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- PDB-7c8o: Crystal structure of IscU D40A/H106A variant -

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Basic information

Entry
Database: PDB / ID: 7c8o
TitleCrystal structure of IscU D40A/H106A variant
ComponentsNitrogen-fixing NifU domain protein
KeywordsBIOSYNTHETIC PROTEIN / Iron-sulfur cluster biogenesis
Function / homologyNIF system FeS cluster assembly, NifU-like / NIF system FeS cluster assembly, NifU, N-terminal / NifU-like N terminal domain / iron-sulfur cluster assembly / ferrous iron binding / 2 iron, 2 sulfur cluster binding / intracellular iron ion homeostasis / FE2/S2 (INORGANIC) CLUSTER / Nitrogen-fixing NifU domain protein
Function and homology information
Biological speciesMethanothrix thermoacetophila (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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
DepositionJun 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 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 / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9656
Polymers60,6144
Non-polymers3522
Water3,369187
1
A: Nitrogen-fixing NifU domain protein
D: Nitrogen-fixing NifU domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4833
Polymers30,3072
Non-polymers1761
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nitrogen-fixing NifU domain protein
C: Nitrogen-fixing NifU domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4833
Polymers30,3072
Non-polymers1761
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.678, 60.376, 64.562
Angle α, β, γ (deg.)90.000, 95.780, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSSERSERAA10 - 12410 - 124
21LYSLYSSERSERBB10 - 12410 - 124
12SERSERSERSERAA8 - 1248 - 124
22SERSERSERSERCC8 - 1248 - 124
13PHEPHESERSERAA15 - 12415 - 124
23PHEPHESERSERDD15 - 12415 - 124
14LYSLYSSERSERBB10 - 12410 - 124
24LYSLYSSERSERCC10 - 12410 - 124
15PHEPHELYSLYSBB15 - 12515 - 125
25PHEPHELYSLYSDD15 - 12515 - 125
16PHEPHESERSERCC15 - 12415 - 124
26PHEPHESERSERDD15 - 12415 - 124

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 15153.384 Da / Num. of mol.: 4 / Mutation: D40A, H106A
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
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
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: 1.93 Å3/Da / Density % sol: 36.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 0.2 M Potassium iodide, 20 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 7, 2020
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.84→42.26 Å / Num. obs: 40163 / % possible obs: 99.81 % / Redundancy: 3.469 % / Biso Wilson estimate: 36.288 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.09137 / Rpim(I) all: 0.03835 / Rrim(I) all: 0.09928 / Χ2: 0.982 / Net I/σ(I): 13.08 / Num. measured all: 271483 / Scaling rejects: 65
Reflection shellResolution: 1.84→1.86 Å / Redundancy: 3.602 % / Rmerge(I) obs: 0.9103 / Mean I/σ(I) obs: 3.53 / Num. possible: 2428 / Num. unique obs: 3984 / CC1/2: 0.866 / CC star: 0.963 / Rpim(I) all: 0.368 / Rrim(I) all: 0.9831 / % possible all: 99.95

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z7E

2z7e


Resolution: 1.84→42.26 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.978 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2225 2008 5 %RANDOM
Rwork0.1937 ---
obs0.2008 40156 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.98 Å2 / Biso mean: 39.939 Å2 / Biso min: 9.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.01 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.84→42.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3497 0 8 187 3692
Biso mean--22.78 39.89 -
Num. residues----467
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0123563
X-RAY DIFFRACTIONr_angle_refined_deg2.1351.6344777
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7575463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.18523.293167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.91315644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8171520
X-RAY DIFFRACTIONr_chiral_restr0.1290.2478
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022658
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A29140.22
12B29140.22
21A33580.15
22C33580.15
31A28650.2
32D28650.2
41B29390.21
42C29390.21
51B30460.15
52D30460.15
61C28680.2
62D28680.2
LS refinement shellResolution: 1.84→1.906 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2836 200 -
Rwork0.2499 2790 -
all-3983 -
obs--99.97 %
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)
12.4779-1.1962-2.97812.8947-1.93758.5236-0.0281-0.0207-0.44720.05980.22980.7355-0.0479-0.2366-0.20170.06280.0215-0.04670.18040.04040.2601-28.107-13.34128.8323
21.4853-0.98443.21261.4437-1.91437.06680.0590.07560.0652-0.1815-0.1517-0.02530.01770.09550.09270.18370.0688-0.02250.20610.05420.1495-15.1973-9.8794-0.0265
31.0073-1.33030.65712.1495-1.40472.4675-0.05080.10980.003-0.0968-0.14890.23570.1446-0.04780.19970.07640.0205-0.11570.1704-0.02120.3641-22.5329-9.58553.3355
40.2563-1.2488-1.27286.9355.29369.09150.08950.0481-0.0033-0.1035-0.1650.4254-0.7675-0.09890.07560.24870.0387-0.02980.03730.06050.4387-23.17772.08962.1499
53.7942.2886-0.973812.9293-2.21180.481-0.2851-0.61240.0851-0.45180.2785-0.00250.10660.06340.00660.15280.0821-0.02220.1751-0.02560.1792-25.7768-0.86814.9594
60.3212-0.27261.13330.5698-1.20237.1937-0.0010.12420.18490.0023-0.13980.069-0.02520.37010.14080.17050.0217-0.04050.10920.0610.3098-14.6608-3.55794.7772
70.9595-1.018-1.68713.06474.79967.5313-0.16640.30810.24040.1493-0.28290.32520.2477-0.46540.44940.1875-0.0207-0.03160.23150.04390.2857-22.0066-26.53148.7243
81.3653-0.57172.34830.3709-1.20284.41230.09480.0161-0.0962-0.06450.02220.01630.2306-0.0191-0.11690.15960.0014-0.04540.2222-0.00710.1416-10.7462-38.95061.5066
90.0353-0.05040.17040.9692-0.47033.38290.05230.0063-0.0238-0.01050.0853-0.0126-0.1798-0.1916-0.13750.15030.0285-0.02380.21720.01370.1339-14.0057-29.2298-0.9763
100.41640.6176-0.67823.00372.65567.54020.01610.0031-0.0923-0.04180.2295-0.364-0.12290.3393-0.24560.07920.0064-0.00070.2371-0.02870.1924-5.3976-21.30380.8977
113.0838-2.02840.48071.3811-0.3140.0756-0.0829-0.07630.1948-0.00430.0644-0.2076-0.0074-0.01160.01850.184-0.00850.01260.2061-0.00370.2093-1.1928-27.934811.883
120.1898-0.0015-0.58021.44391.9457.33180.08950.0338-0.12520.00170.163-0.0361-0.17140.0877-0.25250.11770.0199-0.050.2263-0.02160.2108-7.154-35.1562-8.3256
135.3673-0.0569-0.10492.311-0.52811.2302-0.00320.1802-0.0535-0.01540.05090.08660.14740.0352-0.04760.1935-0.0234-0.03710.1399-0.01980.1465-11.1697-49.8928.5412
140.39890.3971-0.28341.5201-1.16491.1230.0816-0.054-0.13250.0984-0.05480.0236-0.0981-0.067-0.02680.1372-0.0164-0.03030.2020.00610.1542-14.6077-45.686327.2796
152.17760.81793.57449.201-4.21429.37320.1615-0.14860.0557-0.2302-0.0450.32870.5268-0.2608-0.11650.2313-0.01850.01170.15620.02830.1431-18.7842-61.114833.4876
160.19980.4868-0.03772.1086-0.90961.17320.0679-0.0298-0.0078-0.1263-0.04540.04980.0818-0.1418-0.02250.1838-0.0196-0.05060.1846-0.00510.1752-14.275-48.78721.8827
175.61310.47990.17531.3612-3.10117.426-0.0246-0.05110.2443-0.2147-0.1712-0.06790.66230.41970.19580.43790.0824-0.06290.03390.01620.0992-7.7206-60.211427.6858
180.89940.7716-0.06120.7838-0.25570.35790.1264-0.1034-0.2770.0499-0.1536-0.23010.03680.13050.02730.18270.0196-0.06460.15530.04670.2105-5.6972-51.436424.2185
199.0175-3.4185-1.66481.30470.51142.46920.04590.106-0.3972-0.006-0.02110.1572-0.08360.0559-0.02470.16480.0216-0.02210.15160.00190.1943-18.6946-34.491815.8459
200.67761.3739-1.16163.311-2.90022.5693-0.1290.05930.27230.01470.47390.4431-0.0962-0.4373-0.3450.29110.1641-0.04630.31620.02290.2615-24.9357-20.159626.1917
210.32040.0854-0.64691.8211-0.88511.6019-0.08830.05120.01780.05280.16310.11730.1051-0.1594-0.07490.13980.01820.00280.21890.03590.1841-22.9623-28.876927.1842
226.3989-1.8608-2.71711.34140.0471.8527-0.3108-0.3556-0.06730.33330.1824-0.0975-0.10150.12240.12840.18720.04130.00710.2739-0.03690.0396-15.7884-31.854434.7475
230.2909-0.6390.37351.4477-0.83610.4853-0.17140.00050.05050.41210.0843-0.1495-0.2309-0.02740.08710.22270.03950.010.1792-0.03010.1528-16.437-22.508630.8741
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 25
2X-RAY DIFFRACTION2A26 - 50
3X-RAY DIFFRACTION3A51 - 75
4X-RAY DIFFRACTION4A76 - 91
5X-RAY DIFFRACTION5A92 - 100
6X-RAY DIFFRACTION6A101 - 125
7X-RAY DIFFRACTION7B10 - 21
8X-RAY DIFFRACTION8B22 - 46
9X-RAY DIFFRACTION9B47 - 83
10X-RAY DIFFRACTION10B84 - 97
11X-RAY DIFFRACTION11B98 - 111
12X-RAY DIFFRACTION12B112 - 126
13X-RAY DIFFRACTION13C6 - 15
14X-RAY DIFFRACTION14C16 - 49
15X-RAY DIFFRACTION15C50 - 54
16X-RAY DIFFRACTION16C55 - 79
17X-RAY DIFFRACTION17C80 - 90
18X-RAY DIFFRACTION18C91 - 125
19X-RAY DIFFRACTION19D15 - 19
20X-RAY DIFFRACTION20D20 - 45
21X-RAY DIFFRACTION21D46 - 77
22X-RAY DIFFRACTION22D78 - 95
23X-RAY DIFFRACTION23D96 - 126

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