PDB-2ia0: Transcriptional Regulatory Protein PF0864 From Pyrococcus Furiosu...

ID or keywords:

Entry

Database: PDB / ID: 2ia0

Title

Transcriptional Regulatory Protein PF0864 From Pyrococcus Furiosus a Member of the ASNC Family (PF0864)

Components

Putative HTH-type transcriptional regulator PF0864

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF0864 / ASNC /

PYROCOCCUS FURIOSUS / PSI / SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS /

Protein Structure Initiative / SECSG

Function / homology

Function and homology information

sequence-specific DNA binding / DNA-binding transcription factor activity
Similarity search - Function

Biological species

Pyrococcus furiosus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / AU SAD / Resolution: 2.37 Å

Authors

Yang, H. / Chang, J. / Liu, Z.J. / Rose, J.P. / Wang, B.C. / Southeast Collaboratory for Structural Genomics / Southeast Collaboratory for Structural Genomics (SECSG)

Citation

Journal: To be Published
Title: Crystal Structure of the Transcriptional Regulatory Protein PF0864: an Asnc Family member from Pyrococcus Furiosus
Authors: Yang, H. / Chang, J. / Liu, Z.J. / Rose, J.P. / Wang, B.C. / Southeast Collaboratory for Structural Genomics

History

Deposition	Sep 6, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 31, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Advisory / Category: pdbx_unobs_or_zero_occ_atoms
Revision 1.4	Feb 21, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2ia0.cif.gz	76.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2ia0.ent.gz	59 KB	Display	PDB format
PDBx/mmJSON format	2ia0.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ia/2ia0 ftp://data.pdbj.org/pub/pdb/validation_reports/ia/2ia0	HTTPS FTP

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Related structure data

Similar structure data	3r3m-d 3e3q-5 5qsw-2 3hw8-d 5izn-2 5ey4-2 3mda-d 4cz2-3 3lm8-5 3uq0-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
Other databases	TargetDB: Pfu-839232-001

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#107 - Nov 2008 Mechanosensitive Channels similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1)

Deposited unit

A: Putative HTH-type transcriptional regulator PF0864

B: Putative HTH-type transcriptional regulator PF0864

hetero molecules

39.5 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)	58.074, 70.372, 96.536
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Putative HTH-type transcriptional regulator PF0864 Mass: 19528.738 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: PF0864 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8U2H1
#2: Chemical	ChemComp-AU / GOLD ION Mass: 196.967 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Au
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.52 Å³/Da / Density % sol: 51.28 %
Crystal grow	Temperature: 291 K / Method: modified microbatch Details: MODIFIED MICROBACTH UNDER 0IL USING 1 MICROLITER DROPS CONTAING EQUAL VOLUMES OF PROTEIN 100 MM NAAC/HCL, 16% W/V PEG4000, PH4.5, TEMPERATURE 291K, MODIFIED MICROBATCH

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97 / Wavelength: 0.97 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 17, 2006 / Details: ROSENBAUM
Radiation	Monochromator: SI CHANNEL 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97 Å / Relative weight: 1
Reflection	Resolution: 2.37→56.89 Å / Num. all: 15365 / Num. obs: 14545 / % possible obs: 91.68 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 2 / Redundancy: 6.1 % / R_sym value: 0.114 / Net I/σ(I): 9
Reflection shell	Resolution: 2.37→2.42 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.18 / R_sym value: 0.477 / % possible all: 50.29

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Processing

Software

Name	Version	Classification
SOLVE		phasing
CCP4		model building
REFMAC	5.2.0019	refinement
SERGUI		data collection
HKL-2000		data reduction
HKL-2000		data scaling
SCA2STRUCTURE		phasing

Refinement

Method to determine structure: AU SAD / Resolution: 2.37→56.89 Å / Cor.coef. F_o:F_c: 0.935 / Cor.coef. F_o:F_c free: 0.891 / SU B: 13.794 / SU ML: 0.187 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.391 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26854	776	5.1 %	RANDOM
R_work	0.20541	-	-	-
obs	0.2085	14545	91.68 %	-
all	-	14565	-	-

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: 19.003 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.73 Å²	0 Å²	0 Å²
2-	-	-0.63 Å²	0 Å²
3-	-	-	-1.1 Å²

Refinement step

Cycle: LAST / Resolution: 2.37→56.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2473	0	2	97	2572

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	2483
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.793	2.006	3337
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	11.924	5	303
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.821	24.95	101
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.338	15	502
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.764	15	13
X-RAY DIFFRACTION	r_chiral_restr	0.173	0.2	405
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	1743
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.227	0.2	971
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.302	0.2	1644
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.173	0.2	95
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	0.286	0.2	33
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.24	0.2	6
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	1.062	1.5	1587
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.136	2	2483
X-RAY DIFFRACTION	r_scbond_it	2.044	3	990
X-RAY DIFFRACTION	r_scangle_it	3.289	4.5	854
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.367→2.429 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.275	36	-
R_work	0.238	580	-
obs	-	-	50.29 %

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	4.8267	0.455	1.1828	1.9876	0.438	4.2405	0.1032	-0.0815	-0.0406	-0.0124	-0.0357	0.1636	0.1111	-0.2843	-0.0675	0.1235	-0.0098	-0.0065	0.0335	0.0281	0.028	19.4832	65.4338	7.1124
2	1.5158	1.6145	2.6268	2.8559	1.5287	5.9695	-0.0889	0.1075	0.6203	-0.2753	-0.0135	0.1788	-0.4899	-0.0743	0.1023	0.1642	0.0257	-0.0374	0.1137	0.0358	0.0784	18.3722	76.0681	6.8079
3	0.2584	0.2901	-0.1165	0.326	-0.0913	5.3026	-0.0353	-0.1007	-0.1966	0.068	-0.0022	-0.1005	0.2331	0.3168	0.0374	0.156	0.0013	0.0113	0.1168	-0.0083	0.1404	36.3632	68.8084	24.9022
4	1.8595	0.0115	-1.0336	4.0084	-1.3093	0.9981	-0.1971	-0.2366	0.1797	0.6183	0.2848	0.6836	-0.3721	0.0172	-0.0877	0.2329	-0.013	-0.0112	0.181	-0.0206	0.1539	27.146	86.0546	47.3449
5	1.3263	0.2573	-0.8252	4.7015	1.3189	3.2078	-0.1327	0.0073	0.0615	0.0657	0.1167	-0.0671	0.1057	0.0109	0.0161	0.132	-0.0138	-0.0241	0.0657	0.0119	0.0352	32.8652	80.8546	38.9539
6	7.2503	-0.4632	-0.9082	4.0258	1.0279	5.8747	-0.233	-0.3915	-0.2336	-0.119	0.2675	-0.0787	-0.0651	0.713	-0.0345	0.1561	-0.0242	-0.0435	0.0934	0.0115	0.0209	39.6971	77.4917	46.4844
7	1.1099	0.1788	0.4499	1.6048	0.8036	3.3897	-0.0854	0.1547	-0.1135	-0.0801	-0.0448	-0.1645	0.2333	0.3057	0.1302	0.1081	0.0085	-0.008	0.115	-0.0034	0.054	32.4654	66.9479	33.3012
8	7.1141	1.0776	-0.3742	0.7232	-0.2169	3.7187	0.2218	-0.4204	0.0512	-0.0161	-0.0684	-0.2453	-0.0359	0.3924	-0.1533	0.1659	-0.0209	0.0355	0.0704	-0.0421	0.0342	42.4418	75.3576	13.5839
9	4.0621	-1.2028	-1.8851	3.525	-1.983	4.4151	0.1082	-0.0882	0.095	-0.1006	0.0084	-0.3562	-0.0994	0.2507	-0.1166	0.1718	-0.0053	0.0208	0.1271	-0.0555	0.0502	46.6119	73.4255	7.1383
10	13.5366	-3.4993	-0.6747	5.3815	0.2596	4.7282	0.0623	-0.2369	-0.3022	-0.0221	-0.0177	0.1179	0.1079	-0.0277	-0.0446	0.1839	-0.0711	-0.0184	0.0161	0.0331	-0.0424	30.7911	68.8018	16.6556
11	1.5091	0.7148	0.1037	2.0945	1.8755	1.9069	-0.0992	-0.0035	-0.105	0.3877	0.0527	-0.1793	-0.0859	-0.1334	0.0465	0.1384	-0.0113	0.0523	0.1533	-0.0157	0.1318	21.3376	63.473	39.6765
12	0.9539	-0.302	-0.492	4.5314	-1.3056	3.1456	-0.0302	-0.0557	-0.1077	0.0877	-0.0237	-0.0414	0.1901	0.0196	0.0539	0.1224	-0.0114	0.0332	0.043	-0.0115	0.0414	23.1175	57.974	38.0533
13	3.4043	0.4894	-0.2407	2.8625	-1.3008	4.157	-0.1113	-0.2653	0.0804	-0.0809	0.1895	0.381	-0.0014	-0.7724	-0.0782	0.149	-0.01	0.0134	0.1199	-0.0489	0.0701	12.6597	66.121	39.575
14	0.5455	0.2436	-0.996	2.3776	-0.2141	2.5242	0.0057	0.0451	0.0653	-0.1495	-0.0543	0.1032	-0.2692	-0.1132	0.0486	0.0922	0.0033	0.0006	0.1164	0.0136	0.0295	23.2938	74.7386	31.95

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	5 - 38	14 - 47
2	X-RAY DIFFRACTION	2	A	A	39 - 52	48 - 61
3	X-RAY DIFFRACTION	3	A	A	53 - 70	62 - 79
4	X-RAY DIFFRACTION	4	A	A	71 - 83	80 - 92
5	X-RAY DIFFRACTION	5	A	A	84 - 121	93 - 130
6	X-RAY DIFFRACTION	6	A	A	122 - 140	131 - 149
7	X-RAY DIFFRACTION	7	A	A	141 - 162	150 - 171
8	X-RAY DIFFRACTION	8	B	B	5 - 27	14 - 36
9	X-RAY DIFFRACTION	9	B	B	28 - 47	37 - 56
10	X-RAY DIFFRACTION	10	B	B	48 - 62	57 - 71
11	X-RAY DIFFRACTION	11	B	B	63 - 83	72 - 92
12	X-RAY DIFFRACTION	12	B	B	84 - 114	93 - 123
13	X-RAY DIFFRACTION	13	B	B	115 - 140	124 - 149
14	X-RAY DIFFRACTION	14	B	B	141 - 162	150 - 171

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