PDB-4ndk: Crystal structure of a computational designed engrailed homeodoma...

ID or keywords:

Entry

Database: PDB / ID: 4ndk

Title

Crystal structure of a computational designed engrailed homeodomain variant fused with YFP

Components

E23P-YFP, GFP-like fluorescent chromoprotein FP506, related, chimeric construct,

Keywords

fluorescent protein / de novo protein / helix-turn-helix

Function / homology

Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / GFP-like fluorescent chromoprotein FP506, related

Function and homology information

Biological species

Aequorea victoria (jellyfish)

Eimeria acervulina (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Mou, Y. / Mayo, S.L.

Citation

Journal: J.Mol.Biol. / Year: 2015
Title: Using Molecular Dynamics Simulations as an Aid in the Prediction of Domain Swapping of Computationally Designed Protein Variants.
Authors: Mou, Y. / Huang, P.S. / Thomas, L.M. / Mayo, S.L.

History

Deposition	Oct 26, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 5, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jul 15, 2015	Group: Database references
Revision 1.2	Aug 19, 2015	Group: Database references
Revision 1.3	Oct 18, 2017	Group: Advisory / Database references ...Advisory / Database references / Source and taxonomy / Structure summary Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_distant_solvent_atoms / struct_ref / struct_ref_seq / struct_ref_seq_dif Item: _entity.pdbx_description / _struct_ref.db_code ..._entity.pdbx_description / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.db_mon_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.mon_id / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_ref_seq_dif.pdbx_seq_db_name / _struct_ref_seq_dif.pdbx_seq_db_seq_num / _struct_ref_seq_dif.seq_num

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ndk.cif.gz	236.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4ndk.ent.gz	201.6 KB	Display	PDB format
PDBx/mmJSON format	4ndk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4ndk_validation.pdf.gz	442.2 KB	Display	wwPDB validaton report
Full document	4ndk_full_validation.pdf.gz	450.3 KB	Display
Data in XML	4ndk_validation.xml.gz	27.1 KB	Display
Data in CIF	4ndk_validation.cif.gz	38.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nd/4ndk ftp://data.pdbj.org/pub/pdb/validation_reports/nd/4ndk	HTTPS FTP

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Related structure data

Related structure data	4ndjC 4zn8C C: citing same article (ref.)
Similar structure data	4ny9-2 4xhd-2 4lya-d 7axi-2 6v33-d 7axl-2 7ax9-2 4yfy-d 7axb-2 4yfv-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
Related items in Molecule of the Month	#70 - Oct 2005 Designer Proteins similarity (1) #174 - Jun 2014 GFP-like Proteins similarity (4) #42 - Jun 2003 Green Fluorescent Protein similarity (4)

Deposited unit

A: E23P-YFP, GFP-like fluorescent chromoprotein FP506, related, chimeric construct,

B: E23P-YFP, GFP-like fluorescent chromoprotein FP506, related, chimeric construct,

69 kDa, 2 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)	75.890, 192.650, 107.610
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	E23P-YFP, GFP-like fluorescent chromoprotein FP506, related, chimeric construct, Mass: 34510.871 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Eimeria acervulina (eukaryote) Gene: GFP, EAH_00062270 / Production host: Escherichia coli (E. coli) / References: UniProt: U6GSR1
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	THE CRYSTALLIZED SEQUENCE REPRESENTS A FUSED PROTEIN. THE N-TERMINAL SEQUENCE, WHICH IS ...THE CRYSTALLIZED SEQUENCE REPRESENTS A FUSED PROTEIN. THE N-TERMINAL SEQUENCE, WHICH IS COMPUTATIONALLY DESIGNED, IS BASED ON THE WILD-TYPE PROTEIN ENGRAILED HOMEODOMAIN (UNIPROT P02836). THE COMPUTATIONAL DESIGN PROCESS IS PURELY PHYSICAL-BASED WITHOUT USING ANY DATABASE ALIGNMENTS

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.85 Å³/Da / Density % sol: 56.83 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1 M sodium chloride, 12% v/v 2-propanol, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 150 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.0332 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 2.3→34 Å / Num. obs: 35208

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Processing

Software

Name	Version	Classification
BlueIce		data collection
PHENIX		model building
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
MOSFLM		data reduction
SCALA		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.3→34 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 27 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2473	1756	4.99 %
R_work	0.1901	-	-
obs	0.1929	35178	99.3 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.3→34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4454	0	0	398	4852

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4558
X-RAY DIFFRACTION	f_angle_d	1.155	6149
X-RAY DIFFRACTION	f_dihedral_angle_d	16.596	1723
X-RAY DIFFRACTION	f_chiral_restr	0.068	642
X-RAY DIFFRACTION	f_plane_restr	0.005	801

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 (%)
2.3-2.3622	0.3623	143	0.273	2522	X-RAY DIFFRACTION	100
2.3622-2.4317	0.3036	133	0.2465	2525	X-RAY DIFFRACTION	100
2.4317-2.5102	0.2838	135	0.2204	2559	X-RAY DIFFRACTION	100
2.5102-2.5999	0.2553	133	0.217	2559	X-RAY DIFFRACTION	100
2.5999-2.7039	0.2967	143	0.2219	2567	X-RAY DIFFRACTION	100
2.7039-2.8269	0.2741	142	0.2169	2558	X-RAY DIFFRACTION	100
2.8269-2.9759	0.3066	120	0.2199	2568	X-RAY DIFFRACTION	100
2.9759-3.1622	0.2733	152	0.2127	2565	X-RAY DIFFRACTION	100
3.1622-3.4062	0.2777	120	0.2022	2590	X-RAY DIFFRACTION	100
3.4062-3.7486	0.2697	159	0.1928	2554	X-RAY DIFFRACTION	99
3.7486-4.2901	0.1777	125	0.1603	2597	X-RAY DIFFRACTION	99
4.2901-5.4017	0.1847	132	0.1406	2603	X-RAY DIFFRACTION	98
5.4017-34.3595	0.2281	119	0.1812	2655	X-RAY DIFFRACTION	96

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	0.0009	-0.0005	0.0022	-0.0006	0.0008	0.0059	0.054	0.0098	0.0268	0.0334	0.0387	-0.0074	0.014	-0.0313	-0.0003	0.6496	-0.0154	0.0864	0.2695	-0.0069	0.2532	17.4839	98.3966	83.1962
2	0.0374	-0.0123	-0.0203	0.0062	0.0052	0.0143	-0.028	0.0157	0.0026	0.0756	0.017	-0.0543	0.0089	0.0418	-0.0107	0.7207	-0.1737	-0.3327	0.3648	0.164	0.196	27.519	98.1746	79.7395
3	0.0368	-0.0319	-0.0419	0.3273	0.2443	0.1854	-0.1516	-0.0042	0.0246	0.1306	-0.1559	-0.1052	-0.0446	0.0876	-0.0928	0.7042	-0.1478	-0.0356	0.2569	0.0656	0.2003	18.6896	86.2953	80.7803
4	0.018	0.0433	-0.0126	0.1242	0.0175	0.0179	-0.0132	-0.0163	-0.0319	-0.0825	0.0355	-0.0207	-0.0375	-0.0078	-0.0337	0.0433	-0.1443	0.2669	0.099	0.1394	-0.0561	8.1015	60.7147	59.4078
5	0.0932	0.1028	-0.0124	0.1491	-0.0292	0.0098	-0.0326	0.0274	-0.2172	0.1494	-0.0758	-0.1369	-0.1372	0.1136	-0.0242	0.1328	-0.2177	0.0868	0.3339	0.0773	0.1383	16.7378	67.1114	70.5885
6	0.0182	0.0031	-0.0213	0.0176	0.0147	0.0396	-0.0169	-0.0046	-0.0885	-0.0147	0.0427	-0.0178	-0.0599	0.0049	0.0229	0.1758	-0.129	0.1095	0.2686	0.0382	0.1634	17.2422	67.0733	59.1093
7	0.1063	0.1182	0.0198	0.2904	0.1097	0.077	0.1099	-0.1152	-0.1831	-0.1418	0.1128	-0.1852	-0.1305	0.0004	0.276	0.067	-0.1108	0.1272	0.1279	0.074	0.261	15.0768	53.714	58.8032
8	0.0048	0.0042	-0.0019	0.004	-0	0.0179	-0.0162	-0.0365	0.0193	0.0285	0.0365	-0.0627	0.0463	-0.0059	-0.0029	0.2443	-0.1455	-0.1341	0.4391	0.0353	0.3035	24.2407	65.5165	74.2331
9	0.1276	-0.0235	-0.0732	0.0195	0.0663	0.3145	0.1866	-0.1459	-0.1656	-0.0083	0.1258	-0.0409	0.0229	0.1061	0.3429	0.0796	-0.1977	-0.1143	0.3267	0.1992	0.5641	20.9596	55.0073	68.2382
10	0.0065	0.014	0.0011	0.0436	0.0143	0.0025	-0.0097	-0.0246	-0.0015	0.0763	0.0105	-0.0239	-0.0869	0.013	0.0095	0.2448	-0.1763	-0.0146	0.2037	0.0967	0.1663	15.9853	67.0631	73.8246
11	0.0378	0.0249	-0.0304	0.0593	-0.0285	0.025	0.0366	-0.0018	0.0203	0.0546	-0.0023	0.0425	-0.0032	-0.0838	0.0486	0.0398	-0.0718	-0.0004	0.3483	0.0552	0.0919	2.4132	56.3104	63.801
12	0.0111	0.0044	-0.0076	0.0085	-0.0048	0.0046	0.0514	-0.0324	-0.0181	-0.0952	-0.0388	0.0854	-0.1078	-0.0245	0.0001	0.5167	-0.063	-0.0189	0.2353	0.038	0.3055	6.0668	88.5602	66.0793
13	0.0855	-0.0687	-0.0356	0.0648	0.0261	0.0178	0.0998	-0.0539	-0.0637	-0.0586	0.0772	0.2251	0.0024	-0.0727	0.0483	0.4732	-0.1027	-0.0408	0.1959	0.0833	0.2155	11.5536	101.1857	66.8851
14	0.0103	-0.041	0.0322	0.2045	-0.0936	0.1136	-0.0086	-0.1013	-0.0442	0.2871	-0.2294	-0.5084	-0.0121	0.1204	-0.6415	0.3479	-0.0309	-0.4562	0.1396	0.1794	0.3674	41.081	118.7581	70.0245
15	0.236	-0.1714	0.1435	0.8596	0.1962	0.2865	0.166	-0.1293	-0.1005	0.113	-0.0216	-0.6388	0.1088	-0.0083	0.3128	0.0251	0.0418	-0.0942	0.0276	0.0566	0.1294	35.5763	116.2449	62.2408
16	0.019	-0.0009	0.005	0.0005	-0.0005	0.0048	0.0139	0.0292	-0.0487	-0.0154	-0.0225	-0.0064	0.0332	-0.01	-0.0265	0.2127	0.0768	-0.1503	0.2214	0.0054	0.1484	24.8655	113.447	54.8369
17	0.0935	-0.0045	0.0296	0.1585	-0.0065	0.0547	-0.0124	0.0671	0.0117	-0.0095	-0.0007	-0.0061	0.0103	-0.0201	0.0024	0.1553	0.027	-0.0758	0.1537	-0.038	0.1115	31.5657	120.1722	54.9235
18	0.1395	-0.0251	-0.0422	0.1316	0.1809	0.3174	0.0422	-0.0019	-0.088	-0.1072	0.0246	-0.0014	-0.0188	-0.0606	0.1959	0.1813	-0.0115	-0.0709	0.1304	0.0141	0.1017	30.2576	118.6169	59.2274
19	0.1474	-0.0723	-0.0048	0.1585	0.1469	0.1639	-0.0673	-0.0283	0.0501	0.1636	-0.1822	-0.1093	-0.2026	0.1267	-0.363	0.3545	-0.1489	-0.3778	0.1746	0.0645	0.3091	37.0748	125.7096	72.521

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 8:18 )	A	8 - 18
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 19:37 )	A	19 - 37
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 38:60 )	A	38 - 60
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 61:117 )	A	61 - 117
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 121:157 )	A	121 - 157
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 158:168 )	A	158 - 168
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 169:200 )	A	169 - 200
8	X-RAY DIFFRACTION	8	( CHAIN A AND RESID 201:211 )	A	201 - 211
9	X-RAY DIFFRACTION	9	( CHAIN A AND RESID 212:240 )	A	212 - 240
10	X-RAY DIFFRACTION	10	( CHAIN A AND RESID 241:261 )	A	241 - 261
11	X-RAY DIFFRACTION	11	( CHAIN A AND RESID 262:281 )	A	262 - 281
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 8:37 )	B	8 - 37
13	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 38:61 )	B	38 - 61
14	X-RAY DIFFRACTION	14	( CHAIN B AND RESID 62:117 )	B	62 - 117
15	X-RAY DIFFRACTION	15	( CHAIN B AND RESID 121:200 )	B	121 - 200
16	X-RAY DIFFRACTION	16	( CHAIN B AND RESID 201:211 )	B	201 - 211
17	X-RAY DIFFRACTION	17	( CHAIN B AND RESID 212:223 )	B	212 - 223
18	X-RAY DIFFRACTION	18	( CHAIN B AND RESID 224:261 )	B	224 - 261
19	X-RAY DIFFRACTION	19	( CHAIN B AND RESID 262:282 )	B	262 - 282

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