resid 242 through 278 )A242 - 278
8X-RAY DIFFRACTION8chain 'A' and (resid 279 through 305 )A279 - 305
9X-RAY DIFFRACTION9chain 'A' and (resid 306 through 329 )A306 - 329
10X-RAY DIFFRACTION10chain 'A' and (resid 330 through 360 )A330 - 360
11X-RAY DIFFRACTION11chain 'A' and (resid 361 through 386 )A361 - 386
12X-RAY DIFFRACTION12chain 'B' and (resid 0 through 36 )B0 - 36
13X-RAY DIFFRACTION13chain 'B' and (resid 37 through 131 )B37 - 131
14X-RAY DIFFRACTION14chain 'B' and (resid 132 through 201 )B132 - 201
15X-RAY DIFFRACTION15chain 'B' and (resid 202 through 241 )B202 - 241
16X-RAY DIFFRACTION16chain 'B' and (resid 242 through 305 )B242 - 305
17X-RAY DIFFRACTION17chain 'B' and (resid 306 through 360 )B306 - 360
18X-RAY DIFFRACTION18chain 'B' and (resid 361 through 384 )B361 - 384

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