PDB-4dzl: A de novo designed Coiled Coil CC-Tri

ID or keywords:

Entry

Database: PDB / ID: 4dzl

Title

A de novo designed Coiled Coil CC-Tri

Components

COILED-COIL PEPTIDE CC-TRI

Keywords

DE NOVO PROTEIN

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.3 Å

Authors

Bruning, M. / Thomson, A.R. / Zaccai, N.R. / Brady, R.L. / Woolfson, D.N.

Citation

Journal: ACS Synth Biol / Year: 2012
Title: A basis set of de novo coiled-coil Peptide oligomers for rational protein design and synthetic biology.
Authors: Fletcher, J.M. / Boyle, A.L. / Bruning, M. / Bartlett, G.J. / Vincent, T.L. / Zaccai, N.R. / Armstrong, C.T. / Bromley, E.H. / Booth, P.J. / Brady, R.L. / Thomson, A.R. / Woolfson, D.N.

History

Deposition	Mar 1, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 29, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jun 19, 2013	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Refinement description / Source and taxonomy / Category: pdbx_entity_src_syn / software Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4dzl.cif.gz	143.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4dzl.ent.gz	126.2 KB	Display	PDB format
PDBx/mmJSON format	4dzl.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/dz/4dzl ftp://data.pdbj.org/pub/pdb/validation_reports/dz/4dzl	HTTPS FTP

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Related structure data

Related structure data	4dzkC 4dzmC 4dznC C: citing same article (ref.)
Similar structure data	5nqm-d 1kis-d 6hk5-3 1wn0-1 4h6i-1 2jst-d 1wn0-3 7jrq-d 2r2v-2 3moq-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details)

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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: COILED-COIL PEPTIDE CC-TRI

I: COILED-COIL PEPTIDE CC-TRI

C: COILED-COIL PEPTIDE CC-TRI

B: COILED-COIL PEPTIDE CC-TRI

E: COILED-COIL PEPTIDE CC-TRI

F: COILED-COIL PEPTIDE CC-TRI

G: COILED-COIL PEPTIDE CC-TRI

H: COILED-COIL PEPTIDE CC-TRI

J: COILED-COIL PEPTIDE CC-TRI

D: COILED-COIL PEPTIDE CC-TRI

K: COILED-COIL PEPTIDE CC-TRI

L: COILED-COIL PEPTIDE CC-TRI

42.5 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: COILED-COIL PEPTIDE CC-TRI

C: COILED-COIL PEPTIDE CC-TRI

B: COILED-COIL PEPTIDE CC-TRI

defined by author&software
10.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

I: COILED-COIL PEPTIDE CC-TRI

G: COILED-COIL PEPTIDE CC-TRI

H: COILED-COIL PEPTIDE CC-TRI

defined by author&software
10.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: COILED-COIL PEPTIDE CC-TRI

F: COILED-COIL PEPTIDE CC-TRI

D: COILED-COIL PEPTIDE CC-TRI

defined by author&software
10.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

J: COILED-COIL PEPTIDE CC-TRI

K: COILED-COIL PEPTIDE CC-TRI

L: COILED-COIL PEPTIDE CC-TRI

defined by author&software
10.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	102.761, 108.441, 41.608
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:
NCS ensembles :

ID
1
2
3
4
5

#1: Protein/peptide	COILED-COIL PEPTIDE CC-TRI Mass: 3543.950 Da / Num. of mol.: 12 / Source method: obtained synthetically / Details: Solid state peptide synthesis / Source: (synth.) synthetic construct (others)
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.73 Å³/Da / Density % sol: 54.87 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2 M C4H4KNaO6, 20 % w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.7 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 17, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.7 Å / Relative weight: 1
Reflection	Resolution: 2.3→20 Å / Num. obs: 21306 / % possible obs: 99.6 % / Observed criterion σ(I): 2
Reflection shell	Resolution: 2.3→2.4 Å / % possible all: 99.5

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Processing

Software

Name	Version	Classification
PHENIX		model building
REFMAC	5.5.0109	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.3→19.42 Å / Cor.coef. F_o:F_c: 0.909 / Cor.coef. F_o:F_c free: 0.863 / SU B: 13.568 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.342 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28759	1085	5.1 %	RANDOM
R_work	0.24802	-	-	-
obs	0.24998	20157	99.37 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 25.613 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.2 Å²	-0 Å²	-0 Å²
2-	-	-0.52 Å²	0 Å²
3-	-	-	-0.68 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→19.42 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2730	0	0	188	2918

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.023	2743
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1895
X-RAY DIFFRACTION	r_angle_refined_deg	1.021	2.038	3647
X-RAY DIFFRACTION	r_angle_other_deg	0.786	3	4742
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.752	5	350
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	48.708	29.221	77
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.784	15	578
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.05	0.2	434
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	2871
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	421
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	2.439	8	1790
X-RAY DIFFRACTION	r_mcbond_other	1.003	8	738
X-RAY DIFFRACTION	r_mcangle_it	3.905	12	2812
X-RAY DIFFRACTION	r_scbond_it	6.106	16	953
X-RAY DIFFRACTION	r_scangle_it	10.367	24	834
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	275	medium positional	0.88	0.5
1	1	B	275	medium positional	0.55	0.5
1	1	C	275	medium positional	0.51	0.5
1	1	D	275	medium positional	0.88	0.5
1	1	E	275	medium positional	0.65	0.5
1	1	F	275	medium positional	0.67	0.5
1	1	G	275	medium positional	0.62	0.5
1	1	H	275	medium positional	0.53	0.5
1	1	I	275	medium positional	0.53	0.5
1	1	J	275	medium positional	0.87	0.5
1	1	K	275	medium positional	0.73	0.5
1	1	L	275	medium positional	0.7	0.5
2	2	A	337	medium positional	0.71	0.5
2	2	B	337	medium positional	0.62	0.5
2	2	C	337	medium positional	0.46	0.5
3	3	D	337	medium positional	0.83	0.5
3	3	E	337	medium positional	0.62	0.5
3	3	F	337	medium positional	0.72	0.5
4	4	G	326	medium positional	0.5	0.5
4	4	H	326	medium positional	0.44	0.5
4	4	I	326	medium positional	0.5	0.5
5	5	J	329	medium positional	0.82	0.5
5	5	K	329	medium positional	0.61	0.5
5	5	L	329	medium positional	0.63	0.5
1	1	A	275	medium thermal	0.63	2
1	1	B	275	medium thermal	0.69	2
1	1	C	275	medium thermal	0.69	2
1	1	D	275	medium thermal	0.6	2
1	1	E	275	medium thermal	0.77	2
1	1	F	275	medium thermal	0.59	2
1	1	G	275	medium thermal	0.63	2
1	1	H	275	medium thermal	1.01	2
1	1	I	275	medium thermal	0.65	2
1	1	J	275	medium thermal	1.03	2
1	1	K	275	medium thermal	0.86	2
1	1	L	275	medium thermal	0.49	2
2	2	A	337	medium thermal	0.57	2
2	2	B	337	medium thermal	0.56	2
2	2	C	337	medium thermal	0.51	2
3	3	D	337	medium thermal	0.65	2
3	3	E	337	medium thermal	0.63	2
3	3	F	337	medium thermal	0.53	2
4	4	G	326	medium thermal	0.7	2
4	4	H	326	medium thermal	0.72	2
4	4	I	326	medium thermal	0.72	2
5	5	J	329	medium thermal	0.81	2
5	5	K	329	medium thermal	0.7	2
5	5	L	329	medium thermal	0.41	2

LS refinement shell

Resolution: 2.3→2.359 Å / Num. reflection R_work: 1353 / Total num. of bins used: 20

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	1.3491	1.8205	-0.0766	4.1009	0.8121	2.428	-0.1083	-0.0092	0.0723	-0.1121	0.1074	0.0861	0.0045	0.1263	0.0008	0.0275	0.0279	-0.0072	0.0454	0.0011	0.0433	31.752	21.9408	29.6976
2	0.0773	-0.3476	-0.3875	0.6162	1.0811	1.373	0.011	-0.0275	0.0411	-0.0239	0.0446	-0.0456	-0.0531	0.0584	-0.0556	0.0943	0.0161	0.0055	0.0173	-0.0132	0.0594	25.8956	23.3202	38.5792
3	0.569	0.0505	-0.5836	3.9209	-1.3152	1.0214	-0.0239	0.0691	-0.0637	0.0129	0.0869	0.1117	-0.0178	-0.0989	-0.0631	0.079	-0.0141	0.0011	0.0365	0.0099	0.0776	22.0552	24.7942	29.0467
4	1.0957	-2.6119	0.2607	6.2241	1.3513	1.992	0.0827	0.0201	0.2779	-0.4654	-0.0113	-0.5357	-0.3978	0.0913	-0.0714	0.1117	-0.041	0.053	0.0218	0.0084	0.129	31.1647	49.2232	8.9827
5	3.5593	-0.5296	1.1313	1.8604	-0.243	1.2762	-0.0248	0.1632	0.1083	0.0005	0.0888	-0.265	0.1102	0.1338	-0.064	0.0522	0.0109	0.0032	0.0652	-0.0232	0.058	27.9811	39.472	7.6087
6	5.3899	1.5506	-2.5119	2.7055	0.1095	2.5669	0.1682	-0.1659	-0.0909	-0.0161	0.0719	-0.3562	-0.1764	0.239	-0.2401	0.0763	-0.0322	-0.0127	0.0995	-0.0145	0.0872	31.5349	42.6069	16.812
7	6.1041	0.9261	-1.7625	2.0117	0.4662	0.7069	0.2078	0.1278	0.4098	-0.1109	-0.0888	0.1674	-0.0739	-0.0736	-0.119	0.058	-0.0106	-0.0205	0.027	0.0192	0.047	8.6889	31.3926	7.7813
8	24.9757	-1.4433	9.2797	0.6256	-0.561	4.6411	0.024	0.3116	-0.4655	-0.0504	-0.0189	-0.2474	0.2647	0.2092	-0.0051	0.063	-0.009	0.0542	0.0787	-0.0091	0.1541	8.0703	21.6473	8.9317
9	14.3048	4.8389	1.8126	1.592	0.6469	0.1597	0.184	-0.2247	-0.3939	0.074	-0.1099	-0.1126	0.0238	-0.0429	-0.0741	0.054	-0.0302	-0.012	0.1059	0.0263	0.0444	8.0165	28.424	17.3616
10	2.8868	0.8238	0.0042	5.041	0.2832	1.4104	0.0107	0.2203	0.208	-0.2687	-0.0667	0.3226	-0.0809	-0.2358	0.0559	0.2056	0.038	-0.0239	0.1509	0.041	0.104	5.014	49.9344	30.0108
11	0.6786	-1.8125	0.9934	3.8341	-1.9546	1.9902	-0.1291	0.0007	0.1659	0.175	-0.0653	-0.364	-0.172	-0.0496	0.1944	0.1103	-0.0133	-0.0402	0.0717	0.0146	0.0863	10.8792	50.1335	38.2769
12	2.1407	5.9259	-0.9703	23.9055	-0.0923	2.2798	0.1713	-0.141	0.0605	-0.9806	-0.6755	0.1189	-0.0651	0.3255	0.5042	0.3049	0.0912	0.118	0.1981	0.147	0.1411	14.4191	44.0293	29.1469

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 30
2	X-RAY DIFFRACTION	2	B	1 - 32
3	X-RAY DIFFRACTION	3	C	1 - 32
4	X-RAY DIFFRACTION	4	D	3 - 29
5	X-RAY DIFFRACTION	5	E	2 - 32
6	X-RAY DIFFRACTION	6	F	1 - 32
7	X-RAY DIFFRACTION	7	G	2 - 29
8	X-RAY DIFFRACTION	8	H	1 - 30
9	X-RAY DIFFRACTION	9	I	1 - 31
10	X-RAY DIFFRACTION	10	J	1 - 30
11	X-RAY DIFFRACTION	11	K	1 - 30
12	X-RAY DIFFRACTION	12	L	5 - 31

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