PDB-2r5f: Putative sugar-binding domain of transcriptional regulator DeoR f...

ID or keywords:

Entry

Database: PDB / ID: 2r5f

Title

Putative sugar-binding domain of transcriptional regulator DeoR from Pseudomonas syringae pv. tomato

Components

Transcriptional regulator, putative

Keywords

TRANSCRIPTION / transcription regulator / sugar-binding domain / structural genomics / pfam04198 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

carbohydrate binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function

Biological species

Pseudomonas syringae pv. tomato (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.1 Å

Authors

Cuff, M.E. / Duggan, E. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: Putative sugar-binding domain of trancsriptional regulator DeoR from Pseudomonas syringae pv. tomato.
Authors: Cuff, M.E. / Duggan, E. / Clancy, S. / Joachimiak, A.

History

Deposition	Sep 3, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 18, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2r5f.cif.gz	57 KB	Display	PDBx/mmCIF format
PDB format	pdb2r5f.ent.gz	42.3 KB	Display	PDB format
PDBx/mmJSON format	2r5f.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2r5f_validation.pdf.gz	438 KB	Display	wwPDB validaton report
Full document	2r5f_full_validation.pdf.gz	439.5 KB	Display
Data in XML	2r5f_validation.xml.gz	11.1 KB	Display
Data in CIF	2r5f_validation.cif.gz	15.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r5/2r5f ftp://data.pdbj.org/pub/pdb/validation_reports/r5/2r5f	HTTPS FTP

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Related structure data

Similar structure data	5k09-7 4h7m-2 4pm5-d 4de0-1 1scr-d 4ua9-2 3hlw-1 4kmx-d 2g4i-d 2b2a-1 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: APC84820

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Transcriptional regulator, putative

hetero molecules

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	42.112, 42.112, 144.782
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	78
Space group name H-M	P4₃

Details

Authors state that the biological unit of this polypeptide is unknown.

#1: Protein	Transcriptional regulator, putative Mass: 28917.014 Da / Num. of mol.: 1 / Fragment: Putative sugar-binding domain: Residues 57-317 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria) Species: Pseudomonas syringae group genomosp. 3 / Strain: DC3000 / Gene: DeoR, PSPTO_2395 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q883G8
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.22 Å³/Da / Density % sol: 44.59 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M Bis-Tris pH 6.5, 2M Ammonium sulfate, 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-BM / Wavelength: 0.97907, 0.97921

Detector

Type: CUSTOM-MADE / Detector: CCD / Date: Jun 14, 2006

Radiation

Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97907	1
2	0.97921	1

Reflection

Redundancy: 7.7 % / Av σ(I) over netI: 10.6 / Number: 100848 / R_merge(I) obs: 0.081 / Χ²: 1.86 / D res high: 2.1 Å / D res low: 50 Å / Num. obs: 13180 / % possible obs: 89.5

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.52	50	87.2	1	0.068	5.54	8
3.59	4.52	92	1	0.057	2.858	8.3
3.14	3.59	92.6	1	0.071	1.952	8.5
2.85	3.14	95.8	1	0.092	1.406	8.4
2.65	2.85	95.7	1	0.129	1.264	8.3
2.49	2.65	96.1	1	0.163	0.995	8.4
2.37	2.49	94.1	1	0.198	0.908	8.2
2.26	2.37	88.5	1	0.25	0.923	7.5
2.18	2.26	79.9	1	0.343	0.994	5.4
2.1	2.18	72.7	1	0.434	0.871	4.4

Reflection

Resolution: 2.1→50 Å / Num. all: 13180 / Num. obs: 13180 / % possible obs: 89.5 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / B_iso Wilson estimate: 36.2 Å² / R_merge(I) obs: 0.081 / Χ²: 1.856 / Net I/σ(I): 10.6

Reflection shell

Resolution: 2.1→2.18 Å / Redundancy: 4.4 % / R_merge(I) obs: 0.434 / Mean I/σ(I) obs: 2.65 / Num. unique all: 1052 / Χ²: 0.871 / % possible all: 72.7

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 2.1 Å / D res low: 42.11 Å / FOM : 0.296 / FOM acentric: 0.296 / FOM centric: 0.219 / Reflection: 13121 / Reflection acentric: 12982 / Reflection centric: 139

Phasing MAD set

Highest resolution: 2.1 Å / Lowest resolution: 42.11 Å

ID	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	1.52	1	0.1	0.1	0	0	12982	139
2	0.93	0.89	13.9	15.3	0.51	0.51	10768	118

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	12.45-42.11	2.71	1	1.1	0.4	0	0	51	1
1	7.31-12.45	1.08	1	0.5	0.3	0	0	234	5
1	5.17-7.31	1.7	1	0.5	0.2	0	0	559	13
1	4-5.17	1.1	1	0.3	0.2	0	0	1017	15
1	3.26-4	1.17	1	0.2	0.1	0	0	1642	25
1	2.75-3.26	1.85	1	0.1	0	0	0	2412	33
1	2.38-2.75	7.17	1	0.1	0	0	0	3346	29
1	2.1-2.38	1.95	1	0	0	0	0	3721	18
2	12.45-42.11	0.69	0.56	16.3	29.1	2.13	0.78	50	1
2	7.31-12.45	0.68	0.77	14.8	18.5	1.73	1.4	233	5
2	5.17-7.31	0.76	0.75	14.9	23.5	1.34	0.63	559	13
2	4-5.17	0.88	0.99	16.5	15.6	0.89	0.78	1017	15
2	3.26-4	0.92	0.85	14.9	13.4	0.63	0.63	1641	25
2	2.75-3.26	0.95	0.97	11.7	13.9	0.47	0.28	2412	33
2	2.38-2.75	0.99	1.01	12.6	11.3	0.25	0.19	3270	23
2	2.1-2.38	1	1	16.8	29.6	0.13	0.04	1586	3

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	78.31342	-0.215	-0.749	-0.184	0
2	Se	73.04219	-0.469	-0.768	-0.025	0
3	Se	86.98933	-0.289	-0.104	-0.251	0
4	Se	75.62676	-0.189	-0.546	-0.253	0
5	Se	67.71538	-0.563	-0.012	-0.123	0
6	Se	639.30438	-0.092	-0.192	-0.011	0
7	Se	77.12099	-0.215	-0.749	-0.184	-0.207
8	Se	60.76777	-0.471	-0.766	-0.025	-0.275
9	Se	84.10966	-0.29	-0.102	-0.25	-0.286
10	Se	76.52405	-0.189	-0.547	-0.253	-0.264
11	Se	67.04011	-0.564	-0.013	-0.123	-0.203
12	Se	620.20215	-0.085	-0.189	-0.01	-0.1

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
12.45-42.11	0.807	0.803	0.987	52	51	1
7.31-12.45	0.803	0.805	0.687	239	234	5
5.17-7.31	0.751	0.754	0.587	572	559	13
4-5.17	0.672	0.677	0.309	1032	1017	15
3.26-4	0.539	0.542	0.291	1667	1642	25
2.75-3.26	0.368	0.37	0.167	2445	2412	33
2.38-2.75	0.15	0.151	0.032	3375	3346	29
2.1-2.38	0.059	0.059	0.002	3739	3721	18

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 13121

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
6.16-100	48.5	0.88	506
4.89-6.16	43	0.913	511
4.29-4.89	42.4	0.93	508
3.9-4.29	42.5	0.921	519
3.64-3.9	45.5	0.916	501
3.43-3.64	47.8	0.908	511
3.26-3.43	50.8	0.919	508
3.12-3.26	55.2	0.863	506
3.01-3.12	55.6	0.885	501
2.91-3.01	62.6	0.875	514
2.82-2.91	63.2	0.861	523
2.73-2.82	64.2	0.816	527
2.66-2.73	66.8	0.799	565
2.59-2.66	71.9	0.81	556
2.53-2.59	72	0.812	607
2.47-2.53	73.9	0.805	581
2.41-2.47	77.6	0.818	619
2.36-2.41	78.1	0.792	618
2.31-2.36	82.9	0.723	606
2.26-2.31	80.6	0.747	594
2.22-2.26	79.9	0.668	602
2.18-2.22	84	0.758	546
2.14-2.18	83.2	0.694	553
2.1-2.14	84.7	0.671	539

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
DM	5	phasing
REFMAC		refinement
PDB_EXTRACT	3	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
SHELXD		phasing
SHELXE		model building
SOLVE		phasing
RESOLVE		phasing
ARP/wARP		model building
CCP4		phasing
O		model building
Coot		model building

Refinement

Method to determine structure:

MAD / Resolution: 2.1→36.4 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.927 / SU B: 15.43 / SU ML: 0.204 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.246 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.252	658	5 %	RANDOM
R_work	0.195	-	-	-
all	0.197	13120	-	-
obs	0.197	13120	89.48 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 42.944 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.84 Å²	0 Å²	0 Å²
2-	-	1.84 Å²	0 Å²
3-	-	-	-3.68 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→36.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1635	0	10	108	1753

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	1670
X-RAY DIFFRACTION	r_angle_refined_deg	1.477	1.985	2250
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.569	5	214
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.925	23.939	66
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.229	15	299
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	24.166	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	268
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	1200
X-RAY DIFFRACTION	r_nbd_refined	0.2	0.2	699
X-RAY DIFFRACTION	r_nbtor_refined	0.298	0.2	1129
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.165	0.2	84
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.155	0.2	24
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.121	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	0.916	1.5	1112
X-RAY DIFFRACTION	r_mcangle_it	1.306	2	1702
X-RAY DIFFRACTION	r_scbond_it	2.127	3	626
X-RAY DIFFRACTION	r_scangle_it	3.2	4.5	548

LS refinement shell

Resolution: 2.1→2.155 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.321	36	-
R_work	0.239	732	-
all	-	768	-
obs	-	-	72.18 %

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	1.6204	0.306	-0.4263	2.1248	0.3439	7.5657	0.0367	0.0242	0.0768	0.0027	0.0364	-0.0506	-0.3588	0.0422	-0.0731	-0.1832	-0.0099	0.0001	-0.1205	-0.0205	-0.0818	10.6446	18.7933	74.9177
2	0.7381	-0.3976	0.9824	1.9998	-1.0577	6.1228	-0.0082	-0.0068	-0.0968	-0.0023	-0.1515	-0.1978	0.7808	0.4433	0.1596	-0.0664	0.0287	0.0194	-0.0947	0.0086	-0.111	16.9093	6.9709	73.5901

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	59 - 121	6 - 68
2	X-RAY DIFFRACTION	2	A	A	132 - 217	79 - 164

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