PDB-2idg: Crystal Structure of hypothetical protein AF0160 from Archaeoglob...

ID or keywords:

Entry

Database: PDB / ID: 2idg

Title

Crystal Structure of hypothetical protein AF0160 from Archaeoglobus fulgidus

Components

Hypothetical protein AF0160

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / AF0160 / Archaeoglobus fulgidus / PROTEIN STRUCTURE INITIATIVE / SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS / SECSG / PSI

Function / homology

TorD-like / TorD-like / DMSO/Nitrate reductase chaperone / TorD-like superfamily / Nitrate reductase delta subunit / Orthogonal Bundle / Mainly Alpha / cytoplasm / Tat proofreading chaperone TtrD

Function and homology information

Biological species

Archaeoglobus fulgidus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.69 Å

Authors

Zhao, M. / Zhang, M. / Chang, J. / Chen, L. / Xu, H. / Li, Y. / Liu, Z.J. / Rose, J.P. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG)

Citation

Journal: To be Published
Title: Crystal structure of Hypothetical Protein AF0160 from Archaeoglobus fulgidus at 2.69 Angstrom resolution
Authors: Zhao, M. / Zhang, M. / Chang, J. / Chen, L. / Xu, H. / Li, Y. / Liu, Z.J. / Rose, J.P. / Wang, B.C.

History

Deposition	Sep 15, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 14, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Sep 13, 2017	Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / refine / Item: _refine.pdbx_method_to_determine_struct
Revision 1.4	Oct 16, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2idg.cif.gz	112.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2idg.ent.gz	88.5 KB	Display	PDB format
PDBx/mmJSON format	2idg.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/id/2idg ftp://data.pdbj.org/pub/pdb/validation_reports/id/2idg	HTTPS FTP

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Related structure data

Similar structure data	2wfr-d 6i3h-2 3a1f-d 4y94-2 1n5n-2 2ewr-d 2xpn-d 3mfb-2 1tmj-d 3ga4-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) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: APC5942

Similar structure data

Other databases

TargetDB: APC5942

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Hypothetical protein AF0160

B: Hypothetical protein AF0160

C: Hypothetical protein AF0160

61.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Hypothetical protein AF0160

defined by author&software
20.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Hypothetical protein AF0160

defined by author
20.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Hypothetical protein AF0160

defined by author
20.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

B: Hypothetical protein AF0160

C: Hypothetical protein AF0160

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

Unit cell

Length a, b, c (Å)	65.187, 69.744, 133.978
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLY	GLY	PHE	PHE	A	A	4 - 20	5 - 21
2	1	GLY	GLY	PHE	PHE	B	B	4 - 20	5 - 21
3	1	GLY	GLY	PHE	PHE	C	C	4 - 20	5 - 21
4	2	ARG	ARG	VAL	VAL	A	A	30 - 48	31 - 49
5	2	ARG	ARG	VAL	VAL	B	B	30 - 48	31 - 49
6	2	ARG	ARG	VAL	VAL	C	C	30 - 48	31 - 49
7	3	GLU	GLU	TYR	TYR	A	A	50 - 79	51 - 80
8	3	GLU	GLU	TYR	TYR	B	B	50 - 79	51 - 80
9	3	GLU	GLU	TYR	TYR	C	C	50 - 79	51 - 80
10	4	SER	SER	GLU	GLU	A	A	84 - 103	85 - 104
11	4	SER	SER	GLU	GLU	B	B	84 - 103	85 - 104
12	4	SER	SER	GLU	GLU	C	C	84 - 103	85 - 104
13	5	GLU	GLU	ILE	ILE	A	A	116 - 128	117 - 129
14	5	GLU	GLU	ILE	ILE	B	B	116 - 128	117 - 129
15	5	GLU	GLU	ILE	ILE	C	C	116 - 128	117 - 129
16	6	ALA	ALA	LYS	LYS	A	A	130 - 157	131 - 158
17	6	ALA	ALA	LYS	LYS	B	B	130 - 157	131 - 158
18	6	ALA	ALA	LYS	LYS	C	C	130 - 157	131 - 158

#1: Protein	Hypothetical protein AF0160 Mass: 20589.859 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF_0160 / Production host: Escherichia coli (E. coli) / References: UniProt: O30077
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.59 Å³/Da / Density % sol: 52.6 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: SITTING DROP MODIFIED MICROBATCH USING 0.5 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (40 mg/ml) AND RESERVOIR SOLUTION CONTAINING 30% PEG 3350, 0.15M NASCN, 0.01M ...Details: SITTING DROP MODIFIED MICROBATCH USING 0.5 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (40 mg/ml) AND RESERVOIR SOLUTION CONTAINING 30% PEG 3350, 0.15M NASCN, 0.01M SPERMINE-HCL, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal

Density Matthews: 2.59 Å³/Da / Density % sol: 52.6 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: SITTING DROP MODIFIED MICROBATCH USING 0.5 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (40 mg/ml) AND RESERVOIR SOLUTION CONTAINING 30% PEG 3350, 0.15M NASCN, 0.01M ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97911 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 2006 / Details: Rosenbaum
Radiation	Monochromator: SI CHANNEL 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97911 Å / Relative weight: 1
Reflection	Resolution: 2.69→50 Å / Num. obs: 18724 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 11.9 % / R_sym value: 0.106 / Net I/σ(I): 28.75
Reflection shell	Resolution: 2.69→2.8 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 4.12 / Num. unique all: 1699 / R_sym value: 0.41 / % possible all: 89

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Processing

Software

Name	Version	Classification
Sca2Structure		model building
REFMAC	5.2.0019	refinement
SERGUI		data collection
HKL-2000		data reduction
SCALEPACK		data scaling
SCA2STRUCTURE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.69→36.83 Å / Cor.coef. F_o:F_c: 0.906 / Cor.coef. F_o:F_c free: 0.875 / SU B: 29.127 / SU ML: 0.302 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 3.817 / ESU R Free: 0.407 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.29677	1012	5.9 %	RANDOM
R_work	0.24394	-	-	-
all	0.24701	16116	-	-
obs	0.24701	16116	100 %	-

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: 30.715 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0 Å²	0 Å²	0 Å²
2-	-	0.01 Å²	0 Å²
3-	-	-	-0.01 Å²

Refinement step

Cycle: LAST / Resolution: 2.69→36.83 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3925	0	0	81	4006

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	3998
X-RAY DIFFRACTION	r_angle_refined_deg	1.361	1.966	5396
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.281	5	483
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.179	23.228	189
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.696	15	700
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.772	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.109	0.2	602
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	3004
X-RAY DIFFRACTION	r_nbd_refined	0.244	0.2	1850
X-RAY DIFFRACTION	r_nbtor_refined	0.31	0.2	2824
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.161	0.2	145
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.286	0.2	86
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.45	0.2	13
X-RAY DIFFRACTION	r_mcbond_it	0.569	1.5	2513
X-RAY DIFFRACTION	r_mcangle_it	0.982	2	3900
X-RAY DIFFRACTION	r_scbond_it	1.516	3	1687
X-RAY DIFFRACTION	r_scangle_it	2.313	4.5	1496

Refine LS restraints NCS

Ens-ID: 1 / Number: 1035 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	tight positional	0.05	0.05
2	B	tight positional	0.06	0.05
3	C	tight positional	0.06	0.05
1	A	tight thermal	0.1	0.5
2	B	tight thermal	0.1	0.5
3	C	tight thermal	0.1	0.5

LS refinement shell

Resolution: 2.69→2.77 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.531	66	-
R_work	0.358	1031	-
obs	-	1031	100 %

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	0.4216	-0.0843	0.5372	2.475	2.4003	3.243	0.2649	-0.2229	0.1974	0.0547	0.1105	-0.1868	-0.2503	0.2991	-0.3754	0.1305	-0.043	-0.0262	0.1691	-0.0696	0.12	18.8059	7.4009	24.138
2	20.1842	-7.3432	-9.5929	7.2382	4.174	4.6616	0.3021	-0.7857	2.6806	0.0543	-0.1958	-0.8983	-0.9075	-0.2306	-0.1063	0.1647	-0.1214	-0.1056	0.0539	-0.1051	0.3944	17.2941	17.9029	23.1469
3	2.2233	-2.1682	-1.7493	2.7305	2.9988	4.0892	0.1565	-0.1839	-0.1851	0.2535	-0.162	0.2265	0.196	-0.4126	0.0055	0.0466	-0.046	-0.008	0.1411	-0.0614	0.0604	5.8295	-4.2779	18.3089
4	2.2367	-0.5516	-0.3766	0.7805	1.0797	1.5744	0.1737	-0.2163	0.3676	0.2495	-0.0329	-0.0171	0.0322	-0.0792	-0.1408	0.1104	0.0225	-0.0512	0.1205	-0.0255	0.0275	22.2195	-3.0317	15.6104
5	23.418	-3.1854	-9.6527	0.4372	1.3987	5.8623	0.4761	1.1611	0.279	-0.1763	-0.2533	0.3309	-0.1617	0.1792	-0.2227	0.1554	0.0801	-0.041	0.2092	-0.0154	-0.0307	25.8436	-1.6	3.438
6	2.9682	-2.0535	1.0247	5.9703	0.7915	0.8486	0.1871	0.2446	0.0947	-0.3027	-0.2387	0.5232	-0.3277	-0.2602	0.0516	0.1219	0.0307	0.0113	0.0911	-0.0332	0.1438	8.0587	6.5837	14.009
7	5.005	-1.9717	-6.2575	11.0674	5.7594	12.9326	0.6528	1.2163	0.326	-0.9601	-0.5796	-0.009	-1.9938	-1.6021	-0.0732	0.2387	0.1444	0.0091	0.1588	0.0847	0.1147	15.897	9.3683	6.2067
8	2.1928	-2.3679	0.6423	2.67	-1.17	2.1956	0.0767	0.2793	-0.2646	-0.3098	-0.1046	0.2608	0.0592	-0.5037	0.0279	0.0799	0.027	-0.0531	-0.0025	-0.0212	0.0422	-1.5851	-17.8108	-19.159
9	1.036	-0.7948	0.723	1.6615	-0.1975	1.3819	0.016	-0.1017	-0.1553	-0.117	0.0074	0.1104	0.0605	0.0142	-0.0234	0.0016	-0.0224	-0.0114	0.0448	-0.0214	0.012	2.995	-18.0166	-5.1475
10	5.6631	-1.9613	-0.4163	2.0835	1.4448	2.7759	0.0031	-0.31	0.2009	-0.1389	-0.1746	0.1756	-0.381	-0.2294	0.1715	0.1082	0.0234	-0.0141	-0.0221	-0.0184	0.0437	-3.8326	-6.0675	-8.745
11	1.1204	-0.1688	-1.8128	10.4274	2.7536	3.8976	0.6231	0.3811	0.9582	-1.0169	-0.1471	-1.2163	-0.9266	0.2419	-0.476	0.2115	-0.0212	0.0714	-0.0362	0.0212	0.0472	2.8446	-1.2282	-12.2572
12	3.4421	0.6353	-1.4432	0.12	-0.2133	1.6389	0.0202	-0.4718	0.5717	0.0718	-0.1051	-0.0885	-0.2276	0.0781	0.0849	0.1536	-0.0077	0.0192	0.0617	-0.1274	0.167	-13.2365	10.111	37.4018
13	4.767	-0.3826	-0.1645	3.5238	3.0891	5.5132	0.0453	0.5264	-0.177	-0.4983	-0.0713	0.3463	-0.2071	-0.15	0.026	0.1907	-0.0112	-0.0032	0.0862	-0.0496	0.1215	-13.976	5.2225	20.411
14	7.2425	1.8029	-6.4875	3.9053	-0.1296	10.5817	0.0758	0.4037	-0.1159	0.5071	-0.1822	0.0977	-0.708	-1.0673	0.1064	0.1079	0.1209	-0.0073	0.1367	-0.0546	0.0454	-33.2091	2.6525	34.2237
15	4.5467	2.1076	-1.2402	2.0483	0.3422	1.1234	-0.1113	0.29	-0.1963	-0.057	0.0743	-0.1642	0.036	0.1005	0.0369	0.086	0.0555	-0.0126	0.0167	-0.048	0.0216	-17.3724	-3.1893	31.0114
16	14.4127	14.0668	1.3572	15.9461	2.9764	1.43	-0.6384	-0.449	-0.2228	0.5887	0.2296	1.1758	0.8456	-0.3347	0.4089	0.2155	0.0715	0.0318	0.0052	-0.0652	0.0168	-27.3249	-10.5817	36.4229

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	2 - 28	3 - 29
2	X-RAY DIFFRACTION	2	A	A	29 - 41	30 - 42
3	X-RAY DIFFRACTION	3	A	A	42 - 75	43 - 76
4	X-RAY DIFFRACTION	4	A	A	76 - 111	77 - 112
5	X-RAY DIFFRACTION	5	A	A	112 - 128	113 - 129
6	X-RAY DIFFRACTION	6	A	A	129 - 147	130 - 148
7	X-RAY DIFFRACTION	7	A	A	148 - 160	149 - 161
8	X-RAY DIFFRACTION	8	B	B	1 - 34	2 - 35
9	X-RAY DIFFRACTION	9	B	B	35 - 97	36 - 98
10	X-RAY DIFFRACTION	10	B	B	98 - 147	99 - 148
11	X-RAY DIFFRACTION	11	B	B	148 - 162	149 - 163
12	X-RAY DIFFRACTION	12	C	C	1 - 41	2 - 42
13	X-RAY DIFFRACTION	13	C	C	42 - 96	43 - 97
14	X-RAY DIFFRACTION	14	C	C	97 - 116	98 - 117
15	X-RAY DIFFRACTION	15	C	C	117 - 156	118 - 157
16	X-RAY DIFFRACTION	16	C	C	157 - 164	158 - 165

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