PDB-2gxg: Crystal structure of EmrR homolog from hyperthermophilic archaea ...

ID or keywords:

Entry

Database: PDB / ID: 2gxg

Title

Crystal structure of EmrR homolog from hyperthermophilic archaea Sulfolobus tokodaii strain7

Components

146aa long hypothetical transcriptional regulator

Keywords

TRANSCRIPTION / Winged Helix

Function / homology

Function and homology information

response to stress / DNA-binding transcription factor activity / DNA binding / metal ion binding
Similarity search - Function

Biological species

Sulfolobus tokodaii (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.45 Å

Authors

Miyazono, K. / Tsujimura, M. / Kawarabayasi, Y. / Tanokura, M.

Citation

Journal: To be Published
Title: Crystal structure of archaeal homolog of multi drug resistance repressor protein, EmrR, from hyperthermophilic archaea Sulfolobus tokodaii strain7
Authors: Miyazono, K. / Tsujimura, M. / Kawarabayasi, Y. / Tanokura, M.

History

Deposition	May 8, 2006	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Mar 20, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Derived calculations / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4	Mar 13, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

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Related structure data

Similar structure data	2eb7-1 4ylj-1 6a4m-d 5yni-d 5zrt-d 3gez-1 3zdt-1 3jw9-d 3gfl-1 4pop-d 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

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PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: 146aa long hypothetical transcriptional regulator

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

1

A: 146aa long hypothetical transcriptional regulator

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

Unit cell

Length a, b, c (Å)	46.114, 46.114, 140.257
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

Details

The second part of the biological assembly is generated by the the operations: 1-y,1-x,0.5-z

#1: Protein	146aa long hypothetical transcriptional regulator / TRANSCRIPTIONAL REPRESSOR PROTEIN Mass: 16879.564 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: strain7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96ZY1
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.21 Å³/Da / Density % sol: 44.26 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 21% PEG 2000 monomethyl ethyl, 0.1M Tris-HCl, pH 9, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	95	1
2		1
3		1

Diffraction source

Source:

SYNCHROTRON / Site:

Photon Factory

/ Beamline: BL-5A / Wavelength: 1.0000, 0.9841, 0.9794, 0.9792

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 29, 2004

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1	1
2	0.9841	1
3	0.9794	1
4	0.9792	1

Reflection

D res high: 2 Å / D res low: 25 Å / % possible obs: 99.7

Redundancy (%)	ID	Av σ(I) over netI	Number	R_merge(I) obs	Χ²	Num. obs
12.6	1	13.1	136592	0.084	2.34	10799
13.3	2	14.2	144231	0.092	3.38	10813
13.4	3	13.3	144655	0.089	2.74	10822

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	Num. obs	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.3	25	1203	98.1	1	0.063	3.523	9.7
3.42	4.3	1108	99.2	1	0.069	3.699	10.9
2.99	3.42	1092	99.9	1	0.078	3.27	12
2.71	2.99	1057	100	1	0.092	2.819	12.6
2.52	2.71	1082	100	1	0.103	2.518	13.1
2.37	2.52	1070	100	1	0.115	2.147	13.4
2.25	2.37	1056	100	1	0.128	1.959	13.6
2.15	2.25	1053	100	1	0.138	1.643	13.8
2.07	2.15	1044	100	1	0.16	1.378	13.9
2	2.07	1034	100	1	0.201	1.062	14.1
4.3	25	1205	98.2	2	0.078	7.821	11.3
3.42	4.3	1107	99	2	0.08	6.071	12.2
2.99	3.42	1093	99.9	2	0.088	4.777	13.1
2.71	2.99	1057	100	2	0.098	3.811	13.5
2.52	2.71	1082	100	2	0.105	3.014	13.7
2.37	2.52	1070	100	2	0.118	2.609	13.8
2.25	2.37	1060	100	2	0.126	2.129	13.9
2.15	2.25	1055	100	2	0.135	1.739	14
2.07	2.15	1047	100	2	0.158	1.452	14.1
2	2.07	1037	100	2	0.201	1.124	14.1
4.3	25	1208	98.5	3	0.072	5.906	11.3
3.42	4.3	1111	99.3	3	0.079	4.966	12.2
2.99	3.42	1094	99.9	3	0.087	4.009	13.2
2.71	2.99	1061	100	3	0.094	3.012	13.6
2.52	2.71	1077	100	3	0.101	2.438	13.7
2.37	2.52	1070	100	3	0.114	2.077	13.9
2.25	2.37	1062	100	3	0.123	1.793	13.9
2.15	2.25	1055	100	3	0.135	1.516	14
2.07	2.15	1047	100	3	0.154	1.231	14.1
2	2.07	1037	100	3	0.199	0.962	14.1

Reflection

Resolution: 1.45→20 Å / Num. obs: 27739 / % possible obs: 99.5 % / Redundancy: 10.4 % / R_merge(I) obs: 0.072 / Χ²: 2.342 / Net I/σ(I): 16

Reflection shell

Resolution (Å)	% possible obs (%)	Redundancy (%)	R_merge(I) obs	Num. unique obs	Χ²	Diffraction-ID
1.45-1.5	99	5.5	0.223	2661	0.482	1
1.5-1.56	100	7.6	0.184	2719	0.683	1
1.56-1.63	100	11.2	0.154	2732	0.82	1
1.63-1.72	100	11.8	0.132	2753	1.033	1
1.72-1.83	100	11.8	0.111	2727	1.417	1
1.83-1.97	100	11.7	0.095	2749	2.032	1
1.97-2.17	100	11.4	0.083	2782	2.825	1
2.17-2.48	100	11.1	0.075	2799	3.542	1
2.48-3.12	99.9	11.3	0.072	2857	4.227	1
3.12-20	96.9	10.1	0.063	2960	4.788	1

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Phasing

Phasing

Method:

MAD

Phasing set

ID
1
2
3

Phasing MAD

D res high: 2 Å / D res low: 20 Å / FOM : 0.6 / Reflection: 10760

Phasing MAD set

Clust-ID	Expt-ID	Set-ID	Wavelength (Å)	F double prime refined	F prime refined
1	3 wavelength	1	0.9841	-4.83	-5.48
1	3 wavelength	2	0.9794	5.02	-10.57
1	3 wavelength	3	0.9792	4.71	-7.48

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	28.269	0.71	0.128	0.116	1.164
2	Se	32.312	0.115	0.957	0.038	1.18
3	Se	37.698	0.091	0.849	0.04	0.983
4	Se	31.593	0.521	0.823	0.111	0.54

Phasing MAD shell

Resolution (Å)	FOM	Reflection
6.99-20	0.72	598
4.48-6.99	0.67	931
3.53-4.48	0.66	1152
3-3.53	0.67	1343
2.65-3	0.64	1478
2.41-2.65	0.6	1625
2.22-2.41	0.55	1763
2.06-2.22	0.46	1870

Phasing dm

FOM : 0.77 / FOM acentric: 0.79 / FOM centric: 0.68 / Reflection: 10762 / Reflection acentric: 8492 / Reflection centric: 2270

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
5.7-19.722	0.92	0.96	0.88	523	276	247
3.6-5.7	0.93	0.96	0.85	1502	1068	434
2.9-3.6	0.88	0.91	0.78	1816	1405	411
2.5-2.9	0.82	0.85	0.65	1806	1461	345
2.1-2.5	0.71	0.75	0.56	3172	2634	538
2-2.1	0.55	0.58	0.4	1943	1648	295

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SOLVE	2.06	phasing
RESOLVE	2.06	phasing
REFMAC	refmac_5.1.24	refinement
PDB_EXTRACT	1.701	data extraction
ADSC		data collection

Refinement

Method to determine structure:

MAD / Resolution: 1.45→20 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.943 / SU B: 1.237 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.239	1394	5 %	RANDOM
R_work	0.22252	-	-	-
all	0.22333	-	-	-
obs	0.22333	26266	99.54 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 19.653 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.05 Å²	0 Å²	0 Å²
2-	-	-0.05 Å²	0 Å²
3-	-	-	0.09 Å²

Refinement step

Cycle: LAST / Resolution: 1.45→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1132	0	0	124	1256

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	1140
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	1121
X-RAY DIFFRACTION	r_angle_refined_deg	1.558	1.993	1528
X-RAY DIFFRACTION	r_angle_other_deg	0.856	3	2596
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.251	5	139
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	183
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1224
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	225
X-RAY DIFFRACTION	r_nbd_refined	0.227	0.2	237
X-RAY DIFFRACTION	r_nbd_other	0.238	0.2	1210
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other	0.082	0.2	682
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.114	0.2	67
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	0.187	0.2	13
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.272	0.2	93
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.181	0.2	11
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	0.971	1.5	694
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.692	2	1126
X-RAY DIFFRACTION	r_scbond_it	2.696	3	446
X-RAY DIFFRACTION	r_scangle_it	4.545	4.5	402
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.45→1.488 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.299	98
R_work	0.241	1881

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