PDB-2p4w: Crystal structure of heat shock regulator from Pyrococcus furiosus

ID or keywords:

Entry

Database: PDB / ID: 2p4w

Title

Crystal structure of heat shock regulator from Pyrococcus furiosus

Components

Transcriptional regulatory protein arsR family

Keywords

TRANSCRIPTION / archaea / Phr / heat shock / transcriptional regulation / winged helix / DNA binding

Function / homology

Function and homology information

DNA-binding transcription factor activity
Similarity search - Function

Biological species

Pyrococcus furiosus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Liu, W. / Vierke, G. / Panjikar, S. / Thomm, M. / Ladenstein, R.

Citation

Journal: J.Mol.Biol. / Year: 2007
Title: Crystal Structure of the Archaeal Heat Shock Regulator from Pyrococcus furiosus: A Molecular Chimera Representing Eukaryal and Bacterial Features.
Authors: Liu, W. / Vierke, G. / Wenke, A.K. / Thomm, M. / Ladenstein, R.

History

Deposition	Mar 13, 2007	Deposition site: RCSB / Processing site: RCSB
Supersession	Mar 27, 2007	ID: 1XNP
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 / Version format compliance
Revision 1.3	Aug 30, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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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Download

PDBx/mmCIF format	2p4w.cif.gz	94.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2p4w.ent.gz	73.9 KB	Display	PDB format
PDBx/mmJSON format	2p4w.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2p4w_validation.pdf.gz	450.7 KB	Display	wwPDB validaton report
Full document	2p4w_full_validation.pdf.gz	470.2 KB	Display
Data in XML	2p4w_validation.xml.gz	18.5 KB	Display
Data in CIF	2p4w_validation.cif.gz	24.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p4/2p4w ftp://data.pdbj.org/pub/pdb/validation_reports/p4/2p4w	HTTPS FTP

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Related structure data

Related structure data	1xnp PDB Unreleased entryS S: Starting model for refinement
Similar structure data	1wl2-2 6mvg-1 5v58-d 2azl-2 1wkz-d 5lmj-d 1qup-d 3mav-2 1ais-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

Deposited unit

A: Transcriptional regulatory protein arsR family

B: Transcriptional regulatory protein arsR family

hetero molecules

48.2 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)	52.389, 82.854, 114.492
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	B

NCS domain segments:

Component-ID: 1

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	MET	MET	ALA	ALA	2	A	A	1 - 98	1 - 98
2	1	MET	MET	ALA	ALA	2	B	B	1 - 98	1 - 98
1	2	LYS	LYS	PHE	PHE	3	A	A	103 - 197	103 - 197
2	2	LYS	LYS	PHE	PHE	3	B	B	103 - 197	103 - 197

NCS ensembles :

ID
1
2

#1: Protein	Transcriptional regulatory protein arsR family Mass: 24074.094 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: PF1790 / Plasmid: pET-17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysE / References: UniProt: Q8U030
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.58 Å³/Da / Density % sol: 52.32 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 1.5 M lithium sulfate, 25% ethylene glycol, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9198 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 20, 2006 / Details: mirrors
Radiation	Monochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9198 Å / Relative weight: 1
Reflection	Resolution: 2.47→38.66 Å / Num. all: 17812 / Num. obs: 17812 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.7 % / B_iso Wilson estimate: 74 Å² / R_merge(I) obs: 0.086 / R_sym value: 0.086 / Net I/σ(I): 17.87
Reflection shell	Resolution: 2.47→2.51 Å / Redundancy: 6.2 % / R_merge(I) obs: 0.634 / Mean I/σ(I) obs: 5.79 / Num. unique all: 682 / R_sym value: 0.634 / % possible all: 73.3

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
MxCuBE		data collection
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XNP

1xnp
PDB Unreleased entry

Resolution: 2.6→38.66 Å / Cor.coef. F_o:F_c: 0.925 / Cor.coef. F_o:F_c free: 0.886 / SU B: 28.02 / SU ML: 0.293 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.969 / ESU R Free: 0.383 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: Use TLS refinement at the last round of refinement

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.30517	786	5 %	RANDOM
R_work	0.25239	-	-	-
obs	0.255	14972	98.79 %	-
all	-	14972	-	-

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: 32.156 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.42 Å²	0 Å²	0 Å²
2-	-	-0.39 Å²	0 Å²
3-	-	-	-3.03 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→38.66 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3308	0	5	47	3360

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.032	0.022	3339
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.128	2.016	4466
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.007	5	393
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.371	22.738	168
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	22.825	15	707
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.663	15	46
X-RAY DIFFRACTION	r_chiral_restr	0.121	0.2	488
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	2462
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.27	0.2	1558
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.332	0.2	2314
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.202	0.2	99
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	0.316	0.2	72
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.288	0.2	4
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	0.828	1.5	2032
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.209	2	3181
X-RAY DIFFRACTION	r_scbond_it	2.603	3	1445
X-RAY DIFFRACTION	r_scangle_it	4.309	4.5	1285
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Number	Type	Rms dev position (Å)	Weight position
1	392	tight positional	0.09	0.05
2	380	tight positional	0.1	0.05
1	406	medium positional	0.31	0.5
2	422	loose positional	0.65	5
1	392	tight thermal	0.19	0.5
2	380	tight thermal	0.17	0.5
1	406	medium thermal	1.04	2
2	422	loose thermal	2.38	10

LS refinement shell

Resolution: 2.6→2.667 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.347	43	-
R_work	0.318	1003	-
obs	-	-	90.09 %

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	10.2698	-0.3931	-7.1278	3.3436	1.4603	13.1515	-0.7119	-0.2138	-0.1507	-0.1326	0.0692	0.1275	-0.0224	-0.5774	0.6427	0.1745	0.0954	0.0785	0.044	-0.0478	0.18	-8.1097	31.5732	36.9817
2	6.1697	2.16	-3.5108	4.3053	0.5628	9.6661	-0.2786	-0.7748	0.3144	0.094	-0.0558	0.28	-0.5166	-1.2889	0.3344	0.292	0.2238	-0.005	0.286	-0.1238	0.2885	-16.6048	35.8917	40.8493
3	6.1512	0.5647	-2.5887	0.1212	0.3359	5.8358	-0.0619	-0.0056	-0.1669	0.0368	-0.1858	0.5072	-0.4787	-1.0127	0.2477	0.212	0.0629	0.1369	0.1344	-0.0221	0.2985	-13.0525	26.4165	35.6424
4	8.0896	5.2312	1.7141	38.9979	-4.9553	6.8323	0.0438	-0.1162	0.5583	-0.4922	1.0296	3.1512	-0.3211	-0.4961	-1.0735	0.1698	-0.055	-0.0101	0.164	-0.0389	0.3936	-13.6031	12.3968	29.6941
5	5.8911	4.7015	1.576	8.123	-1.5918	16.03	0.3276	-1.199	-0.3071	1.0218	-0.6047	0.2076	0.4328	-0.3829	0.2771	0.231	-0.1531	0.0276	0.0096	-0.0023	0.1728	-5.4215	3.7637	46.9439
6	3.354	1.0005	-7.3098	2.3683	-8.27	33.8458	0.0626	0.3864	0.0401	-0.0818	-0.0704	0.0605	-0.7751	0.5009	0.0078	0.1785	-0.032	-0.057	-0.0132	-0.0601	0.1157	4.4293	10.1496	19.0193
7	12.1413	21.8559	-9.5149	40.6552	-7.1996	82.6014	-2.5615	0.138	0.9496	-3.7863	1.5784	-1.5767	0.7606	-3.4192	0.9831	0.8885	-0.0954	0.0377	0.7632	0.3915	0.6098	4.7727	18.9816	-6.2426
8	10.2314	2.7313	-1.7366	12.611	2.0687	35.8726	-0.1003	0.2571	0.9017	-0.2141	-0.1432	1.0789	-1.5441	-0.7779	0.2436	0.2864	0.2146	-0.1335	0.7204	0.0088	0.4181	-6.1226	15.0676	-2.0445
9	10.3038	-1.7697	-4.3162	1.6441	3.5529	7.7066	-0.3256	-0.2328	-0.0044	0.3144	-0.1912	0.2276	0.0169	0.1256	0.5168	0.1827	-0.0769	0.0525	-0.0965	0.0963	0.1641	7.5381	31.1395	26.5162
10	8.0684	-2.0895	-0.3036	6.2079	-1.6085	11.347	-0.1068	0.2723	0.5838	-0.0303	-0.1178	-0.6451	-1.0378	1.3842	0.2245	0.2629	-0.2865	0.0593	0.1317	0.0196	0.2476	16.8385	34.6124	23.0294
11	4.5895	-1.3179	-2.75	2.0798	0.6709	6.4087	-0.0989	-0.1391	-0.3425	0.3092	-0.0546	-0.4027	-0.1404	0.8225	0.1534	0.1586	-0.0062	-0.013	0.0856	0.0087	0.1034	11.4512	24.8838	27.8824
12	18.2526	-26.726	-18.225	46.5578	50.5004	94.582	-1.6643	0.0831	-3.8572	0.3507	2.0565	1.7031	3.9295	7.4555	-0.3922	0.6164	-0.0646	0.2655	0.7044	-0.3526	1.1795	13.1922	9.621	25.6316
13	12.508	-1.8027	-0.5253	4.2732	-0.5085	11.5042	0.0127	1.462	-0.3425	-0.6741	-0.3791	-0.048	0.1732	0.522	0.3664	0.182	0.0899	-0.0254	0.3684	-0.1484	0.2481	4.8174	4.5183	3.6204
14	4.0238	-2.4063	-10.2278	3.2233	5.934	26.0163	0.1489	-0.0171	-0.0317	0.0555	-0.2414	0.0417	-0.3542	-0.1757	0.0926	0.0575	-0.0099	-0.0249	-0.0747	-0.0314	0.1204	-5.6604	9.4227	31.7825
15	4.9335	2.8774	-3.3904	20.4434	37.3521	84.7601	-2.3064	-3.7258	0.438	1.3292	-0.0126	2.2812	2.3065	1.1313	2.319	0.7841	0.1915	-0.1003	1.0001	-0.135	0.6211	-7.1091	18.0038	57.5795
16	9.9577	-0.2985	2.3354	25.5102	-1.6748	24.8877	-0.8297	-0.1685	0.6682	1.48	-0.1982	-1.3441	-1.4786	0.329	1.028	0.3733	-0.231	-0.2521	0.3829	0.0631	0.3998	4.2275	15.7786	52.8562

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 - 32	1 - 32
2	X-RAY DIFFRACTION	2	A	A	33 - 65	33 - 65
3	X-RAY DIFFRACTION	3	A	A	66 - 93	66 - 93
4	X-RAY DIFFRACTION	4	A	A	94 - 104	94 - 104
5	X-RAY DIFFRACTION	5	A	A	105 - 134	105 - 134
6	X-RAY DIFFRACTION	6	A	A	135 - 160	135 - 160
7	X-RAY DIFFRACTION	7	A	A	161 - 170	161 - 170
8	X-RAY DIFFRACTION	8	A	A	171 - 197	171 - 197
9	X-RAY DIFFRACTION	9	B	B	1 - 32	1 - 32
10	X-RAY DIFFRACTION	10	B	B	33 - 65	33 - 65
11	X-RAY DIFFRACTION	11	B	B	66 - 95	66 - 95
12	X-RAY DIFFRACTION	12	B	B	96 - 104	96 - 104
13	X-RAY DIFFRACTION	13	B	B	105 - 134	105 - 134
14	X-RAY DIFFRACTION	14	B	B	135 - 160	135 - 160
15	X-RAY DIFFRACTION	15	B	B	161 - 170	161 - 170
16	X-RAY DIFFRACTION	16	B	B	171 - 198	171 - 198

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