PDB-8u79: Crystal Structure of Substrate Binding Protein of Thermus thermop...

ID or keywords:

Entry

Database: PDB / ID: 8u79

Title

Crystal Structure of Substrate Binding Protein of Thermus thermophilus TAXI-TRAP protein with L-glutamate

Components

Immunogenic protein

Keywords

TRANSPORT PROTEIN / substrate binding protein / TRAP protein / glutamine / TAXI-TRAP

Function / homology

TRAP transporter solute receptor, TAXI family / NMT1-like family / CITRIC ACID / GLUTAMIC ACID / Immunogenic protein

Function and homology information

Biological species

Thermus thermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.11 Å

Authors

Antony, I.R. / Currie, M. / Dobson, R.

Funding support

New Zealand, 1items

Citation

Journal: To be published
Title: Crystal structure of a glutamate-binding subunit from a TAXI-TRAP transporter
Authors: Antony, I.R. / Currie, M.J. / Newton-Vesty, M.C. / Tillett, Z.D. / Allison, T.M. / Dobson, R.C.J.

History

Deposition	Sep 14, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 19, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8u79.cif.gz	352.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8u79.ent.gz	219 KB	Display	PDB format
PDBx/mmJSON format	8u79.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8u79_validation.pdf.gz	726.8 KB	Display	wwPDB validaton report
Full document	8u79_full_validation.pdf.gz	732.9 KB	Display
Data in XML	8u79_validation.xml.gz	20.1 KB	Display
Data in CIF	8u79_validation.cif.gz	28.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u7/8u79 ftp://data.pdbj.org/pub/pdb/validation_reports/u7/8u79	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#235 - Jul 2019 AMPA Receptor similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1)

Deposited unit

A: Immunogenic protein

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	51.547, 67.913, 81.170
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Immunogenic protein Mass: 34135.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA1157 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q5SJ57
#2: Chemical	ChemComp-GLU / GLUTAMIC ACID Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₅H₉NO₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₈O₇
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.12 Å³/Da / Density % sol: 42.05 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: Ammonium citrate dibasic, PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953732 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 5, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.953732 Å / Relative weight: 1
Reflection	Resolution: 1.11→43.552 Å / Num. obs: 112678 / % possible obs: 99.7 % / Redundancy: 12.8 % / CC_1/2: 0.999 / R_merge(I) obs: 0.08 / R_pim(I) all: 0.033 / R_rim(I) all: 0.087 / Net I/σ(I): 14.1
Reflection shell	Resolution: 1.11→1.13 Å / Redundancy: 11.2 % / R_merge(I) obs: 1.449 / Num. unique obs: 58184 / CC_1/2: 0.637 / R_pim(I) all: 0.65 / R_rim(I) all: 0.061

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
MOLREP		phasing
Coot		model building
XDS		data reduction
Aimless		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.11→43.51 Å / Cor.coef. F_o:F_c: 0.984 / Cor.coef. F_o:F_c free: 0.981 / SU B: 0.827 / SU ML: 0.017 / Cross valid method: FREE R-VALUE / ESU R: 0.026 / ESU R Free: 0.026
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1378	5583	4.959 %
R_work	0.1201	107007	-
all	0.121	-	-
obs	-	112590	99.705 %

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: 14.478 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.505 Å²	-0 Å²	0 Å²
2-	-	0.195 Å²	-0 Å²
3-	-	-	0.31 Å²

Refinement step

Cycle: LAST / Resolution: 1.11→43.51 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2241	0	27	324	2592

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.012	2642
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2569
X-RAY DIFFRACTION	r_angle_refined_deg	2.03	1.816	3619
X-RAY DIFFRACTION	r_angle_other_deg	0.672	1.752	5927
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.734	5	363
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	11.063	5	15
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.464	10	453
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.832	10	114
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	403
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	3281
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	619
X-RAY DIFFRACTION	r_nbd_refined	0.281	0.2	602
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.206	0.2	2388
X-RAY DIFFRACTION	r_nbtor_refined	0.185	0.2	1295
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	1359
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.23	0.2	228
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.169	0.2	5
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.367	0.2	35
X-RAY DIFFRACTION	r_nbd_other	0.217	0.2	76
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.548	0.2	46
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.402	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	4.336	1.266	1356
X-RAY DIFFRACTION	r_mcbond_other	4.334	1.266	1356
X-RAY DIFFRACTION	r_mcangle_it	6.331	2.288	1741
X-RAY DIFFRACTION	r_mcangle_other	6.329	2.288	1742
X-RAY DIFFRACTION	r_scbond_it	6.492	1.59	1286
X-RAY DIFFRACTION	r_scbond_other	6.49	1.59	1285
X-RAY DIFFRACTION	r_scangle_it	9.36	2.774	1874
X-RAY DIFFRACTION	r_scangle_other	9.358	2.773	1875
X-RAY DIFFRACTION	r_lrange_it	34.018	24.855	3193
X-RAY DIFFRACTION	r_lrange_other	30.771	20.345	3088
X-RAY DIFFRACTION	r_rigid_bond_restr	4.146	3	5211

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 (%)
1.11-1.139	0.243	426	0.231	7493	X-RAY DIFFRACTION	96.0577
1.139-1.17	0.22	389	0.192	7669	X-RAY DIFFRACTION	100
1.17-1.204	0.174	395	0.173	7441	X-RAY DIFFRACTION	100
1.204-1.241	0.181	401	0.157	7201	X-RAY DIFFRACTION	99.9868
1.241-1.282	0.183	340	0.145	7071	X-RAY DIFFRACTION	100
1.282-1.327	0.157	319	0.127	6801	X-RAY DIFFRACTION	100
1.327-1.377	0.145	360	0.116	6565	X-RAY DIFFRACTION	99.9856
1.377-1.433	0.128	318	0.102	6344	X-RAY DIFFRACTION	100
1.433-1.496	0.124	308	0.092	6056	X-RAY DIFFRACTION	100
1.496-1.569	0.113	306	0.088	5825	X-RAY DIFFRACTION	100
1.569-1.654	0.113	305	0.088	5532	X-RAY DIFFRACTION	100
1.654-1.754	0.113	301	0.088	5210	X-RAY DIFFRACTION	100
1.754-1.875	0.119	259	0.094	4954	X-RAY DIFFRACTION	100
1.875-2.025	0.112	248	0.096	4603	X-RAY DIFFRACTION	100
2.025-2.218	0.119	214	0.102	4268	X-RAY DIFFRACTION	100
2.218-2.479	0.118	206	0.104	3881	X-RAY DIFFRACTION	100
2.479-2.861	0.122	178	0.111	3443	X-RAY DIFFRACTION	99.9724
2.861-3.5	0.127	141	0.123	2941	X-RAY DIFFRACTION	100
3.5-4.934	0.145	111	0.127	2327	X-RAY DIFFRACTION	99.918

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