PDB-3bs3: Crystal structure of a putative DNA-binding protein from Bacteroi...

ID or keywords:

Entry

Database: PDB / ID: 3bs3

Title

Crystal structure of a putative DNA-binding protein from Bacteroides fragilis

Components

Putative DNA-binding protein

Keywords

DNA BINDING PROTEIN / DNA-binding / XRE-family / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

Biological species

Bacteroides fragilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.65 Å

Authors

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

Citation

Journal: TO BE PUBLISHED
Title: The structure of a putative DNA-binding protein from Bacteroides fragilis.
Authors: Cuff, M.E. / Bigelow, L. / Clancy, S. / Joachimiak, A.

History

Deposition	Dec 21, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 15, 2008	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
Revision 1.3	Oct 30, 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_leaving_atom_flag / _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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Download

PDBx/mmCIF format	3bs3.cif.gz	31.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3bs3.ent.gz	19.3 KB	Display	PDB format
PDBx/mmJSON format	3bs3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3bs3_validation.pdf.gz	432.1 KB	Display	wwPDB validaton report
Full document	3bs3_full_validation.pdf.gz	432.1 KB	Display
Data in XML	3bs3_validation.xml.gz	6.7 KB	Display
Data in CIF	3bs3_validation.cif.gz	8.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bs/3bs3 ftp://data.pdbj.org/pub/pdb/validation_reports/bs/3bs3	HTTPS FTP

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Related structure data

Similar structure data	2z0u-1 5nc0-d 1nbb-1 1nbb-2 1rcp-1 4icw-d 6cxw-d 2qho-4 2k3h-d 1sd9-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
Other databases	TargetDB: APC89109

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#144 - Dec 2011 Complex I similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (5)

Deposited unit

A: Putative DNA-binding protein

hetero molecules

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

1

A: Putative DNA-binding protein

hetero molecules

A: Putative DNA-binding protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	63.337, 63.337, 34.706
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

Components on special symmetry positions

ID	Model	Components
1	1	A-137- HOH

Details

AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

#1: Protein	Putative DNA-binding protein Mass: 8987.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: NCTC 9343 / Gene: BF1076 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5LGD2
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.24 Å³/Da / Density % sol: 44.99 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Tris-HCl pH 8.5, 0.2M LiSO4, 1.25M (NH4)2SO4, 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: 0.97931, 0.97945

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 17, 2007

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	0.97931	1
2	0.97945	1

Reflection

Redundancy: 11.9 % / Av σ(I) over netI: 9.2 / Number: 115860 / R_merge(I) obs: 0.094 / Χ²: 2.07 / D res high: 1.65 Å / D res low: 50 Å / Num. obs: 9728 / % possible obs: 98

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.07	50	92.8	1	0.078	6.447	11.7
3.23	4.07	96.5	1	0.075	4.041	12
2.82	3.23	96.1	1	0.095	4.13	12.3
2.56	2.82	98	1	0.101	3.009	12.2
2.38	2.56	98	1	0.098	2.262	12.2
2.24	2.38	98.2	1	0.109	2.022	12.3
2.13	2.24	98.3	1	0.129	1.784	12.3
2.03	2.13	99.1	1	0.143	1.387	12.3
1.96	2.03	99.4	1	0.171	1.184	12.1
1.89	1.96	98.6	1	0.225	0.915	12.3
1.83	1.89	100	1	0.274	0.789	12.2
1.78	1.83	98.8	1	0.349	0.83	11.9
1.73	1.78	98.9	1	0.396	0.663	11.8
1.69	1.73	99.8	1	0.475	0.592	11
1.65	1.69	98	1	0.509	0.514	10

Reflection

Resolution: 1.65→50 Å / Num. all: 9728 / Num. obs: 9728 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 11.9 % / B_iso Wilson estimate: 26.1 Å² / R_merge(I) obs: 0.094 / Χ²: 2.071 / Net I/σ(I): 9.2

Reflection shell

Resolution: 1.65→1.69 Å / Redundancy: 10 % / R_merge(I) obs: 0.509 / Mean I/σ(I) obs: 2.9 / Num. unique all: 632 / Χ²: 0.514 / % possible all: 98

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 1.65 Å / D res low: 50 Å / FOM : 0.473 / FOM acentric: 0.493 / FOM centric: 0.294 / Reflection: 9715 / Reflection acentric: 8755 / Reflection centric: 960

Phasing MAD set

Highest resolution: 1.65 Å / Lowest resolution: 50 Å

ID	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	1.44	1	0.1	0.1	0	0	8755	960
2	0.86	0.81	2.3	3.6	0.95	0.73	8736	951

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	10.72-50	0.9	1	0.5	0.4	0	0	20	16
1	6.01-10.72	1.45	1	0.5	0.4	0	0	132	44
1	4.17-6.01	1.09	1	0.4	0.4	0	0	337	75
1	3.19-4.17	1.01	1	0.3	0.3	0	0	647	100
1	2.59-3.19	1.32	1	0.2	0.1	0	0	1027	135
1	2.18-2.59	1.6	1	0.1	0.1	0	0	1566	162
1	1.88-2.18	2.16	1	0.1	0	0	0	2171	203
1	1.65-1.88	9.91	1	0	0	0	0	2855	225
2	10.72-50	0.47	0.7	4.5	6.8	3.21	1.88	12	11
2	6.01-10.72	0.68	0.71	5.2	6.7	1.97	1.34	124	42
2	4.17-6.01	0.74	0.74	4.6	5.9	1.67	1.17	336	74
2	3.19-4.17	0.82	0.72	4.3	5.8	1.25	0.84	647	100
2	2.59-3.19	0.82	0.77	2.9	3.5	1.21	0.82	1027	135
2	2.18-2.59	0.82	0.81	2.1	3.3	1.04	0.57	1566	162
2	1.88-2.18	0.92	0.94	1.9	2.7	0.64	0.34	2171	203
2	1.65-1.88	0.99	1	1.7	2.4	0.41	0.22	2853	224

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	24.8394	0.81	0.175	0.038	0
2	Se	22.10381	0.796	0.075	-0.083	0
3	Se	49.32137	0.583	0.015	-0.059	0
4	Se	19.157	0.803	0.093	0.013	0
5	Se	130.8812	0.517	-0.175	0.162	0
6	Se	25.84744	0.81	0.175	0.039	-0.132
7	Se	25.15341	0.796	0.075	-0.083	-0.083
8	Se	56.66603	0.584	0.015	-0.059	-0.077
9	Se	20.08065	0.803	0.092	0.011	-0.029
10	Se	132.87267	0.519	-0.173	0.164	-0.042

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
10.72-50	0.597	0.767	0.384	36	20	16
6.01-10.72	0.711	0.768	0.54	176	132	44
4.17-6.01	0.695	0.733	0.525	412	337	75
3.19-4.17	0.692	0.724	0.484	747	647	100
2.59-3.19	0.681	0.717	0.402	1162	1027	135
2.18-2.59	0.628	0.654	0.376	1728	1566	162
1.88-2.18	0.442	0.468	0.168	2374	2171	203
1.65-1.88	0.234	0.247	0.068	3080	2855	225

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 9715

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
4.47-100	40.6	0.879	506
3.54-4.47	42.3	0.941	508
3.08-3.54	43.3	0.928	503
2.8-3.08	45	0.918	508
2.59-2.8	45	0.925	503
2.44-2.59	41.4	0.927	512
2.31-2.44	42.7	0.929	515
2.21-2.31	44.7	0.925	504
2.13-2.21	46.3	0.92	509
2.05-2.13	46.6	0.913	507
1.99-2.05	54.5	0.904	512
1.93-1.99	56.8	0.914	506
1.88-1.93	58	0.901	512
1.83-1.88	58.4	0.912	506
1.79-1.83	66.8	0.888	503
1.75-1.79	64.1	0.9	516
1.72-1.75	68.1	0.894	504
1.69-1.72	68.4	0.873	510
1.65-1.69	71.2	0.841	571

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
DM	5	phasing
REFMAC		refinement
PDB_EXTRACT	3.004	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: 1.65→29.32 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.958 / SU B: 3.505 / SU ML: 0.06 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.099
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.219	463	4.8 %	RANDOM
R_work	0.183	-	-	-
all	0.185	9714	-	-
obs	0.185	9714	98.02 %	-

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: 32.059 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.1 Å²	-0.55 Å²	0 Å²
2-	-	-1.1 Å²	0 Å²
3-	-	-	1.66 Å²

Refinement step

Cycle: LAST / Resolution: 1.65→29.32 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	502	0	9	83	594

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	600
X-RAY DIFFRACTION	r_angle_refined_deg	1.346	1.99	820
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.079	5	85
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	43.062	24.483	29
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.635	15	141
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.164	15	7
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	92
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	439
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	243
X-RAY DIFFRACTION	r_nbtor_refined	0.305	0.2	407
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.153	0.2	50
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.207	0.2	33
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.189	0.2	10
X-RAY DIFFRACTION	r_mcbond_it	0.989	1.5	358
X-RAY DIFFRACTION	r_mcangle_it	1.355	2	581
X-RAY DIFFRACTION	r_scbond_it	2.266	3	269
X-RAY DIFFRACTION	r_scangle_it	3.348	4.5	226

LS refinement shell

Resolution: 1.65→1.69 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.276	37	-
R_work	0.256	682	-
all	-	719	-
obs	-	-	98.09 %

Refinement TLS params.

Method: refined / Origin x: 10.1757 Å / Origin y: 43.7762 Å / Origin z: -7.2521 Å

	11	12	13	21	22	23	31	32	33
T	-0.1121 Å²	0.016 Å²	-0.0072 Å²	-	-0.1013 Å²	0.0006 Å²	-	-	-0.109 Å²
L	2.6955 °²	0.6023 °²	-0.1516 °²	-	5.0508 °²	1.1381 °²	-	-	2.1305 °²
S	-0.0418 Å °	-0.0456 Å °	0.0341 Å °	0.1772 Å °	0.145 Å °	-0.2005 Å °	-0.0202 Å °	0.0953 Å °	-0.1032 Å °

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