PDB-9eie: Trypanosomatid-specific protein of unknown function

ID or keywords:

Entry

Database: PDB / ID: 9eie

Title

Trypanosomatid-specific protein of unknown function

Components

Trypanosomatid-specific protein of unknown function

Keywords

UNKNOWN FUNCTION / Trypanosome structure prediction SGPP / Structural Genomics / PSI-2 / Protein Structure Initiative / Structural Genomics of Pathogenic Protozoa Consortium

Function / homology

: / Uncharacterized protein

Function and homology information

Biological species

Trypanosoma cruzi (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.45 Å

Authors

Merritt, E.A. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Funding support

1items

Citation

Journal: To Be Published
Title: Prediction and determination of a Structure Genomics target after 20 years
Authors: Merritt, E.A. / Anderson, L. / Boni, E. / Buckner, F.S. / Earnest, T.N. / Hol, W.G. / Holmes, M.A. / Kim, D. / Mehlin, C. / Neely, H. / Van Voorhis, W.C. / Zucker, F.

History

Deposition	Nov 25, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 26, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9eie.cif.gz	139.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9eie.ent.gz	105.6 KB	Display	PDB format
PDBx/mmJSON format	9eie.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9eie_validation.pdf.gz	453.5 KB	Display	wwPDB validaton report
Full document	9eie_full_validation.pdf.gz	459.9 KB	Display
Data in XML	9eie_validation.xml.gz	18 KB	Display
Data in CIF	9eie_validation.cif.gz	22.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ei/9eie ftp://data.pdbj.org/pub/pdb/validation_reports/ei/9eie	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: Tcru006532

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Trypanosomatid-specific protein of unknown function

B: Trypanosomatid-specific protein of unknown function

hetero molecules

47.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Trypanosomatid-specific protein of unknown function

hetero molecules

defined by author
Evidence: dimer interface is mediated by two K+ ions from the crystallization buffer
23.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Trypanosomatid-specific protein of unknown function

hetero molecules

defined by author
23.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	110.225, 71.647, 67.084
Angle α, β, γ (deg.)	90.000, 94.616, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-418- HOH

#1: Protein	Trypanosomatid-specific protein of unknown function Mass: 23645.236 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: Tc00.1047053506679.130 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4E090
#2: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.84 Å³/Da / Density % sol: 57 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M K2HPO4, 0.1 M Tris pH 8, 30% PEG 20000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 1, 2004
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.42→45.714 Å / Num. obs: 17796 / % possible obs: 88.8 % / Redundancy: 3.3 % / CC_1/2: 0.996 / R_merge(I) obs: 0.099 / R_pim(I) all: 0.062 / R_rim(I) all: 0.118 / Χ²: 0.93 / Net I/σ(I): 8.3
Reflection shell	Resolution: 2.42→2.51 Å / % possible obs: 40.3 % / Redundancy: 1.7 % / R_merge(I) obs: 0.482 / Num. measured all: 1471 / Num. unique obs: 851 / CC_1/2: 0.702 / R_pim(I) all: 0.398 / R_rim(I) all: 0.629 / Χ²: 0.83 / Net I/σ(I) obs: 1.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
Aimless		data scaling
PHASER		phasing
DENZO		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: AlphaFold3-generated model, from run in Oct 2024

Resolution: 2.45→45.714 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.911 / SU B: 18.467 / SU ML: 0.197 / Cross valid method: FREE R-VALUE / ESU R: 0.368 / ESU R Free: 0.242
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.231	908	5.166 %
R_work	0.2025	16668	-
all	0.204	-	-
obs	-	17576	91.115 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 43.325 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.34 Å²	0 Å²	-0.368 Å²
2-	-	0.188 Å²	-0 Å²
3-	-	-	0.209 Å²

Refinement step

Cycle: LAST / Resolution: 2.45→45.714 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2662	0	14	78	2754

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.013	2729
X-RAY DIFFRACTION	r_bond_other_d	0.018	0.017	2518
X-RAY DIFFRACTION	r_angle_refined_deg	2.15	1.641	3655
X-RAY DIFFRACTION	r_angle_other_deg	1.551	1.579	5847
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.929	5	336
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.856	22.841	176
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.945	15	523
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	26.192	15	23
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	339
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	3091
X-RAY DIFFRACTION	r_gen_planes_other	0.02	0.02	586
X-RAY DIFFRACTION	r_nbd_refined	0.241	0.2	569
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.202	0.2	2189
X-RAY DIFFRACTION	r_nbtor_refined	0.168	0.2	1243
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.089	0.2	1370
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.198	0.2	66
X-RAY DIFFRACTION	r_metal_ion_refined	0.174	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.22	0.2	25
X-RAY DIFFRACTION	r_nbd_other	0.199	0.2	70
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.149	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	2.79	3.522	1332
X-RAY DIFFRACTION	r_mcbond_other	2.786	3.519	1331
X-RAY DIFFRACTION	r_mcangle_it	4.579	5.266	1663
X-RAY DIFFRACTION	r_mcangle_other	4.578	5.269	1664
X-RAY DIFFRACTION	r_scbond_it	3.175	3.968	1397
X-RAY DIFFRACTION	r_scbond_other	3.174	3.97	1398
X-RAY DIFFRACTION	r_scangle_it	5.379	5.795	1989
X-RAY DIFFRACTION	r_scangle_other	5.377	5.797	1990
X-RAY DIFFRACTION	r_lrange_it	8.004	39.514	2916
X-RAY DIFFRACTION	r_lrange_other	8	39.485	2911
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.082	0.05	5009

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.45-2.514	0.277	28	0.321	644	X-RAY DIFFRACTION	47.4912
2.514-2.582	0.316	51	0.33	790	X-RAY DIFFRACTION	62.1582
2.582-2.657	0.27	66	0.298	987	X-RAY DIFFRACTION	77.5976
2.657-2.739	0.216	59	0.279	1152	X-RAY DIFFRACTION	92.5134
2.739-2.828	0.319	55	0.249	1182	X-RAY DIFFRACTION	98.8019
2.828-2.927	0.26	67	0.246	1158	X-RAY DIFFRACTION	99.4318
2.927-3.038	0.297	44	0.218	1141	X-RAY DIFFRACTION	99.7475
3.038-3.162	0.266	52	0.21	1082	X-RAY DIFFRACTION	99.9119
3.162-3.302	0.218	69	0.206	1007	X-RAY DIFFRACTION	99.9072
3.302-3.462	0.25	54	0.216	1020	X-RAY DIFFRACTION	99.7215
3.462-3.649	0.293	44	0.213	930	X-RAY DIFFRACTION	99.7951
3.649-3.87	0.238	42	0.193	889	X-RAY DIFFRACTION	99.4658
3.87-4.136	0.163	51	0.171	841	X-RAY DIFFRACTION	99.7763
4.136-4.466	0.201	55	0.149	778	X-RAY DIFFRACTION	99.7605
4.466-4.89	0.165	35	0.123	706	X-RAY DIFFRACTION	99.5968
4.89-5.464	0.197	42	0.169	673	X-RAY DIFFRACTION	100
5.464-6.302	0.316	42	0.228	558	X-RAY DIFFRACTION	99.8336
6.302-7.701	0.158	19	0.186	506	X-RAY DIFFRACTION	100
7.701-10.82	0.139	20	0.136	394	X-RAY DIFFRACTION	99.5192
10.82-45.714	0.325	12	0.266	226	X-RAY DIFFRACTION	97.541

Refinement TLS params.

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

ID	L11 (°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)
1	0.166	-0.0255	-0.4157	0.3484	-0.2413	1.3678	0.0092	0.0833	0.0049	0.0085	0.0005	-0.0178	-0.0589	-0.133	-0.0097	0.0681	-0.0204	0.0083	0.1846	-0.0161	0.004	37.3761	7.2325	17.9321
2	0.0283	0.0129	0.1489	0.3372	-0.1558	1.4548	0.0057	-0.0564	0.0077	0.0186	-0.0292	-0.021	0.109	-0.1231	0.0235	0.0798	0.0135	-0.0069	0.1826	-0.024	0.0063	34.6654	16.981	50.8147

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	1 - 204
2	X-RAY DIFFRACTION	2	ALL	BBB	1 - 204

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