PDB-9dcl: [2Fe-2S] SufU from Mycobacterium tuberculosis

Basic information

• Entry: Database: PDB / ID: 9dcl
• Title: [2Fe-2S] SufU from Mycobacterium tuberculosis
• Components: Possible nitrogen fixation related protein
• Keywords: BIOSYNTHETIC PROTEIN / Fe-S cluster biogenesis Fe-S binding
• Function / homology: 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 / cytoplasm / FE2/S2 (INORGANIC) CLUSTER / Possible nitrogen fixation related protein
• Biological species: Mycobacterium tuberculosis H37Rv (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
• Authors: Stuteley, S.M. / Bashiri, G.

Funding support

New Zealand, 1items

Organization	Grant number	Country
Health Research Council (HRC)		New Zealand

• Citation: Journal: Biorxiv / Year: 2025; Title: Feedback regulation of iron-sulfur cluster biogenesis.; Authors: Stuteley, S.M. / Chen, J. / Wang, J. / Dawes, S. / Baker, E.N. / Squire, C.J. / Pandelia, M.E. / Bashiri, G.

History

Deposition	Aug 26, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 30, 2025	Provider: repository / Type: Initial release

Assembly

Deposited unit

A: Possible nitrogen fixation related protein

hetero molecules

Summary:

• 17.9 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	17,874	2
Polymers	17,698	1
Non-polymers	176	1
Water	649	36

1

A: Possible nitrogen fixation related protein

hetero molecules

A: Possible nitrogen fixation related protein

hetero molecules

A: Possible nitrogen fixation related protein

hetero molecules

A: Possible nitrogen fixation related protein

hetero molecules

Summary:

• defined by author&software
• Evidence: light scattering, SEC-MALS
• 71.5 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	71,494	8
Polymers	70,791	4
Non-polymers	703	4
Water	72	4

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_555	-x,-y,z	1
crystal symmetry operation	3_555	-y,x,z	1
crystal symmetry operation	4_555	y,-x,z	1

Calculated values:

Buried area	5020 Å2
ΔGint	-80 kcal/mol
Surface area	26130 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	100.118, 100.118, 31.333
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	79
Space group name H-M	I4

Components

#1: Protein

A Possible nitrogen fixation related protein

Details:

Mass: 17697.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: Rv1465 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): LOBSTR / References: UniProt: O53156

#2: Chemical

A-201 ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER

Details:

Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe₂S₂ / Feature type: SUBJECT OF INVESTIGATION

#3: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H₂O

• Has ligand of interest: Y
• Has protein modification: N

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

• Crystal: Density Matthews: 2.23 ų/Da / Density % sol: 44.79 %
• Crystal grow: Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 ; Details: 0.2 M calcium acetate hydrate, 0.1 M sodium cacodylate pH 6.5, 40% v/v PEG 3000

Data collection

• Diffraction: Mean temperature: 100 K / Serial crystal experiment: N
• Diffraction source: Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
• Detector: Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2022
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.9537 Å / Relative weight: 1
• Reflection: Resolution: 1.95→35.42 Å / Num. obs: 11785 / % possible obs: 100 % / Redundancy: 27.3 % / CC_1/2: 0.995 / Net I/σ(I): 7.8
• Reflection shell: Resolution: 1.95→2.05 Å / Num. unique obs: 796 / CC_1/2: 0.699 / % possible all: 100

Processing

Software

Name	Version	Classification
REFMAC	5.8.0349	refinement
XDS		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→35.42 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.945 / SU B: 4.08 / SU ML: 0.111 / Cross valid method: FREE R-VALUE / ESU R: 0.15 / ESU R Free: 0.135
Details: Hydrogens have been added in their riding positions

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.2099	578	4.981 %	Random
Rwork	0.1786	11027	-	-
all	0.18	-	-	-
obs	-	11605	99.983 %	-

• Solvent computation: Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 31.577 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-0.48 Å2	0 Å2	0 Å2
2-	-	-0.48 Å2	0 Å2
3-	-	-	0.961 Å2

Refinement step

Cycle: LAST / Resolution: 1.95→35.42 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1110	0	4	36	1150

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.012	1139
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	1020
X-RAY DIFFRACTION	r_angle_refined_deg	1.289	1.635	1542
X-RAY DIFFRACTION	r_angle_other_deg	0.397	1.553	2366
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.72	5	146
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.32	10	7
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.242	10	175
X-RAY DIFFRACTION	r_dihedral_angle_other_3_deg	12.965	10	3
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.978	10	52
X-RAY DIFFRACTION	r_chiral_restr	0.054	0.2	175
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	1320
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	220
X-RAY DIFFRACTION	r_nbd_refined	0.208	0.2	212
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.184	0.2	922
X-RAY DIFFRACTION	r_nbtor_refined	0.172	0.2	563
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.074	0.2	595
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.105	0.2	28
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.199	0.2	3
X-RAY DIFFRACTION	r_nbd_other	0.098	0.2	23
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.092	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	3.258	3.039	587
X-RAY DIFFRACTION	r_mcbond_other	3.259	3.039	587
X-RAY DIFFRACTION	r_mcangle_it	4.147	4.533	732
X-RAY DIFFRACTION	r_mcangle_other	4.145	4.54	733
X-RAY DIFFRACTION	r_scbond_it	5.073	3.692	552
X-RAY DIFFRACTION	r_scbond_other	5.088	3.691	547
X-RAY DIFFRACTION	r_scangle_it	7.889	5.317	808
X-RAY DIFFRACTION	r_scangle_other	7.894	5.331	807
X-RAY DIFFRACTION	r_lrange_it	8.662	42.516	1222
X-RAY DIFFRACTION	r_lrange_other	8.715	42.094	1218

LS refinement shell

Resolution (Å)	Rfactor Rfree	Num. reflection Rfree	Rfactor Rwork	Num. reflection Rwork	Refine-ID	% reflection obs (%)
1.95-2.001	0.281	43	0.273	789	X-RAY DIFFRACTION	100
2.001-2.055	0.282	48	0.247	784	X-RAY DIFFRACTION	100
2.055-2.115	0.184	56	0.236	758	X-RAY DIFFRACTION	100
2.115-2.18	0.238	38	0.214	735	X-RAY DIFFRACTION	100
2.18-2.251	0.239	40	0.203	713	X-RAY DIFFRACTION	100
2.251-2.33	0.256	22	0.191	713	X-RAY DIFFRACTION	100
2.33-2.417	0.198	37	0.182	684	X-RAY DIFFRACTION	100
2.417-2.515	0.211	38	0.166	630	X-RAY DIFFRACTION	100
2.515-2.627	0.201	27	0.182	637	X-RAY DIFFRACTION	100
2.627-2.754	0.296	32	0.178	578	X-RAY DIFFRACTION	100
2.754-2.902	0.201	37	0.179	573	X-RAY DIFFRACTION	100
2.902-3.077	0.208	30	0.183	525	X-RAY DIFFRACTION	100
3.077-3.287	0.253	21	0.177	521	X-RAY DIFFRACTION	100
3.287-3.548	0.28	13	0.168	484	X-RAY DIFFRACTION	100
3.548-3.883	0.168	31	0.159	433	X-RAY DIFFRACTION	100
3.883-4.335	0.124	25	0.145	390	X-RAY DIFFRACTION	100
4.335-4.993	0.209	9	0.128	370	X-RAY DIFFRACTION	100
4.993-6.085	0.205	9	0.19	319	X-RAY DIFFRACTION	100
6.085-8.481	0.075	11	0.152	240	X-RAY DIFFRACTION	100
8.481-35.42	0.371	11	0.198	151	X-RAY DIFFRACTION	100