PDB-4di3: Crystal structure of a 2:1 complex of Treponema pallidum TatP(T) ...

ID or keywords:

Entry

Database: PDB / ID: 4di3

Title

Crystal structure of a 2:1 complex of Treponema pallidum TatP(T) (Tp0957) bound to TatT (Tp0956)

Components

TatP(T) (Tp0957)
TatT (Tp0956)

Keywords

TRANSPORT PROTEIN / protein-protein complex / TRAP transporter / TPAT

Function / homology

Function and homology information

transmembrane transport
Similarity search - Function

Biological species

Treponema pallidum subsp. pallidum (syphilis treponeme)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.05 Å

Authors

Brautigam, C.A. / Deka, R.K. / Norgard, M.V.

Citation

Journal: J.Mol.Biol. / Year: 2012
Title: Structural and Thermodynamic Characterization of the Interaction between Two Periplasmic Treponema pallidum Lipoproteins that are Components of a TPR-Protein-Associated TRAP Transporter (TPAT).
Authors: Brautigam, C.A. / Deka, R.K. / Schuck, P. / Tomchick, D.R. / Norgard, M.V.

History

Deposition	Jan 30, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 23, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jun 20, 2012	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Refinement description / Structure summary / Category: entity / entity_name_com / software Item: _entity.pdbx_description / _software.classification ..._entity.pdbx_description / _software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3	Sep 13, 2023	Group: 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_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4di3.cif.gz	592 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/di/4di3 ftp://data.pdbj.org/pub/pdb/validation_reports/di/4di3	HTTPS FTP

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Related structure data

Related structure data	4di4C 3u64S 3di4 3u65 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4r6e-d 5cod-2 23419 7c01-d 6r9w-d 6v76-d 4rtd-d 3a16-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

D: TatP(T) (Tp0957)

E: TatP(T) (Tp0957)

A: TatT (Tp0956)

B: TatT (Tp0956)

C: TatT (Tp0956)

174 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	148.934, 148.934, 212.805
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	91
Space group name H-M	P4₁22

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	1
1	2
2	2

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	Chain A and not (resid 28:32 or resid 96 or...
2	1	1	Chain B and not (resid 28:32 or resid 96 or...
3	1	1	Chain C and not (resid 28:32 or resid 96 or...
1	1	2	Chain D and not (resid 21:22 or resid 93 or...
2	1	2	Chain E and not (resid 21:22 or resid 93 or...

NCS ensembles :

ID
1
2

#1: Protein	TatP(T) (Tp0957) / TRAP-T family tripartite ATP-independent periplasmic transporter / binding protein Mass: 36278.836 Da / Num. of mol.: 2 / Fragment: soluble fragment, UNP residues 21-342 / Mutation: A185V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Treponema pallidum subsp. pallidum (syphilis treponeme) Strain: Nichols / Gene: TP_0957 / Production host: Escherichia coli (E. coli) / References: UniProt: O83923
#2: Protein	TatT (Tp0956) Mass: 33716.078 Da / Num. of mol.: 3 / Fragment: soluble fragment, UNP residues 23-323 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Treponema pallidum subsp. pallidum (syphilis treponeme) Strain: Nichols / Gene: TP_0956 / Production host: Escherichia coli (E. coli) / References: UniProt: O83922

#1: Protein

TatP(T) (Tp0957) / TRAP-T family tripartite ATP-independent periplasmic transporter / binding protein

Mass: 36278.836 Da / Num. of mol.: 2 / Fragment: soluble fragment, UNP residues 21-342 / Mutation: A185V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Treponema pallidum subsp. pallidum (syphilis treponeme)
Strain: Nichols / Gene: TP_0957 / Production host:

Escherichia coli (E. coli) / References: UniProt: O83923

#2: Protein

TatT (Tp0956)

Mass: 33716.078 Da / Num. of mol.: 3 / Fragment: soluble fragment, UNP residues 23-323
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Treponema pallidum subsp. pallidum (syphilis treponeme)
Strain: Nichols / Gene: TP_0956 / Production host:

Escherichia coli (E. coli) / References: UniProt: O83922

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.4 Å³/Da / Density % sol: 63.79 %
Crystal grow	Temperature: 293 K / pH: 9.5 Details: 0.1 M CHES, 30% PEG400, pH 9.5, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.979347 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 23, 2009

Radiation

Monochromator: sagitally focused Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.979347 Å / Relative weight: 1

Reflection

Resolution: 3.05→50 Å / Num. all: 45743 / Num. obs: 45743 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / R_merge(I) obs: 0.055 / Net I/σ(I): 10

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
3.05-3.16	5.2	0.97	1	98.8
3.16-3.29	5.2	0.621	1	98.8
3.29-3.43	5.2	0.369	1	98.9
3.43-3.62	5.2	0.207	1	99
3.62-3.84	5.2	0.119	1	99.2
3.84-4.14	5.1	0.074	1	99.1
4.14-4.56	5.1	0.046	1	99.2
4.56-5.21	5.1	0.038	1	99.3
5.21-6.57	5	0.041	1	99.4
6.57-50	4.7	0.02	1	98.3

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHENIX	1.7.1_743	refinement
PDB_EXTRACT	3.1	data extraction
SBC-Collect	COLLECT	data collection
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3U64

3u64

Resolution: 3.05→49.65 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 1 / Phase error: 28.98 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.263	2320	5.08 %
R_work	0.203	-	-
obs	0.206	45712	98.9 %
all	-	45713	-

Solvent computation

Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 80.73 Å² / k_sol: 0.32 e/Å³

Displacement parameters

B_iso mean: 117.68 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	8.043 Å²	0 Å²	-0 Å²
2-	-	8.043 Å²	0 Å²
3-	-	-	-16.086 Å²

Refinement step

Cycle: LAST / Resolution: 3.05→49.65 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11376	0	0	0	11376

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	11652
X-RAY DIFFRACTION	f_angle_d	1.233	15825
X-RAY DIFFRACTION	f_dihedral_angle_d	16.817	4214
X-RAY DIFFRACTION	f_chiral_restr	0.088	1753
X-RAY DIFFRACTION	f_plane_restr	0.006	2031

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	1850	X-RAY DIFFRACTION	POSITIONAL
1	2	B	1850	X-RAY DIFFRACTION	POSITIONAL	0.07
1	3	C	1850	X-RAY DIFFRACTION	POSITIONAL	0.057
2	1	D	2065	X-RAY DIFFRACTION	POSITIONAL
2	2	E	2065	X-RAY DIFFRACTION	POSITIONAL	0.064

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 (%)
3.0513-3.1136	0.4707	135	0.3859	2433	X-RAY DIFFRACTION	96
3.1136-3.1813	0.364	136	0.3002	2485	X-RAY DIFFRACTION	99
3.1813-3.2552	0.3589	123	0.2768	2519	X-RAY DIFFRACTION	99
3.2552-3.3366	0.3562	165	0.2703	2496	X-RAY DIFFRACTION	99
3.3366-3.4268	0.3238	133	0.2564	2500	X-RAY DIFFRACTION	99
3.4268-3.5276	0.3089	141	0.2411	2514	X-RAY DIFFRACTION	99
3.5276-3.6415	0.3527	124	0.2463	2538	X-RAY DIFFRACTION	99
3.6415-3.7716	0.295	127	0.2172	2545	X-RAY DIFFRACTION	99
3.7716-3.9225	0.264	151	0.2033	2524	X-RAY DIFFRACTION	99
3.9225-4.101	0.2835	123	0.2009	2552	X-RAY DIFFRACTION	99
4.101-4.3171	0.2314	130	0.1834	2549	X-RAY DIFFRACTION	99
4.3171-4.5874	0.2554	128	0.1637	2575	X-RAY DIFFRACTION	99
4.5874-4.9413	0.2445	140	0.1676	2562	X-RAY DIFFRACTION	99
4.9413-5.438	0.2434	145	0.1982	2586	X-RAY DIFFRACTION	100
5.438-6.2235	0.2874	133	0.2182	2620	X-RAY DIFFRACTION	99
6.2235-7.836	0.2413	140	0.1858	2645	X-RAY DIFFRACTION	99
7.836-49.6512	0.2002	146	0.1829	2749	X-RAY DIFFRACTION	98

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	1.8818	-0.0675	-0.8444	1.194	-1.2481	2.5934	-0.1871	0.3332	0.4314	-0.3583	-0.2783	-0.1287	-0.5333	0.0685	0.4348	0.7141	0.1057	-0.2985	0.9445	-0.1768	1.1247	-6.4466	53.1949	-21.5854
2	2.4589	1.5991	-2.9759	3.1442	0.0764	5.5292	-0.0397	0.1622	-1.6634	-0.8597	-1.3354	-0.3576	1.0266	1.5714	0.0882	1.0123	-0.0389	-0.2692	1.0007	-0.0793	1.6602	-4.7059	34.5048	-19.9117
3	0.605	0.2287	-0.201	0.5237	-0.2816	0.7786	0.352	-0.4239	0.3461	0.1884	-0.2043	-0.2579	0.007	0.4351	0.0964	0.7927	0.1735	-0.5873	0.9944	-0.2231	1.4826	-11.8284	36.9507	-9.943
4	2.9289	-0.7269	1.0641	0.537	0.587	3.4386	0.698	0.9397	-0.0679	-0.5862	-0.2047	-0.481	-0.0557	0.3087	-0.251	1.0792	0.2907	-0.2551	1.0375	-0.2432	1.0597	-26.2266	27.7751	-24.0867
5	0.8664	1.0989	-0.9815	1.6804	-1.2468	1.7801	0.4277	-0.2699	-0.3464	0.3387	-0.3427	-0.4173	0.1601	0.3849	-0.0941	0.8499	0.146	-0.338	0.7771	-0.4176	1.1784	-17.3253	45.904	-12.7401
6	2.6802	-0.0389	0.6731	2.0685	-1.5917	1.3697	0.554	0.3459	-0.4414	-0.1529	-0.6758	-1.0126	1.1118	0.5211	0.0256	1.0214	0.2044	-0.5313	0.973	-0.1148	1.6974	-16.4002	25.1678	-9.1485
7	3.2729	-0.2434	0.1882	4.1244	0.9235	4.2511	-0.0813	-0.3967	0.1728	-0.1264	-0.1554	-0.3382	-0.5192	0.0006	0.1996	0.6968	0.2308	0.0608	0.5441	0.1652	0.7233	12.8259	99.2723	-29.0887
8	1.8155	0.2883	-1.7512	2.7529	-0.3834	2.4416	-0.0938	0.6495	-0.5102	-0.3174	-0.3469	-0.987	0.7748	0.0264	0.54	1.1681	0.4694	0.3186	0.9079	0.1287	1.0802	20.9786	90.9919	-41.9548
9	5.1055	-0.2653	-1.2548	2.1501	-0.9836	1.5482	-0.2186	0.3196	0.5805	-0.1377	0.021	0.2894	-0.1776	-0.188	0.0723	1.2546	0.2849	0.0902	1.125	0.1715	0.9322	8.0883	109.2301	-54.9634
10	3.0594	0.5347	-0.5852	2.9364	0.2316	1.5991	0.0988	0.5194	-0.5866	-0.4958	0.0611	-0.4893	0.3824	0.371	-0.0502	0.7192	0.176	0.1482	0.6879	0.0373	0.8561	13.1042	93.7879	-45.8319
11	0.4978	0.1706	0.6386	0.2942	-0.1219	1.3088	0.9695	0.5822	0.3596	-1.329	-1.2384	-0.5684	-0.3984	0.6563	-0.4633	0.6193	0.27	0.118	1.2954	-0.0842	1.1083	29.0477	96.0925	-50.2524
12	4.5137	2.1856	-2.1488	4.1829	-0.4669	2.914	0.1085	1.0191	-0.1511	-0.4966	0.1672	-0.1276	-0.23	-0.2714	-0.4075	0.8677	0.6653	-0.2168	0.9267	-0.3506	0.6345	-34.4508	83.1298	-28.29
13	2.7625	1.3779	0.5138	3.7628	-0.0766	3.0253	0.1269	-0.1384	-0.0205	0.4603	-0.0221	0.1486	-0.202	-0.3711	-0.1198	0.5614	0.2694	-0.1007	0.7928	-0.4236	0.6666	-34.5897	67.7257	-23.6785
14	3.013	0.105	0.7062	2.3771	0.2508	3.2825	0.5624	0.4559	-0.631	0.1784	-0.0216	-0.1027	0.4336	-0.1078	-0.2376	0.632	0.1518	-0.1803	0.9364	-0.5343	0.7745	-37.875	58.8295	-33.4577
15	3.7288	0.8636	0.3554	3.8665	0.1887	2.467	-0.0821	1.1742	-0.6054	0.1119	0.3382	-0.5538	0.2396	0.018	-0.2307	0.6826	0.0986	-0.1103	1.3314	-0.4568	0.9229	-25.1428	59.1188	-41.4855
16	1.2814	0.7243	-0.6638	6.1798	-1.5822	3.1942	0.7207	0.9572	-0.7326	-1.8003	-1.1403	-0.3139	0.2698	0.4038	0.2242	0.9054	0.3587	-0.0331	1.4643	-0.2992	0.8189	-16.0514	67.9361	-42.2399
17	3.1867	-3.6528	-0.6587	7.327	-1.4908	1.8135	-0.0236	0.0357	-0.0181	0.317	-0.389	-0.8356	-0.2563	0.436	0.1303	0.6881	0.1403	-0.1019	0.8135	-0.4159	0.7313	-13.9753	69.9019	-34.116
18	1.336	-0.1173	0.0521	7.2916	-0.1261	3.0415	-0.4118	0.553	-0.2681	1.1543	0.1518	0.4665	0.3791	-0.158	0.1842	0.82	0.2322	-0.0481	0.8643	-0.285	0.7025	-37.9386	86.6194	-13.6729
19	4.7302	-1.3058	-0.9045	3.2084	0.3701	2.7047	0.5097	0.5118	0.7408	0.1749	-0.4968	-0.1485	0.2644	0.0309	-0.0562	0.8733	0.0843	0.0779	0.4967	-0.2196	0.7142	-32.6395	95.0042	-1.2931
20	4.0937	1.4162	0.0722	8.2504	1.4398	2.8252	0.2843	-0.439	0.1781	1.1869	0.1856	0.2727	-0.7884	0.3699	-0.0098	1.0996	0.101	0.545	0.6564	-0.4096	0.9816	-47.2486	104.1075	13.3695
21	2.7316	-1.0246	-1.5942	2.7956	0.835	1.9947	0.2325	-0.7137	0.3932	0.4095	-0.2414	0.0872	-0.4455	0.3089	-0.2253	1.1629	-0.1893	0.216	0.3286	-0.4006	0.5406	-38.0568	94.9922	9.2749
22	5.2768	-1.9091	-0.5853	2.031	-0.924	1.8183	0.2954	-0.551	-0.7262	0.1549	-0.1813	0.1024	0.2409	0.1447	-0.2983	1.4177	-0.1326	0.0644	0.4136	-0.0731	0.7743	-38.691	82.0432	13.3812
23	1.3413	0.3022	-0.1344	1.3288	-0.5317	4.0133	0.8631	-0.0382	-1.1748	0.1793	-0.2373	0.1857	0.3512	0.5259	-0.3691	1.3433	0.0301	-0.1938	0.4989	-0.1696	0.959	-28.9532	72.2309	6.587
24	6.1548	-0.3809	0.7938	5.1154	1.4863	4.5713	-0.017	-0.2409	-0.4418	0.5602	0.3727	0.2953	0.1101	0.3917	-0.3981	0.5943	0.3593	0.1506	0.5592	-0.0916	0.6245	-29.9433	99.5477	-16.9878
25	0.653	-0.7127	-0.3662	1.985	0.3168	1.7425	-0.007	0.5662	0.105	0.088	-0.114	-0.0488	-0.5922	-0.4721	-0.0517	0.7435	0.6374	0.1336	0.9958	-0.1862	0.6013	-26.7579	97.3447	-29.8612
26	3.6307	-0.4464	0.5663	3.3385	-0.8113	2.0234	0.7941	0.6407	-0.4611	-0.5147	-0.283	-0.3039	0.3248	0.4629	-0.334	0.825	0.4424	-0.0113	0.6244	-0.0301	0.6866	-17.2083	95.2893	-34.2974
27	2.2414	-0.276	-0.0754	1.6756	0.1736	0.7474	0.2776	0.9485	0.3173	-0.1838	-0.1306	-0.1514	-0.4893	-0.6654	-0.0613	1.2602	1.2914	0.0824	1.0966	0.0903	0.5497	-19.7511	111.2851	-41.0954
28	2.0898	-0.3203	0.9108	2.3896	0.2429	2.5332	-0.1231	0.4436	0.4653	0.0073	-0.147	-0.1485	-1.2693	-0.6942	0.074	1.2044	0.3365	-0.0058	0.6669	0.0268	0.6752	-10.4444	115.1957	-22.4327
29	6.3841	1.2518	-2.8005	0.9463	-0.1292	2.0445	-0.9384	-0.3261	0.0285	0.0322	0.5532	-0.1806	0.7622	0.3305	0.0553	0.9897	0.163	0.0762	0.6788	-0.0817	0.6731	-8.1771	104.2949	-16.2172

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'D' and (resseq 10:80)	D	10 - 80
2	X-RAY DIFFRACTION	2	chain 'D' and (resseq 81:95)	D	81 - 95
3	X-RAY DIFFRACTION	3	chain 'D' and (resseq 96:149)	D	96 - 149
4	X-RAY DIFFRACTION	4	chain 'D' and (resseq 150:197)	D	150 - 197
5	X-RAY DIFFRACTION	5	chain 'D' and (resseq 198:276)	D	198 - 276
6	X-RAY DIFFRACTION	6	chain 'D' and (resseq 277:321)	D	277 - 321
7	X-RAY DIFFRACTION	7	chain 'E' and (resseq 9:97)	E	9 - 97
8	X-RAY DIFFRACTION	8	chain 'E' and (resseq 98:135)	E	98 - 135
9	X-RAY DIFFRACTION	9	chain 'E' and (resseq 136:226)	E	136 - 226
10	X-RAY DIFFRACTION	10	chain 'E' and (resseq 227:304)	E	227 - 304
11	X-RAY DIFFRACTION	11	chain 'E' and (resseq 305:325)	E	305 - 325
12	X-RAY DIFFRACTION	12	chain 'A' and (resseq 29:61)	A	29 - 61
13	X-RAY DIFFRACTION	13	chain 'A' and (resseq 62:136)	A	62 - 136
14	X-RAY DIFFRACTION	14	chain 'A' and (resseq 137:211)	A	137 - 211
15	X-RAY DIFFRACTION	15	chain 'A' and (resseq 212:248)	A	212 - 248
16	X-RAY DIFFRACTION	16	chain 'A' and (resseq 249:277)	A	249 - 277
17	X-RAY DIFFRACTION	17	chain 'A' and (resseq 278:300)	A	278 - 300
18	X-RAY DIFFRACTION	18	chain 'B' and (resseq 29:61)	B	29 - 61
19	X-RAY DIFFRACTION	19	chain 'B' and (resseq 62:136)	B	62 - 136
20	X-RAY DIFFRACTION	20	chain 'B' and (resseq 137:148)	B	137 - 148
21	X-RAY DIFFRACTION	21	chain 'B' and (resseq 149:192)	B	149 - 192
22	X-RAY DIFFRACTION	22	chain 'B' and (resseq 193:248)	B	193 - 248
23	X-RAY DIFFRACTION	23	chain 'B' and (resseq 249:300)	B	249 - 300
24	X-RAY DIFFRACTION	24	chain 'C' and (resseq 29:47)	C	29 - 47
25	X-RAY DIFFRACTION	25	chain 'C' and (resseq 48:92)	C	48 - 92
26	X-RAY DIFFRACTION	26	chain 'C' and (resseq 93:124)	C	93 - 124
27	X-RAY DIFFRACTION	27	chain 'C' and (resseq 125:211)	C	125 - 211
28	X-RAY DIFFRACTION	28	chain 'C' and (resseq 212:277)	C	212 - 277
29	X-RAY DIFFRACTION	29	chain 'C' and (resseq 278:300)	C	278 - 300

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