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- PDB-5zsq: NifS from Hydrogenimonas thermophila, soaked with L-cysteine for 4 min -

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Basic information

Entry
Database: PDB / ID: 5zsq
TitleNifS from Hydrogenimonas thermophila, soaked with L-cysteine for 4 min
ComponentsCysteine desulfurase
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
cysteine desulfurase
Similarity search - Component
Biological speciesHydrogenimonas thermophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.211 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: to be published
Title: X-ray snapshots of two classes of cysteine desulfurase enzymes NifS and SufS
Authors: Fujishiro, T. / Nakamura, R. / 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


Theoretical massNumber of molelcules
Total (without water)92,5782
Polymers92,5782
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-31 kcal/mol
Surface area28810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.500, 137.500, 98.700
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 385)
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: TYR / End label comp-ID: TYR / Auth seq-ID: 0 - 385 / Label seq-ID: 3 - 388

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 0 through 385)AA
2chain BBB

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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.: 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: 3.13 Å3/Da / Density % sol: 60.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Magnesium chloride, 0.1M Tris-HCl, 20% (v/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 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: 3.21→45.007 Å / Num. obs: 17458 / % possible obs: 99.9 % / Redundancy: 5.845 % / Biso Wilson estimate: 75.65 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.189 / Rrim(I) all: 0.208 / Χ2: 0.927 / Net I/σ(I): 9.5 / Num. measured all: 199285 / Scaling rejects: 58
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.21-3.315.8640.892.0629900.8340.97899.8
3.31-45.8310.4384.15134780.9440.482100
4-65.8630.16110.44124200.9910.177100
6-105.860.06421.5340960.9980.07100
10-45.0075.7160.03539.6511090.9990.03899.1

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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: 1EG5

1eg5


Resolution: 3.211→45.007 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.59
RfactorNum. reflection% reflection
Rfree0.2447 874 5.01 %
Rwork0.1974 --
obs0.1998 17458 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 159.53 Å2 / Biso mean: 77.3635 Å2 / Biso min: 22.95 Å2
Refinement stepCycle: final / Resolution: 3.211→45.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6022 0 0 12 6034
Biso mean---35.21 -
Num. residues----774
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2358X-RAY DIFFRACTION8.459TORSIONAL
12B2358X-RAY DIFFRACTION8.459TORSIONAL
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
3.2108-3.41190.34551450.290727432888
3.4119-3.67530.29961450.246627552900
3.6753-4.04490.27871450.21227652910
4.0449-4.62970.22531440.179127392883
4.6297-5.8310.22621470.181927812928
5.831-45.01180.20121480.164828012949
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)
13.1818-1.98141.81874.9429-1.59033.1063-0.17290.02560.15520.43040.019-0.1549-0.49850.26520.21230.3429-0.04930.09410.4850.07660.3534-58.342821.90829.5703
22.8840.5121.7150.48940.00442.7880.3-0.4527-0.41970.2293-0.0223-0.0390.6049-0.1617-0.27940.65470.03530.02440.46940.10270.492-69.5757.30868.5289
33.8067-1.49321.0566.80121.05022.3292-0.06110.2519-0.433-0.39110.18380.38670.2745-0.0497-0.18310.7126-0.12860.00150.64330.01560.5108-80.48710.3982-12.6664
40.83730.02981.01994.24670.67322.3612-0.1127-0.2406-0.1916-0.15040.11390.80420.1295-0.30040.03210.4599-0.04180.07820.54480.04040.5147-84.73414.0697-1.1937
57.1974.74592.05643.1371.40953.205-0.0917-0.36540.07140.23840.07480.32780.09050.0635-0.18160.5010.01420.09350.5198-0.08190.5016-71.230813.50634.5019
68.35913.79735.06732.37490.6067.73080.7071-0.7787-1.36420.1286-0.01030.08981.0291-0.1303-0.43450.542-0.00390.04620.51880.10060.7227-64.59140.92734.2447
72.0026-2.73591.71613.6341-2.19912.2137-0.0805-0.2511-0.02490.01780.07340.1862-0.101-0.1719-0.01650.50160.01870.00810.5646-0.06380.4298-76.842333.20493.2117
84.12622.8954.11354.8570.7766.0491-0.32220.48390.0011-0.69930.09780.1495-0.3131-0.12180.29390.56940.08140.08740.6088-0.03110.3778-70.932937.801-13.7034
95.3808-0.34674.37323.5903-0.12367.1222-0.140.07940.2988-0.75290.02660.35170.3489-0.0043-0.12190.5072-0.04480.08130.65290.0270.3715-79.522133.0157-10.2059
104.8902-0.04570.23985.5484-3.17726.9464-0.11990.38690.65620.1475-0.0484-0.2747-0.8081-0.07020.51810.46150.0815-0.01180.3937-0.00760.5678-70.785947.5869-10.262
111.2927-0.31270.42941.9031-0.13351.56870.05030.4001-0.2901-0.4529-0.1199-0.18710.55240.34890.0640.64470.10.17440.6379-0.02230.538-50.86171.2945-5.5138
123.7127-0.38150.79092.57430.44453.18120.270.4032-0.176-0.7039-0.0591-0.35410.47060.2095-0.01730.59060.05480.13210.64010.04860.4569-51.13067.0675-7.1661
132.2959-2.46490.87933.6819-2.10142.3523-0.06150.0839-0.0987-0.4153-0.3335-0.5870.6450.47350.37980.61290.15240.14820.70870.05410.6356-39.3506-6.068511.515
144.0765-0.3901-0.97173.3535-3.47846.1876-0.2328-0.4435-1.15970.1199-0.9026-0.91060.29540.50221.01240.50490.17120.05580.71890.09830.8726-37.7065-9.104926.7247
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 36 )A-1 - 36
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 86 )A37 - 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 301 )A242 - 301
8X-RAY DIFFRACTION8chain 'A' and (resid 302 through 329 )A302 - 329
9X-RAY DIFFRACTION9chain 'A' and (resid 330 through 360 )A330 - 360
10X-RAY DIFFRACTION10chain 'A' and (resid 361 through 386 )A361 - 386
11X-RAY DIFFRACTION11chain 'B' and (resid 0 through 181 )B0 - 181
12X-RAY DIFFRACTION12chain 'B' and (resid 182 through 241 )B182 - 241
13X-RAY DIFFRACTION13chain 'B' and (resid 242 through 360 )B242 - 360
14X-RAY DIFFRACTION14chain 'B' and (resid 361 through 385 )B361 - 385

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