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- PDB-7cnv: Crystal structure of IscU H106C variant -

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Basic information

Entry
Database: PDB / ID: 7cnv
TitleCrystal structure of IscU H106C variant
ComponentsNitrogen-fixing NifU domain protein
KeywordsBIOSYNTHETIC PROTEIN / Iron-sulfur cluster biogenesis
Function / homology
Function and homology information


iron-sulfur cluster assembly / ferrous iron binding / 2 iron, 2 sulfur cluster binding / intracellular iron ion homeostasis / cytoplasm
Similarity search - Function
NIF system FeS cluster assembly, NifU-like / NIF system FeS cluster assembly, NifU, N-terminal / NifU-like N terminal domain
Similarity search - Domain/homology
: / FE2/S2 (INORGANIC) CLUSTER / TRIETHYLENE GLYCOL / Nitrogen-fixing NifU domain protein
Similarity search - Component
Biological speciesMethanothrix thermoacetophila (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsKunichika, K. / Takahashi, Y. / Fujishiro, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17K14510 Japan
CitationJournal: to be published
Title: [2Fe-2S] clusters-assembled dimeric structures of IscU iron-sulfur scaffold
Authors: Kunichika, K. / Fujishiro, T. / Takahashi, Y.
History
DepositionAug 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: Nitrogen-fixing NifU domain protein
B: Nitrogen-fixing NifU domain protein
C: Nitrogen-fixing NifU domain protein
D: Nitrogen-fixing NifU domain protein
E: Nitrogen-fixing NifU domain protein
F: Nitrogen-fixing NifU domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,33025
Polymers87,2326
Non-polymers2,09819
Water1,04558
1
A: Nitrogen-fixing NifU domain protein
B: Nitrogen-fixing NifU domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9319
Polymers29,0772
Non-polymers8547
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-90 kcal/mol
Surface area13070 Å2
MethodPISA
2
C: Nitrogen-fixing NifU domain protein
D: Nitrogen-fixing NifU domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7478
Polymers29,0772
Non-polymers6696
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-74 kcal/mol
Surface area12510 Å2
MethodPISA
3
E: Nitrogen-fixing NifU domain protein
F: Nitrogen-fixing NifU domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6528
Polymers29,0772
Non-polymers5756
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-96 kcal/mol
Surface area13210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.820, 104.080, 65.280
Angle α, β, γ (deg.)90.00, 106.12, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSAA1 - 1261 - 126
21LYSLYSBB1 - 1261 - 126
12LEULEUAA1 - 1231 - 123
22LEULEUCC1 - 1231 - 123
13LYSLYSAA1 - 1261 - 126
23LYSLYSDD1 - 1261 - 126
14HISHISAA1 - 1291 - 129
24HISHISEE1 - 1291 - 129
15GLNGLNAA1 - 1271 - 127
25GLNGLNFF1 - 1271 - 127
16LEULEUBB1 - 1231 - 123
26LEULEUCC1 - 1231 - 123
17GLNGLNBB1 - 1271 - 127
27GLNGLNDD1 - 1271 - 127
18LYSLYSBB1 - 1261 - 126
28LYSLYSEE1 - 1261 - 126
19LYSLYSBB1 - 1261 - 126
29LYSLYSFF1 - 1261 - 126
110LEULEUCC1 - 1231 - 123
210LEULEUDD1 - 1231 - 123
111LEULEUCC1 - 1231 - 123
211LEULEUEE1 - 1231 - 123
112LEULEUCC1 - 1231 - 123
212LEULEUFF1 - 1231 - 123
113LYSLYSDD1 - 1261 - 126
213LYSLYSEE1 - 1261 - 126
114LYSLYSDD1 - 1261 - 126
214LYSLYSFF1 - 1261 - 126
115GLNGLNEE1 - 1271 - 127
215GLNGLNFF1 - 1271 - 127

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Nitrogen-fixing NifU domain protein / IscU


Mass: 14538.724 Da / Num. of mol.: 6 / Mutation: H106C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothrix thermoacetophila (archaea)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: A0B757

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Non-polymers , 6 types, 77 molecules

#2: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.32 Å3/Da / Density % sol: 47.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Lithium sulfate, 0.1 M Sodium cacodylate, 30% (w/v) PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 19, 2020
RadiationMonochromator: A liquid nitrogen cooled Si double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.23→46.51 Å / Num. obs: 40566 / % possible obs: 99.9 % / Redundancy: 7.041 % / Biso Wilson estimate: 57.429 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.084 / Χ2: 0.876 / Net I/σ(I): 13.36 / Num. measured all: 285637 / Scaling rejects: 75
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
2.23-2.337.0050.9712.1234865498149770.8051.04999.9
2.33-2.47.0340.7332.8221144300830060.8780.79199.9
2.4-2.56.9220.5883.4926007375937570.9220.63699.9
2.5-37.2170.2417.488715512089120760.9890.25999.9
3-3.56.90.09316.4142536616961650.9970.199.9
3.5-47.0420.05825.2924442347734710.9980.06399.8
4-57.1510.05130.9324715346534560.9980.05599.7
5-66.6280.04931.2610141153215300.9980.05499.9
6-106.9230.04534.9611464166216560.9990.04999.6
10-46.516.7120.04337.4131684824720.9970.04797.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C8N
Resolution: 2.23→46.51 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 15.262 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.304 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23255 2029 5 %RANDOM
Rwork0.20967 ---
obs0.21082 38536 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.313 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20.05 Å2
2--0.28 Å20 Å2
3----0.24 Å2
Refinement stepCycle: 1 / Resolution: 2.23→46.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5833 0 65 58 5956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.0126034
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0251.648041
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4385772
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.43623.811286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.401151115
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2931530
X-RAY DIFFRACTIONr_chiral_restr0.1610.2797
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024458
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8042.7663085
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.9924.1333852
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.4193.1482948
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.93753.05624902
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A38110.1
12B38110.1
21A37160.11
22C37160.11
31A38580.08
32D38580.08
41A39440.1
42E39440.1
51A38560.09
52F38560.09
61B36640.11
62C36640.11
71B38490.09
72D38490.09
81B37880.1
82E37880.1
91B37690.1
92F37690.1
101C36700.11
102D36700.11
111C36750.11
112E36750.11
121C36700.12
122F36700.12
131D37860.1
132E37860.1
141D37460.1
142F37460.1
151E39250.08
152F39250.08
LS refinement shellResolution: 2.23→2.288 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 149 -
Rwork0.378 2820 -
obs--99.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.4635-0.5603-1.3950.5319-0.03691.12340.23310.06870.4696-0.1277-0.0163-0.16040.044-0.0474-0.21690.55060.01910.00710.32880.01990.5464-20.54311.5022.611
22.6466-1.7147-1.54181.11340.98881.0051-0.1091-0.11240.26430.0720.0934-0.20280.22460.16430.01570.53520.05680.00730.43110.0220.4948-15.6187-4.463.673
30.8215-0.3842-0.10852.4811-0.20570.085-0.0452-0.02760.04650.00180.20310.69840.04740.0746-0.15790.49720.0306-0.04430.30350.07020.6863-44.38683.53866.0986
41.4436-0.89870.2080.73370.1391.0887-0.1595-0.0524-0.21550.0590.19610.38850.00510.1236-0.03660.3985-0.0243-0.01880.26380.19780.8256-49.73141.11037.5453
54.112-0.88021.56063.5656-3.48033.54020.00220.323-1.4198-0.11490.0943-0.18710.0074-0.0388-0.09650.60920.08260.0680.0617-0.130.8231-24.315917.7903-19.5259
60.6923-0.52290.43593.2818-1.65540.93110.0198-0.3162-0.39210.1337-0.2905-0.7768-0.1960.00440.27070.49410.018-0.07410.3150.28280.9402-16.977425.08971.4287
71.15031.5135-0.3232.0096-0.41830.11030.0507-0.2736-0.8140.0238-0.3346-1.0029-0.06470.02970.28390.37570.0588-0.07930.28260.21.0361-16.096620.5827-2.8029
84.5205-0.66093.69083.16192.50276.94890.05310.4366-0.5794-0.29480.2224-0.6716-0.03730.8888-0.27550.07330.0360.27670.16030.14251.2481-6.691221.8041-8.8667
92.6872-1.3084-1.02990.88110.39890.47180.13720.554-0.325-0.0858-0.4262-0.3455-0.1957-0.15180.28910.62270.04070.16210.20050.2331.1167-19.193427.4008-14.8168
109.77573.88854.18341.54841.66371.7940.3113-0.1215-0.72660.1136-0.0242-0.29020.1013-0.0628-0.28710.3975-0.0826-0.15550.40630.09040.6298-6.796429.85172.2286
111.04060.24870.71485.72672.00111.16670.266-0.1576-0.12450.4636-0.1842-0.37570.1835-0.2106-0.08190.5561-0.0446-0.04180.36810.07450.4212-35.346323.68680.2539
121.47390.95880.46291.66610.31410.52560.089-0.1583-0.1074-0.2782-0.07260.0596-0.1957-0.1675-0.01640.51460.0441-0.08920.36380.02360.5065-45.0120.4991-11.8656
132.4602-1.19580.81460.997-1.10962.0717-0.17010.62130.1148-0.0095-0.0597-0.34940.4374-0.17450.22980.4983-0.13430.0460.4191-0.20640.489-34.758532.3769-36.5047
142.9464-0.44551.89430.7232-0.2281.2584-0.0282-0.11360.0890.1225-0.0651-0.02580.0834-0.20940.09330.3922-0.18180.10870.6639-0.17560.3868-46.198140.1125-32.9151
1515.53648.73383.102410.4184-1.86062.9787-1.13650.8431-0.3120.93711.52640.3042-1.2566-0.5169-0.38990.54480.21750.11620.5337-0.09580.5017-63.097155.388-31.9862
163.0004-0.0771-0.51160.12320.16920.4043-0.08390.8066-0.13490.1797-0.0017-0.02720.1041-0.07850.08560.4892-0.0856-0.01370.5214-0.01550.4817-19.840840.1994-34.8059
174.411-1.4576-1.39710.84570.64360.5671-0.05030.30840.00420.10450.0603-0.075-0.04750.0354-0.010.3955-0.12130.01390.49990.00580.4986-13.803640.9252-32.7183
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 89
2X-RAY DIFFRACTION2A90 - 132
3X-RAY DIFFRACTION3B1 - 54
4X-RAY DIFFRACTION4B55 - 127
5X-RAY DIFFRACTION5C1 - 16
6X-RAY DIFFRACTION6C17 - 50
7X-RAY DIFFRACTION7C51 - 75
8X-RAY DIFFRACTION8C76 - 96
9X-RAY DIFFRACTION9C97 - 114
10X-RAY DIFFRACTION10C115 - 124
11X-RAY DIFFRACTION11D1 - 24
12X-RAY DIFFRACTION12D25 - 127
13X-RAY DIFFRACTION13E1 - 25
14X-RAY DIFFRACTION14E26 - 124
15X-RAY DIFFRACTION15E125 - 130
16X-RAY DIFFRACTION16F1 - 53
17X-RAY DIFFRACTION17F54 - 128

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