PDB-2p06: Crystal structure of a predicted coding region AF_0060 from Archa...

ID or keywords:

Entry

Database: PDB / ID: 2p06

Title

Crystal structure of a predicted coding region AF_0060 from Archaeoglobus fulgidus DSM 4304

Components

Hypothetical protein AF_0060

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / MCSG / PSI2 / MAD / singleton / predicted coding region AF_0060 / Protein Structure Initiative / Midwest Center for Structural Genomics

Function / homology

Uncharacterised protein AF_0060, NTP Pyrophosphohydrolase MazG-like domain / NTP pyrophosphohydrolase MazG, putative catalytic core / MazG nucleotide pyrophosphohydrolase domain / MazG-like / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein AF_0060

Function and homology information

Biological species

Archaeoglobus fulgidus DSM 4304 (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.1 Å

Authors

Nocek, B. / Xu, X. / Koniyenko, Y. / Yakounine, A. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of a predicted coding region AF_0060 from Archaeoglobus fulgidus DSM 4304
Authors: Nocek, B. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A.

History

Deposition	Feb 28, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 27, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Derived calculations / Version format compliance
Revision 1.3	Nov 20, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 300

BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2p06.cif.gz	59.1 KB	Display	PDBx/mmCIF format
PDB format	pdb2p06.ent.gz	43.7 KB	Display	PDB format
PDBx/mmJSON format	2p06.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/p0/2p06 ftp://data.pdbj.org/pub/pdb/validation_reports/p0/2p06	HTTPS FTP

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Related structure data

Similar structure data	4avb-2 1avx-d 1c8t-d 5uwm-d 1zj6-2 1z6x-d 4avc-2 6dwu-4 4d86-d 5we9-2 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	TargetDB: APC7408

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Hypothetical protein AF_0060

B: Hypothetical protein AF_0060

hetero molecules

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

1

A: Hypothetical protein AF_0060

B: Hypothetical protein AF_0060

hetero molecules

A: Hypothetical protein AF_0060

B: Hypothetical protein AF_0060

hetero molecules

defined by author&software
56.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	80.083, 80.083, 106.771
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	Hypothetical protein AF_0060 Mass: 14143.105 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea) Species: Archaeoglobus fulgidus / Strain: DSM 4304, VC-16, JCM 9628, NBRC 100126 / Gene: AF_0060 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: O30176
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 124 / 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: 3.49 Å³/Da / Density % sol: 64.79 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.6 Details: 0.2M Potassium thiocyanate, 30% PEG 3350, pH 8.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97920, 0.97940

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2007 / Details: mirrors

Radiation

Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9792	1
2	0.9794	1

Reflection

Resolution: 2.1→35 Å / Num. all: 23576 / Num. obs: 23576 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.6 % / R_merge(I) obs: 0.121 / Net I/σ(I): 30.6

Reflection shell

Resolution: 2.1→2.4 Å / Redundancy: 12.8 % / R_merge(I) obs: 0.79 / Mean I/σ(I) obs: 4.1 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
SHELXD		phasing
MLPHARE		phasing
DM		phasing
RESOLVE		phasing
ARP/wARP		model building

Refinement

Method to determine structure:

MAD / Resolution: 2.1→34.67 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.958 / SU B: 5.263 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.117 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18655	1213	5.1 %	RANDOM
R_work	0.16919	-	-	-
all	0.17006	22363	-	-
obs	0.17006	22363	99.67 %	-

Displacement parameters

B_iso mean: 22.083 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.62 Å²	0.31 Å²	0 Å²
2-	-	0.62 Å²	0 Å²
3-	-	-	-0.93 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→34.67 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1489	0	8	124	1621

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	1571
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	1166
X-RAY DIFFRACTION	r_angle_refined_deg	1.329	1.96	2111
X-RAY DIFFRACTION	r_angle_other_deg	0.898	3	2776
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.308	5	178
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.197	22.473	93
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.421	15	296
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.804	15	21
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	204
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	1738
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	381
X-RAY DIFFRACTION	r_nbd_refined	0.216	0.2	402
X-RAY DIFFRACTION	r_nbd_other	0.189	0.2	1235
X-RAY DIFFRACTION	r_nbtor_refined	0.19	0.2	777
X-RAY DIFFRACTION	r_nbtor_other	0.088	0.2	803
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.19	0.2	90
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	0.199	0.2	8
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.382	0.2	28
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.071	0.2	7
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	0.987	1.5	1095
X-RAY DIFFRACTION	r_mcbond_other	0.193	1.5	347
X-RAY DIFFRACTION	r_mcangle_it	1.275	2	1408
X-RAY DIFFRACTION	r_scbond_it	2.145	3	807
X-RAY DIFFRACTION	r_scangle_it	3.056	4.5	701
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.1→2.154 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.206	96	-
R_work	0.175	1602	-
obs	-	-	99.76 %

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	1.0801	1.0296	-1.6716	11.2034	-2.2089	3.2989	0.149	-0.016	0.4002	-0.8418	-0.345	-0.1072	-0.7731	0.2901	0.196	0.3922	-0.0621	0.0188	0.0425	-0.0126	0.1072	4.0141	84.2025	-14.7867
2	0.0909	-0.4957	-0.5796	9.0912	-0.2393	5.5069	0.0777	0.0203	0.0338	0.0909	-0.1175	-0.1125	-0.0567	0.3156	0.0398	0.2089	-0.0509	-0.0091	0.0517	-0.0022	0.1131	6.0357	71.482	-12.0841
3	37.9026	-13.784	-9.9892	54.5764	10.165	26.5052	0.1717	0.8867	0.4465	-0.3257	0.3607	-0.1703	1.1322	0.3327	-0.5324	0.1814	-0.0604	-0.0261	-0.0499	0.0815	0.0798	7.3744	59.3717	-8.7312
4	92.6129	-33.0344	-8.7527	20.6108	2.8727	0.8343	-1.3324	-2.2734	-2.975	1.1963	0.0687	0.2381	1.4701	0.1064	1.2637	0.5175	-0.0253	0.0384	0.1057	0.149	0.2363	3.8835	54.1923	-6.2808
5	2.6351	2.7391	-2.4815	8.3105	2.2979	12.9807	-0.0685	-0.0432	-0.1535	-0.0285	-0.1996	0.1979	0.1885	-0.1441	0.2681	0.2351	-0.1424	0.0284	0.0381	-0.0002	0.0889	-6.1013	59.76	-1.9378
6	17.3638	10.8763	3.7423	9.4265	1.58	3.7248	0.4188	-0.7889	-0.402	0.9608	-0.2939	-0.3371	0.2903	-0.1843	-0.1249	0.3546	-0.1237	-0.0417	0.0533	0.0327	0.0059	6.3876	67.8923	6.727
7	15.5312	-6.5058	19.5268	51.1878	-10.7851	24.6904	0.1175	1.1197	-0.6481	-0.0128	1.3913	-2.7543	0.0527	0.8393	-1.5088	0.1081	-0.058	0.0029	0.382	-0.037	0.4051	19.5409	73.0534	3.5065
8	16.2525	7.1377	-1.9131	27.3205	-6.8775	12.4189	0.3247	0.1733	-0.6673	-0.1134	-0.4147	-2.4963	0.4739	0.7711	0.09	0.1149	-0.0422	-0.0407	0.1082	-0.0116	0.223	14.9016	71.5982	-2.5048
9	11.1291	0.989	0.7921	0.8156	1.915	4.7316	0.2191	-0.1335	-0.2283	0.145	-0.1415	0.0057	0.2729	0.0655	-0.0776	0.3042	-0.0998	0.0039	0.0451	0.0213	0.1118	4.0905	69.2347	-2.3828
10	0.5709	-3.0961	-0.346	16.7914	1.8667	6.3454	0.1963	-0.111	-0.0479	0.0112	-0.1024	1.2684	0.0652	-0.5817	-0.094	0.2084	-0.1393	0.0414	0.1165	-0.0002	0.1757	-9.4401	67.5592	-2.9447
11	2.3345	2.0375	2.052	6.0883	8.2994	12.8551	0.1661	0.101	-0.4081	0.4197	-0.2227	0.0984	0.7663	-0.2179	0.0566	0.2649	-0.0429	-0.0201	0.0314	-0.0066	0.1496	-4.3775	59.1302	-16.2927
12	4.6835	-9.678	-4.2072	20.6889	12.3125	22.7528	0.3988	0.2648	0.1589	-0.0524	-0.5569	0.8727	0.1742	-1.0256	0.158	0.2407	-0.061	-0.0072	0.0765	-0.0119	0.147	-6.151	69.3011	-13.7344
13	2.2615	0.1507	3.8609	5.7674	1.1097	7.54	0.1611	-0.0104	0.1166	0.0042	-0.2522	0.0987	-0.2821	-0.3775	0.0911	0.2297	-0.0273	0.0303	0.0644	-0.03	0.1201	-5.3326	79.0478	-8.5665
14	27.2571	-5.7132	-29.2007	23.7995	-1.6026	35.2184	-0.0312	0.6056	0.005	0.8286	-0.3655	0.5239	-0.6253	-0.7397	0.3968	0.3218	-0.0266	-0.0253	-0.1072	-0.1328	0.158	-4.3675	87.2156	-4.4923
15	37.2657	-11.3871	7.9958	23.4805	20.4632	40.8587	-1.4914	-3.3038	3.0193	1.51	0.0707	-0.3436	1.3668	-0.5786	1.4207	0.6232	-0.1119	0.0081	0.2164	-0.2407	0.4193	-1.4236	92.8773	-0.5281
16	15.4045	5.1502	9.8559	5.0424	1.785	10.4829	-0.0857	0.1513	0.7847	-0.5466	0.0615	0.3786	-0.7106	0.1379	0.0242	0.3229	-0.1235	0.0001	-0.0002	-0.016	0.1347	7.9299	89.5438	-6.4862
17	16.0157	14.0085	-6.9154	14.7085	-2.8217	7.2268	0.1046	-0.4269	-0.0729	0.4832	-0.1783	-0.3665	0.2262	0.2211	0.0737	0.2973	-0.1456	-0.0224	0.061	-0.0279	0.091	9.6234	83.392	4.417
18	17.7022	9.533	-7.6229	11.8816	-4.6697	12.542	0.4431	-0.6951	0.4508	1.1471	-0.4445	0.4318	-0.1814	0.3255	0.0014	0.3428	-0.1691	0.1077	0.0483	-0.1007	-0.0119	-2.8535	76.141	10.4354
19	3.3121	-5.4906	-6.7256	17.4701	-10.7453	70.9436	0.6763	-0.1233	0.1009	0.6584	0.1354	2.5145	-0.2485	-3.7684	-0.8116	0.2704	-0.2157	0.193	0.2259	-0.1091	0.268	-12.0127	73.4158	6.0505
20	11.0262	4.3956	-1.3557	3.948	-0.148	1.8515	-0.0315	0.0424	0.3382	0.0833	0.0714	0.0558	-0.2251	0.0334	-0.0399	0.2915	-0.1131	0.0015	0.0383	-0.0173	0.0699	4.6244	79.2957	-2.8445

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	1 - 5	22 - 26
2	X-RAY DIFFRACTION	2	A	A	6 - 18	27 - 39
3	X-RAY DIFFRACTION	3	A	A	19 - 23	40 - 44
4	X-RAY DIFFRACTION	4	A	A	24 - 29	45 - 50
5	X-RAY DIFFRACTION	5	A	A	30 - 40	51 - 61
6	X-RAY DIFFRACTION	6	A	A	41 - 56	62 - 77
7	X-RAY DIFFRACTION	7	A	A	57 - 61	78 - 82
8	X-RAY DIFFRACTION	8	A	A	62 - 65	83 - 86
9	X-RAY DIFFRACTION	9	A	A	66 - 75	87 - 96
10	X-RAY DIFFRACTION	10	A	A	76 - 84	97 - 105
11	X-RAY DIFFRACTION	11	B	B	-4 - 3	17 - 24
12	X-RAY DIFFRACTION	12	B	B	4 - 9	25 - 30
13	X-RAY DIFFRACTION	13	B	B	10 - 17	31 - 38
14	X-RAY DIFFRACTION	14	B	B	18 - 21	39 - 42
15	X-RAY DIFFRACTION	15	B	B	22 - 28	43 - 49
16	X-RAY DIFFRACTION	16	B	B	29 - 35	50 - 56
17	X-RAY DIFFRACTION	17	B	B	36 - 45	57 - 66
18	X-RAY DIFFRACTION	18	B	B	46 - 57	67 - 78
19	X-RAY DIFFRACTION	19	B	B	58 - 64	79 - 85
20	X-RAY DIFFRACTION	20	B	B	65 - 83	86 - 104

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