PDB-4rjv: Crystal Structure of a De Novo Designed Ferredoxin Fold, Northeas...

ID or keywords:

Entry

Database: PDB / ID: 4rjv

Title

Crystal Structure of a De Novo Designed Ferredoxin Fold, Northeast Structural Genomics Consortium (NESG) Target OR461

Components

OR461

Keywords

DE NOVO PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium (NESG) Target OR461 / Ferredoxin Fold

Function / homology

Ribosomal protein S10 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.523 Å

Authors

O'Connell, P.T. / Lin, Y.-R. / Guan, R. / Koga, N. / Koga, R. / Seetharaman, J. / Janjua, H. / Xiao, R. / Maglaqui, M. / Everett, J.K. ...

Citation

Journal: To be published
Title: Northeast Structural Genomics Consortium Target OR461
Authors: O'Connell, P.T. / Lin, Y.-R. / Guan, R. / Koga, N. / Koga, R. / Seetharaman, J. / Janjua, H. / Xiao, R. / Maglaqui, M. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / ...

History

Deposition	Oct 9, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 22, 2014	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4rjv.cif.gz	142.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4rjv.ent.gz	114.9 KB	Display	PDB format
PDBx/mmJSON format	4rjv.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/rj/4rjv ftp://data.pdbj.org/pub/pdb/validation_reports/rj/4rjv	HTTPS FTP

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Related structure data

Related structure data	4pwwS S: Starting model for refinement
Similar structure data	6rp3-d 4nft-2 6a7u-d 4dve-1 2m00-d 3pgg-d 4gs4-d 6ucd-1 2czo-d 2moq-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
Other databases	TargetTrack: NESG-OR461

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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: OR461

B: OR461

C: OR461

D: OR461

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

1

A: OR461

B: OR461

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

2

C: OR461

D: OR461

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

Unit cell

Length a, b, c (Å)	37.666, 46.688, 48.066
Angle α, β, γ (deg.)	86.490, 72.890, 72.330
Int Tables number	1
Space group name H-M	P1

#1: Protein	OR461 Mass: 9951.331 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pET21_NESG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 196 / 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: 1.93 Å³/Da / Density % sol: 36.36 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Reservoir solution: 0.5M ADA pH 5.7, 15% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97917 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 19, 2014
Radiation	Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97917 Å / Relative weight: 1
Reflection	Resolution: 1.52277→30.1717 Å / Num. obs: 42569 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.7 % / B_iso Wilson estimate: 18.205 Å² / R_merge(I) obs: 0.1985
Reflection shell	Resolution: 1.52→1.55 Å / Redundancy: 1.2 % / % possible all: 67

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
AMoRE		phasing
RESOLVE		phasing
PHENIX	1.8.2_1309	refinement
PDB_EXTRACT	3.1	data extraction
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB Entry 4PWW

4pww

Resolution: 1.523→30.1717 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0.11 / Phase error: 27.38 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.231	1975	4.64 %	Random
R_work	0.199	-	-	-
obs	0.2	42569	93.25 %	-
all	-	42569	-	-

Solvent computation

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

Displacement parameters

B_iso max: 94 Å² / B_iso mean: 37.204 Å² / B_iso min: 12.9 Å²

Refinement step

Cycle: LAST / Resolution: 1.523→30.1717 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2562	0	0	196	2758

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2582
X-RAY DIFFRACTION	f_angle_d	1.083	3457
X-RAY DIFFRACTION	f_chiral_restr	0.07	400
X-RAY DIFFRACTION	f_plane_restr	0.004	455
X-RAY DIFFRACTION	f_dihedral_angle_d	15.021	1001

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.523-1.561	0.351	117	0.309	2420	2537	77
1.561-1.603	0.288	139	0.266	2788	2927	89
1.603-1.65	0.324	142	0.243	2804	2946	91
1.65-1.704	0.256	134	0.227	2879	3013	93
1.704-1.764	0.284	142	0.219	2909	3051	94
1.764-1.835	0.233	150	0.227	2919	3069	94
1.835-1.918	0.278	136	0.219	2913	3049	93
1.918-2.02	0.252	143	0.218	2934	3077	95
2.02-2.146	0.233	142	0.196	3009	3151	97
2.146-2.312	0.223	146	0.186	2977	3123	96
2.312-2.544	0.229	144	0.192	3027	3171	97
2.544-2.912	0.207	147	0.188	3010	3157	97
2.912-3.668	0.224	148	0.185	3015	3163	97
3.668-30.178	0.21	145	0.189	2990	3135	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	3.5825	-0.6291	1.9514	5.7834	3.7149	4.1014	0.0282	0.5621	0.4071	0.1615	0.1117	-0.5927	0.1417	0.2891	-0.0855	0.3598	0.1279	-0.0218	0.3428	0.0272	0.2168	23.5761	1.9765	12.6682
2	4.6885	-4.0093	-2.8036	7.8494	5.4588	4.967	0.0737	0.0578	-0.1737	-0.2827	-0.1124	0.0639	0.173	-0.2352	0.1714	0.2432	0.035	0.0013	0.1901	0.022	0.1104	13.8923	2.0932	7.6076
3	2.7727	-1.8551	-1.7682	6.9657	-0.0922	9.4949	-0.4499	-0.6925	0.9841	0.5741	0.3493	-1.3184	-0.3012	1.0948	0.1241	0.2747	0.0883	-0.1246	0.3215	0.0166	0.2797	20.815	9.1041	13.6445
4	3.8614	-2.3837	-1.4571	9.3117	5.619	4.2448	0.1792	-0.4047	-0.3015	-0.0517	-0.0327	0.2653	0.504	-0.8617	-0.1394	0.3001	-0.0784	-0.0511	0.3262	0.1005	0.2298	14.6854	-3.8177	16.6934
5	1.4298	1.2063	0.5671	7.8638	6.5219	5.1336	-0.2002	-0.1014	-0.0595	0.0607	0.3766	-0.3173	0.037	0.7831	-0.0699	0.3165	0.1464	-0.01	0.2517	0.015	0.1787	23.812	0.1868	17.9528
6	4.8407	2.7037	1.6888	3.7312	2.8561	3.2044	-0.1576	-0.3852	0.2061	0.3231	-0.2275	0.3916	-0.3062	-0.3564	0.3458	0.2885	0.0608	-0.027	0.2127	-0.0136	0.1729	10.6705	18.8891	2.1447
7	6.236	4.5123	5.2374	4.1926	4.5356	5.3719	-0.1662	-0.0439	-0.0979	-0.0348	0.0245	0.669	0.9517	-0.5307	0.1633	0.3139	-0.0408	-0.016	0.2158	0.0041	0.227	10.8054	3.4537	-3.4659
8	6.3305	4.4441	3.8154	7.6946	3.2133	4.1467	-0.1866	0.2335	0.0476	-0.3011	0.2247	-1.1388	-0.0751	0.4766	-0.2631	0.134	0.0011	-0.019	0.1615	0.0245	0.2934	22.5534	14.6613	2.4662
9	3.7416	2.5843	4.4873	3.8994	3.6064	7.4294	0.1235	-0.5889	0.1146	0.6801	0.0741	1.2381	0.222	-1.9484	0.0306	0.2598	-0.0297	-0.0201	0.5467	0.1078	0.3509	8.1686	13.2485	8.0075
10	3.1192	3.6348	-1.57	6.307	-0.0005	4.7119	0.1966	-0.3411	0.3793	0.5663	-0.0471	-0.0052	-0.1636	0.1093	-0.2029	0.2182	0.023	-0.0519	0.1764	-0.0036	0.2276	19.1286	24.0629	4.4297
11	7.2161	5.1101	4.9308	4.4709	5.2481	8.4281	-0.0966	0.4448	0.4379	-0.1348	0.0896	-0.1857	0.027	0.571	-0.0282	0.1979	0.0215	0.0445	0.2002	0.0377	0.181	17.1349	17.1479	-6.8228
12	1.8656	1.1346	0.7555	4.1233	5.9411	8.8414	-0.1668	-0.1862	0.1983	-0.366	-0.2828	0.59	-0.6404	-0.3016	0.3565	0.22	0.0439	-0.0416	0.1536	-0.0053	0.1389	9.2936	20.7379	-0.6567
13	2.826	-0.3399	-1.2851	7.8877	2.2007	6.2389	0.294	0.0809	-0.051	-0.3361	-0.2504	0.1698	0.0806	-0.3251	-0.0822	0.1823	0.0861	-0.0207	0.2876	0.0155	0.1049	9.7189	34.8156	23.5231
14	7.0004	1.4572	-4.1834	7.2305	-2.0289	3.9066	-0.0081	0.0612	0.0423	-0.0238	0.2141	0.4297	0.0966	-0.1244	-0.1628	0.1904	0.0668	-0.0123	0.2526	0.0146	0.1827	8.2977	37.8251	31.083
15	1.564	-0.0466	-0.1557	3.8128	3.2394	5.9801	0.2603	0.5915	0.2307	-0.46	-0.0357	-0.2078	-0.7273	-0.2229	-0.1593	0.2922	0.0822	0.0355	0.305	0.0259	0.1723	9.6285	42.2534	19.5815
16	4.5914	0.164	-1.0054	4.8999	3.7671	3.7053	0.2191	0.4486	-0.0787	-0.48	-0.0243	-0.0889	0.0134	0.0131	-0.1008	0.3568	0.1174	-0.0179	0.2137	0.0041	0.1523	19.3237	23.9471	34.479
17	5.9838	-1.9415	-4.3601	4.6637	2.7062	9.6498	0.555	0.525	-0.498	-0.7726	-0.1655	0.4653	1.2235	-0.4965	0.6908	0.3642	0.0839	-0.1069	0.1821	-0.0262	0.1858	9.3085	23.6741	30.2411
18	4.3448	-1.417	1.2437	6.0451	0.1455	5.3464	0.527	-0.0088	-0.6335	-0.1614	-0.1935	-0.0771	0.5689	0.121	-0.0777	0.1944	0.0599	-0.089	0.1513	-0.0034	0.2201	13.8668	24.357	37.7167
19	3.0331	0.7351	1.1004	7.5361	5.6841	4.3362	0.3328	0.0123	-0.2009	-0.4673	-0.1444	-0.0117	0.5037	0.1383	-0.318	0.33	0.1248	-0.0779	0.2193	-0.0216	0.1871	20.5686	22.0936	41.305

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 11 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 12 through 29 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 30 through 50 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 51 through 68 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 69 through 79 )	A
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1 through 8 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 9 through 18 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 19 through 33 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 34 through 43 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 44 through 53 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 54 through 68 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 69 through 79 )	B
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 1 through 29 )	C
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 30 through 50 )	C
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 51 through 78 )	C
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 1 through 11 )	D
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 12 through 29 )	D
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 30 through 68 )	D
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 69 through 80 )	D

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