PDB-3dcl: Crystal structure of TM1086

ID or keywords:

Entry

Database: PDB / ID: 3dcl

Title

Crystal structure of TM1086

Components

TM1086

Keywords

structural genomics / unknown function / TM1086 / SAD / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

tm1086 (SG structure) fold / tm1086 (SG structure) domain / tm1086 fold / tm1086 domain / Protein of unknown function DUF4438 / TM_1086 superfamily / TM_1086, SG structure domain / : / Domain of unknown function (DUF4438), N-terminal / Domain of unknown function (DUF4438), C-terminal ...
Similarity search - Domain/homology

Biological species

Thermotoga maritima (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.25 Å

Authors

Chruszcz, M. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of TM1086
Authors: Chruszcz, M. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A. / Minor, W.

History

Deposition	Jun 3, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 5, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Oct 5, 2011	Group: Structure summary
Revision 1.3	Apr 13, 2022	Group: Database references / Derived calculations / Structure summary Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_site Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Oct 30, 2024	Group: Data collection / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3dcl.cif.gz	287.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3dcl.ent.gz	235.3 KB	Display	PDB format
PDBx/mmJSON format	3dcl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dc/3dcl ftp://data.pdbj.org/pub/pdb/validation_reports/dc/3dcl	HTTPS FTP

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Related structure data

Related structure data	3n99C C: citing same article (ref.)
Similar structure data	3n99-2 3n99-3 3n99-1 3kum-d 3k1g-d 10400 6ut3-d 3jw7-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: APC4579

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: TM1086

B: TM1086

C: TM1086

D: TM1086

E: TM1086

hetero molecules

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

1

A: TM1086

B: TM1086

C: TM1086

D: TM1086

E: TM1086

hetero molecules

A: TM1086

B: TM1086

C: TM1086

D: TM1086

E: TM1086

hetero molecules

defined by author&software
312 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	164.578, 164.578, 97.815
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	A
7	1	B
8	1	C
9	1	D
10	1	E

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	2	A	1 - 162
2	1	1	2	B	1 - 162
3	1	1	2	C	1 - 162
4	1	1	2	D	1 - 162
5	1	1	2	E	1 - 162
6	2	1	2	A	170 - 282
7	2	1	2	B	170 - 282
8	2	1	2	C	170 - 282
9	2	1	2	D	170 - 282
10	2	1	2	E	170 - 282

Details

Decamer (two pentamers) Chains A, B, C, D, E present in asymmetric unit plus chains A, B, C, D, E transformed by -x,-x+y,-z-1/3

#1: Protein	TM1086 Mass: 30793.695 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_1086 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RP / References: UniProt: Q9X0H2
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 641 / Source method: isolated from a natural source / Formula: H₂O
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: 2.48 Å³/Da / Density % sol: 50.48 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M K/NA TARTRATE, 2M AMMONIUM SULPHATE,0.1M NA CITRATE PH5.6, VAPOR DIFFUSION - HANGING DROP, TEMPERATURE 293K, pH 6.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.9794 / Wavelength: 0.979 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 2, 2007 / Details: MIRROR

Radiation

Monochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9794	1
2	0.979	1

Reflection

Resolution: 2.25→50 Å / Num. all: 72494 / Num. obs: 72494 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / R_merge(I) obs: 0.101 / R_sym value: 0.101 / Net I/σ(I): 29.451

Reflection shell

Resolution: 2.25→2.29 Å / Redundancy: 5.9 % / R_merge(I) obs: 0.449 / Mean I/σ(I) obs: 3.7 / R_sym value: 0.449 / % possible all: 98.6

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Processing

Software

Name	Version	Classification
HKL-3000		phasing
MLPHARE		phasing
DM		model building
SHELXD		phasing
RESOLVE		model building
ARP	WARP	model building
Coot		model building
REFMAC	5.2.0019	refinement
HKL-3000		data collection
HKL-2000		data reduction
HKL-2000		data scaling
DM		phasing
RESOLVE		phasing
MAIN		refinement

Refinement

Method to determine structure:

SAD / Resolution: 2.25→50 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.948 / SU B: 10.925 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.258 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.212	2862	4 %	RANDOM
R_work	0.164	-	-	-
all	0.166	71836	-	-
obs	0.166	71836	99.16 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 32.72 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.22 Å²	-1.11 Å²	0 Å²
2-	-	-2.22 Å²	0 Å²
3-	-	-	3.33 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10483	0	87	641	11211

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	10809
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.02	7187
X-RAY DIFFRACTION	r_angle_refined_deg	1.568	1.973	14600
X-RAY DIFFRACTION	r_angle_other_deg	1.236	3	17688
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.695	5	1415
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.48	24.579	404
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.654	15	1883
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.924	15	52
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	1667
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	11990
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1944
X-RAY DIFFRACTION	r_nbd_refined	0.202	0.2	1878
X-RAY DIFFRACTION	r_nbd_other	0.21	0.2	7489
X-RAY DIFFRACTION	r_nbtor_refined	0.167	0.2	5117
X-RAY DIFFRACTION	r_nbtor_other	0.085	0.2	5893
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.141	0.2	615
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.019	0.2	2
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.237	0.2	37
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.258	0.2	91
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.121	0.2	20
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.585	1.5	6974
X-RAY DIFFRACTION	r_mcbond_other	0.128	1.5	2936
X-RAY DIFFRACTION	r_mcangle_it	1.181	2	11222
X-RAY DIFFRACTION	r_scbond_it	2.774	3	3870
X-RAY DIFFRACTION	r_scangle_it	4.156	4.5	3378
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	1563	tight positional	0.05	0.05
2	B	1563	tight positional	0.05	0.05
3	C	1563	tight positional	0.05	0.05
4	D	1563	tight positional	0.05	0.05
5	E	1563	tight positional	0.06	0.05
1	A	1752	medium positional	0.42	0.5
2	B	1752	medium positional	0.45	0.5
3	C	1752	medium positional	0.42	0.5
4	D	1752	medium positional	0.38	0.5
5	E	1752	medium positional	0.56	0.5
1	A	1563	tight thermal	0.13	0.5
2	B	1563	tight thermal	0.13	0.5
3	C	1563	tight thermal	0.12	0.5
4	D	1563	tight thermal	0.13	0.5
5	E	1563	tight thermal	0.13	0.5
1	A	1752	medium thermal	0.63	2
2	B	1752	medium thermal	0.65	2
3	C	1752	medium thermal	0.64	2
4	D	1752	medium thermal	0.66	2
5	E	1752	medium thermal	0.77	2

LS refinement shell

Resolution: 2.25→2.31 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.259	196	-
R_work	0.197	5015	-
obs	-	-	98.6 %

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	0.235	0.0673	-0.2933	1.3524	1.1103	1.436	-0.018	-0.0884	-0.109	0.1549	0.0162	-0.0322	0.0544	0.2346	0.0018	-0.0382	-0.0113	-0.0308	0.0216	0.0478	0.0162	-24.184	42.949	4.714
2	1.1857	0.1488	0.4392	1.5981	0.2396	1.3637	0.0448	-0.2045	-0.0823	0.1539	-0.0958	0.0709	0.0696	0.0045	0.051	-0.0621	-0.0598	0.0126	-0.0227	0.0518	-0.0457	-26.684	43.548	12.491
3	2.3991	-0.4297	-0.5886	2.1472	-0.3658	1.0414	0.0305	-0.1749	-0.3191	0.0437	-0.1121	-0.2426	0.1084	0.1588	0.0817	-0.0564	-0.0233	-0.0386	0.0036	0.1111	0.0059	-10.531	37.683	9.512
4	0.8796	-0.2402	-1.1192	1.3664	0.4638	1.4433	0.0675	-0.2097	-0.1246	0.3045	-0.0693	-0.1921	0.1752	0.1614	0.0017	-0.0166	-0.031	-0.048	0.0275	0.1184	0.0295	-11.572	38.579	13.855
5	1.0673	-0.737	0.045	0.6445	-0.2311	0.3471	0.1282	-0.1927	-0.0892	-0.003	-0.0701	0.0504	-0.0658	0.0271	-0.0581	-0.0236	-0.0561	0.0171	-0.0428	-0.0394	-0.0199	-33.41	71.747	11.571
6	1.3091	-0.1418	0.2361	1.1356	0.1557	0.9294	0.1001	-0.1649	-0.0447	0.1327	-0.0942	0.1971	-0.0304	-0.029	-0.0059	-0.0477	-0.0874	0.0624	-0.0579	-0.0162	-0.0214	-40.11	73.221	15.896
7	1.4741	0.5472	-0.6633	2.1199	0.0208	0.8041	0.1386	-0.1852	-0.0056	0.2236	-0.0788	-0.0873	-0.0369	0.2003	-0.0598	-0.0076	-0.0774	0.0349	-0.0341	-0.0501	-0.0961	-25.888	82.741	19.207
8	1.1548	-0.2886	-0.3667	0.8616	0.4882	1.35	0.1223	-0.253	0.0949	0.2044	-0.0787	0.0084	-0.0352	0.0323	-0.0436	0.0021	-0.1144	0.061	-0.0308	-0.0515	-0.0693	-29.56	84.349	21.063
9	0.3537	0.2737	0.0701	0.26	-0.0575	0.2735	0.0562	-0.0473	0.212	0.1175	-0.0235	0.1165	-0.0021	-0.0749	-0.0327	-0.0562	-0.01	0.025	-0.0595	-0.0426	0.0804	-57.397	78.742	-6.724
10	0.9139	0.0364	0.449	1.2313	0.1735	1.0734	0.0131	-0.0971	0.0672	0.1254	-0.0235	0.1829	0.0599	-0.1225	0.0104	-0.1193	-0.045	0.0411	-0.0684	-0.0116	0.0041	-64.872	75.802	-5.293
11	1.3802	0.0377	0.0455	1.3076	0.0959	2.2052	0.0017	-0.0229	0.2728	0.0708	-0.0419	0.1143	-0.1241	-0.093	0.0403	-0.128	0.007	0.0019	-0.0846	-0.0365	0.097	-63.315	92.517	-9.946
12	2.3377	0.0077	0.3751	1.1636	0.0965	0.7221	-0.0466	-0.1626	0.3212	0.0506	-0.0709	0.2259	-0.1333	-0.1925	0.1175	-0.0976	0.0125	0.0168	-0.0709	-0.0455	0.1093	-67.387	91.335	-10.373
13	0.9771	-0.0957	0.514	0.0538	-0.2061	1.4517	-0.0533	0.0346	-0.1216	-0.0257	-0.0496	-0.0384	0.139	-0.0333	0.1029	-0.0386	-0.0339	0.0136	-0.094	0.015	0.0119	-42.54	32.088	-17.868
14	1.4192	0.0188	0.1346	1.0686	0.2752	1.0812	-0.0642	-0.0726	-0.1717	0.0935	0.0248	-0.035	0.1429	-0.0168	0.0394	-0.0784	-0.0287	0.017	-0.0923	0.0333	-0.0126	-43.135	27.557	-11.106
15	3.1264	0.3968	-0.5394	1.975	0.869	2.0912	-0.1366	0.2312	-0.3592	-0.0665	-0.0609	0.1622	0.0702	0.0216	0.1975	-0.0566	-0.0256	0.055	-0.1198	-0.0206	0.0593	-38.493	19.578	-25.94
16	1.3105	0.2556	-0.2255	1.68	-0.8475	1.355	-0.0485	0.0746	-0.4564	-0.0022	-0.0421	-0.1308	0.1563	0.0363	0.0906	-0.0446	-0.039	0.0537	-0.097	-0.027	0.0767	-37.974	17.016	-22.347
17	0.1217	-0.2845	0.1984	2.0686	-0.1135	0.411	-0.0464	0.0142	0.0392	-0.0399	0.061	0.1009	0.0297	-0.1164	-0.0146	-0.134	-0.0493	0.0144	-0.0413	0.0133	0.0031	-63.029	54.144	-24.936
18	0.5591	-0.0873	-0.0248	1.8621	0.3408	0.9391	0.0027	0.0287	-0.0159	0.0126	-0.0188	0.1299	0.1488	-0.1126	0.0162	-0.1209	-0.0539	0.0066	-0.06	0.0344	-0.0492	-66.825	47.471	-22.194
19	1.3675	-0.3729	-0.1772	1.5967	-0.0958	0.9617	0.0013	0.1089	-0.0335	-0.1009	-0.0031	0.1423	0.0164	-0.1368	0.0018	-0.1162	-0.0444	-0.0337	-0.0375	0.0322	-0.0536	-71.261	53.602	-37.86
20	1.9266	0.708	-0.3305	2.265	-0.3631	0.5889	0.006	0.1419	-0.0945	-0.1656	-0.0257	0.2119	0.1068	-0.1374	0.0197	-0.1188	-0.0274	-0.0397	-0.0295	0.0109	-0.0299	-72.909	49.373	-36.764

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 38
2	X-RAY DIFFRACTION	2	A	39 - 169
3	X-RAY DIFFRACTION	3	A	170 - 228
4	X-RAY DIFFRACTION	4	A	229 - 281
5	X-RAY DIFFRACTION	5	B	1 - 38
6	X-RAY DIFFRACTION	6	B	39 - 169
7	X-RAY DIFFRACTION	7	B	170 - 228
8	X-RAY DIFFRACTION	8	B	229 - 280
9	X-RAY DIFFRACTION	9	C	1 - 38
10	X-RAY DIFFRACTION	10	C	39 - 169
11	X-RAY DIFFRACTION	11	C	170 - 228
12	X-RAY DIFFRACTION	12	C	229 - 279
13	X-RAY DIFFRACTION	13	D	1 - 38
14	X-RAY DIFFRACTION	14	D	39 - 169
15	X-RAY DIFFRACTION	15	D	170 - 228
16	X-RAY DIFFRACTION	16	D	229 - 280
17	X-RAY DIFFRACTION	17	E	1 - 38
18	X-RAY DIFFRACTION	18	E	39 - 169
19	X-RAY DIFFRACTION	19	E	170 - 228
20	X-RAY DIFFRACTION	20	E	229 - 281

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-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

-
Basic information

-
Structure visualization

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Downloads & links

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Download

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Validation report

-
Related structure data

-
Links

-
Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi