PDB-3tdm: Computationally designed TIM-barrel protein, HalfFLR

ID or keywords:

Entry

Database: PDB / ID: 3tdm

Title

Computationally designed TIM-barrel protein, HalfFLR

Components

Computationally designed two-fold symmetric TIM-barrel protein, FLR (half molecule)

Keywords

DE NOVO PROTEIN / TIM-BARREL / SYMMETRIC SUPERFOLD

Function / homology

Rossmann fold - #12600 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / PHOSPHATE ION

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Harp, J.M. / Fortenberry, C. / Bowman, E. / Profitt, W. / Dorr, B. / Mizoue, L.

Citation

Journal: J.Am.Chem.Soc. / Year: 2011
Title: Exploring symmetry as an avenue to the computational design of large protein domains.
Authors: Fortenberry, C. / Bowman, E.A. / Proffitt, W. / Dorr, B. / Combs, S. / Harp, J. / Mizoue, L. / Meiler, J.

History

Deposition	Aug 11, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 16, 2011	Provider: repository / Type: Initial release
Revision 1.1	Nov 23, 2011	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3tdm.cif.gz	200.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3tdm.ent.gz	164.7 KB	Display	PDB format
PDBx/mmJSON format	3tdm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3tdm_validation.pdf.gz	470.5 KB	Display	wwPDB validaton report
Full document	3tdm_full_validation.pdf.gz	497.5 KB	Display
Data in XML	3tdm_validation.xml.gz	23.9 KB	Display
Data in CIF	3tdm_validation.cif.gz	32 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/td/3tdm ftp://data.pdbj.org/pub/pdb/validation_reports/td/3tdm	HTTPS FTP

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Related structure data

Related structure data	3tdnC C: citing same article (ref.)
Similar structure data	4fx7-1 4fx7-2 4fx7-4 4fx7-3 5ac6-d 1h5y-2 5g4w-d 5ahi-d 1viz-2 5l6u-d Search similar-shape structures by Omokage search (details) 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

A: Computationally designed two-fold symmetric TIM-barrel protein, FLR (half molecule)

B: Computationally designed two-fold symmetric TIM-barrel protein, FLR (half molecule)

C: Computationally designed two-fold symmetric TIM-barrel protein, FLR (half molecule)

D: Computationally designed two-fold symmetric TIM-barrel protein, FLR (half molecule)

hetero molecules

54.7 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Computationally designed two-fold symmetric TIM-barrel protein, FLR (half molecule)

B: Computationally designed two-fold symmetric TIM-barrel protein, FLR (half molecule)

hetero molecules

defined by author&software
27.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Computationally designed two-fold symmetric TIM-barrel protein, FLR (half molecule)

hetero molecules

D: Computationally designed two-fold symmetric TIM-barrel protein, FLR (half molecule)

hetero molecules

defined by author&software
27.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	60.493, 60.493, 140.200
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	78
Space group name H-M	P4₃

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	B
2	1	A
1	2	D
2	2	C

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	B	2 - 115
2	1	1	1	A	2 - 115
1	1	2	4	D	2 - 115
2	1	2	4	C	2 - 115

NCS ensembles :

ID
1
2

#1: Protein	Computationally designed two-fold symmetric TIM-barrel protein, FLR (half molecule) Mass: 13581.423 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.36 Å³/Da / Density % sol: 47.9 %
Crystal grow	Temperature: 291 K / Method: microbatch / pH: 4.2 Details: 20% PEG 1000, 0.1M SODIUM CITRATE, 0.1M AMMONIUM CHLORIDE, pH 4.2, Microbatch, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 21, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 2.4→36.98 Å / Num. obs: 19865 / % possible obs: 99.9 % / Redundancy: 15 % / B_iso Wilson estimate: 57.2 Å² / R_merge(I) obs: 0.074 / Net I/σ(I): 33.66
Reflection shell	Resolution: 2.4→2.44 Å / Redundancy: 12.3 % / R_merge(I) obs: 0.32 / Mean I/σ(I) obs: 8.48 / % possible all: 100

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Processing

Software

Name	Version	Classification
MOLREP		phasing
REFMAC	5.5.0102	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: COMPUTATIONAL MODEL

Resolution: 2.4→36.98 Å / Cor.coef. F_o:F_c: 0.928 / Cor.coef. F_o:F_c free: 0.899 / SU B: 19.428 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.288	1011	5.1 %	RANDOM
R_work	0.242	-	-	-
obs	0.244	18627	99.7 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 82.29 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	11.09 Å²	0 Å²	-0 Å²
2-	-	11.09 Å²	0 Å²
3-	-	-	-22.19 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→36.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3598	0	20	66	3684

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.024	0.022	3665
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.139	1.969	4949
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.958	5	467
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.298	23.624	149
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.661	15	650
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.95	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.132	0.2	581
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	2673
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	4.337	1.5	2318
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	7.033	2	3734
X-RAY DIFFRACTION	r_scbond_it	5.155	3	1347
X-RAY DIFFRACTION	r_scangle_it	8.249	4.5	1215
X-RAY DIFFRACTION	r_rigid_bond_restr	2.679	3	3665
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

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

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	B	872	tight positional	0.34	0.05
2	D	840	medium positional	0.68	0.5
1	B	872	tight thermal	10.43	0.5
2	D	840	medium thermal	19.44	2

LS refinement shell

Resolution: 2.4→2.46 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.333	84	-
R_work	0.299	1322	-
obs	-	-	97.84 %

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	6.7859	2.8994	5.4421	9.6861	6.9351	8.4734	-0.2171	-0.2489	0.1916	-0.7489	-0.0898	-0.4247	-0.7535	0.1856	0.307	0.2061	-0.0085	0.0054	0.2177	0.0383	0.1833	-11.888	22.462	16.557
2	2.0151	0.7304	-0.144	2.8555	0.4144	1.6434	-0.0148	0.1878	-0.121	-0.3896	0.0522	0.1324	0.0609	-0.1695	-0.0374	0.1635	-0.0106	-0.0275	0.1776	0.0047	0.1712	-19.858	16.192	8.71
3	2.3109	-0.0472	-0.1503	3.7878	0.9381	1.4467	-0.0732	0.1321	-0.3168	-0.3313	0.0731	-0.2321	0.0237	-0.137	0.0001	0.2055	-0.0262	0.0478	0.1582	-0.0064	0.2129	-8.454	15.372	5.826
4	2.1973	0.7583	0.5012	2.6295	0.3729	2.351	-0.0682	0.169	-0.4256	-0.2011	0.1878	-0.5978	0.1164	0.2987	-0.1195	0.1889	0.0093	0.0817	0.1599	-0.0452	0.3847	3.178	12.265	8.827
5	46.6171	-3.5138	-38.1418	1.3245	2.4178	26.5154	0.0053	2.8811	0.2323	-0.5729	0.2925	-1.3376	-0.133	-2.3911	-0.2978	0.2764	-0.2548	0.5772	0.6631	-0.656	1.7466	10.057	18.692	9.716
6	9.339	-6.0145	4.008	2.4459	0.1225	13.152	-0.3336	0.2261	0.274	0.0795	-0.1023	-0.1635	-0.783	0.3878	0.4358	0.2002	-0.0683	-0.1237	0.2399	0.275	0.8209	0.733	16.064	17.469
7	2.4529	0.9863	0.7106	1.6751	0.3646	2.6892	0.2844	-0.5017	-1.0856	0.2256	-0.0522	-0.3001	0.3085	-0.0875	-0.2322	0.1987	-0.001	-0.089	0.2256	0.1888	0.5974	0.253	6.125	25.593
8	6.2247	1.858	-0.7495	1.2557	-0.4202	1.3204	0.1058	-0.7168	-0.5635	0.0826	-0.1523	-0.1786	0.0616	-0.0066	0.0465	0.1653	-0.0258	-0.0264	0.2415	0.1083	0.2381	-6.998	14.858	28.386
9	1.3634	0.3702	0.3231	1.7723	0.1746	1.9847	0.1829	-0.4908	0.015	0.2044	-0.0965	0.0958	-0.1077	-0.0935	-0.0864	0.1564	-0.0351	0.0142	0.3322	0.0133	0.1604	-13.685	21.493	27.709
10	6.0975	2.7993	-1.7474	2.7624	0.1682	1.0611	0.3878	-0.7426	0.4486	0.2799	-0.6875	0.7243	-0.0133	-0.1086	0.2998	0.1485	-0.0315	0.029	0.4653	-0.2686	0.4233	-21.402	25.552	20.784
11	5.6432	0.7315	3.5606	2.0601	-2.4623	10.4838	-0.1925	-0.4313	-0.1588	0.2129	-0.0051	0.0688	-0.2118	-0.201	0.1977	0.135	-0.0267	0.0396	0.1895	-0.0311	0.1442	22.91	28.468	-10.347
12	2.8015	1.1213	-1.1064	1.8123	-0.4034	2.0395	-0.0966	-0.1302	-0.0766	0.1003	-0.1352	-0.0336	0.008	-0.0204	0.2318	0.1376	-0.0351	0.0171	0.1525	-0.0185	0.1698	23.795	31.246	-12.894
13	-0.556	0.6485	4.828	0.7199	5.1524	18.0837	0.7244	0.7384	-0.3584	0.8138	0.7268	-0.2001	2.6184	2.6828	-1.4511	1.2557	0.5773	0.9059	0.5493	0.1178	1.5695	21.246	15.109	-6.681
14	4.9962	3.787	-2.9075	2.8758	-2.7155	3.603	0.0491	-0.3236	-0.0874	0.0241	-0.2283	-0.0725	0.0867	0.0398	0.1793	0.2958	-0.0675	0.2092	0.2486	-0.0959	0.3755	12.722	23.021	-4.781
15	16.0752	-0.9553	-10.0634	4.3026	4.2459	8.4797	-0.7472	-0.3263	-0.092	-0.0175	0.4249	0.4439	0.4778	0.5813	0.3223	0.3992	-0.0741	-0.0974	0.2628	0.1336	0.4816	9.586	8.908	-13.855
16	6.2721	-0.1143	-17.0405	-1.7931	-2.4078	36.6072	-0.4209	0.2046	0.0842	0.0178	0.1889	0.0498	1.4561	-0.4831	0.232	0.5633	0.2352	0.1239	0.2384	-0.0577	0.527	16.606	49.691	14.963
17	5.8151	-0.3547	-2.3544	11.0102	6.1414	4.0017	-0.2411	1.8288	-0.3414	0.0858	-0.2972	0.7214	0.2449	-0.9243	0.5383	0.4862	-0.4366	0.001	1.0055	-0.2797	0.2646	7.464	42.358	7.248
18	6.079	-1.0909	-4.2567	1.9736	0.4534	6.1808	0.0413	0.6716	-0.1696	0.1192	-0.1205	0.1479	0.3349	-0.3502	0.0793	0.1951	0.0967	0.0217	0.258	0.0313	0.2187	17.311	46.819	7.414
19	5.4212	-2.3472	-3.7429	5.2794	-1.2704	6.97	0.0152	0.0673	0.137	0.0168	-0.0962	-0.0892	0.3274	0.2141	0.081	0.2211	0.0636	0.0009	0.1961	0.031	0.167	25.882	47.905	4.84
20	8.0762	0.7124	-0.8052	5.712	3.9862	4.0325	0.1504	0.6418	0.4771	-0.6369	0.1448	-0.4022	-0.6962	0.0093	-0.2952	0.2308	0.0214	0.0421	0.1565	0.0368	0.2133	35.649	40.001	11.574

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 9
2	X-RAY DIFFRACTION	2	A	10 - 46
3	X-RAY DIFFRACTION	3	A	47 - 82
4	X-RAY DIFFRACTION	4	A	83 - 115
5	X-RAY DIFFRACTION	5	A	116 - 121
6	X-RAY DIFFRACTION	6	B	1 - 9
7	X-RAY DIFFRACTION	7	B	10 - 46
8	X-RAY DIFFRACTION	8	B	47 - 80
9	X-RAY DIFFRACTION	9	B	81 - 104
10	X-RAY DIFFRACTION	10	B	105 - 119
11	X-RAY DIFFRACTION	11	C	1 - 18
12	X-RAY DIFFRACTION	12	C	19 - 51
13	X-RAY DIFFRACTION	13	C	52 - 62
14	X-RAY DIFFRACTION	14	C	63 - 99
15	X-RAY DIFFRACTION	15	C	100 - 111
16	X-RAY DIFFRACTION	16	D	1 - 11
17	X-RAY DIFFRACTION	17	D	12 - 34
18	X-RAY DIFFRACTION	18	D	35 - 68
19	X-RAY DIFFRACTION	19	D	69 - 100
20	X-RAY DIFFRACTION	20	D	101 - 120

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