PDB-4yvz: Structure of Thermotoga maritima DisA in complex with 3'-dATP/Mn2+

Basic information

• Entry: Database: PDB / ID: 4yvz
• Title: Structure of Thermotoga maritima DisA in complex with 3'-dATP/Mn2+
• Components: DNA integrity scanning protein DisA
• Keywords: DNA BINDING PROTEIN / c-di-AMP synthesis / DAC domain / Inhibitor / pre-reaction state / TRANSFERASE

Function / homology

Function:

catalytic activity, acting on DNA / diadenylate cyclase / diadenylate cyclase activity / adenylate cyclase activity / hydrolase activity / DNA repair / DNA binding / ATP binding

Domain/homology:

DNA integrity scanning linker region / DNA integrity scanning, DisA, linker region / DNA integrity scanning protein, DisA / DisA, linker domain superfamily / DisA bacterial checkpoint controller linker region / YojJ-like (1 / DNA integrity scanning protein, DisA, N-terminal domain / Helix-hairpin-helix motif / Helix-hairpin-helix motif / : / DNA integrity scanning protein, DisA, N-terminal / DNA integrity scanning protein, DisA, N-terminal domain superfamily / DisA bacterial checkpoint controller nucleotide-binding / Diadenylate cyclase (DAC) domain profile. / RuvA domain 2-like / Ferritin / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Up-down Bundle / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta

Component:

3'-DEOXYADENOSINE-5'-TRIPHOSPHATE / : / DNA integrity scanning protein DisA

• Biological species: Thermotoga maritima (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.495 Å
• Authors: Mueller, M. / Deimling, T. / Hopfner, K.-P. / Witte, G.

Funding support

Germany, 2items

Organization	Grant number	Country
German Research Foundation	3717/2-1	Germany
German Research Foundation	GRK1721	Germany

• Citation: Journal: Biochem.J. / Year: 2015; Title: Structural analysis of the diadenylate cyclase reaction of DNA-integrity scanning protein A (DisA) and its inhibition by 3'-dATP.; Authors: Muller, M. / Deimling, T. / Hopfner, K.P. / Witte, G.

History

Deposition	Mar 20, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jun 3, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jun 10, 2015	Group: Database references
Revision 1.2	Aug 5, 2015	Group: Database references
Revision 1.3	Sep 6, 2017	Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.4	Jan 10, 2024	Group: Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Assembly

Deposited unit

A: DNA integrity scanning protein DisA

B: DNA integrity scanning protein DisA

hetero molecules

Summary:

• 86.7 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	86,730	8
Polymers	85,528	2
Non-polymers	1,202	6
Water	2,000	111

1

A: DNA integrity scanning protein DisA

B: DNA integrity scanning protein DisA

hetero molecules

A: DNA integrity scanning protein DisA

B: DNA integrity scanning protein DisA

hetero molecules

A: DNA integrity scanning protein DisA

B: DNA integrity scanning protein DisA

hetero molecules

A: DNA integrity scanning protein DisA

B: DNA integrity scanning protein DisA

hetero molecules

Summary:

• defined by author&software
• 347 kDa, 8 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	346,920	32
Polymers	342,112	8
Non-polymers	4,808	24
Water	144	8

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_545	-x,-y-1,z	1
crystal symmetry operation	3_445	-y-1/2,x-1/2,z	1
crystal symmetry operation	4_545	y+1/2,-x-1/2,z	1

Calculated values:

Buried area	37280 Å2
ΔGint	-129 kcal/mol
Surface area	111110 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	107.490, 107.490, 168.790
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	90
Space group name H-M	P4212

Components

#1: Protein

A B DNA integrity scanning protein DisA / Cyclic di-AMP synthase / c-di-AMP synthase / Diadenylate cyclase

Details:

Mass: 42763.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: disA, TM_0200 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q9WY43, diadenylate cyclase

#2: Chemical

A-401 A-402 B-402 B-403
ChemComp-MN / MANGANESE (II) ION

Details:

Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn

#3: Chemical

A-403 B-401 ChemComp-3AT / 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE / CORDYCEPIN TRIPHOSPHATE

Details:

Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₂P₃

#4: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION

Sample preparation

• Crystal: Density Matthews: 2.85 ų/Da / Density % sol: 56.85 %
• Crystal grow: Temperature: 288 K / Method: vapor diffusion, hanging drop; Details: 30% (v/v) MPD, 200 mM ammoniumacetate, 100 mM Tris-HCl; PH range: 8.0-8.3

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.23953 Å
• Detector: Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2013
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 1.23953 Å / Relative weight: 1
• Reflection: Resolution: 2.495→168.8 Å / Num. obs: 65492 / % possible obs: 99.6 % / Redundancy: 7.6 % / R_merge(I) obs: 0.108 / Net I/σ(I): 15.9
• Reflection shell: Resolution: 2.495→2.56 Å / Redundancy: 7.2 % / R_merge(I) obs: 1.052 / Mean I/σ(I) obs: 2.8 / % possible all: 94.5

Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.9_1692)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 3c1z

3c1z

Resolution: 2.495→168.79 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.1 / Stereochemistry target values: ML

	Rfactor	Num. reflection	% reflection
Rfree	0.2189	3255	4.97 %
Rwork	0.1642	-	-
obs	0.167	65492	99.58 %

• Solvent computation: Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.495→168.79 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5594	0	64	111	5769

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	5739
X-RAY DIFFRACTION	f_angle_d	1.103	7769
X-RAY DIFFRACTION	f_dihedral_angle_d	15.981	2199
X-RAY DIFFRACTION	f_chiral_restr	0.044	917
X-RAY DIFFRACTION	f_plane_restr	0.004	978

LS refinement shell

Resolution (Å)	Rfactor Rfree	Num. reflection Rfree	Rfactor Rwork	Num. reflection Rwork	Refine-ID	% reflection obs (%)
2.4953-2.5326	0.3339	127	0.288	2464	X-RAY DIFFRACTION	91
2.5326-2.5722	0.3086	140	0.2468	2710	X-RAY DIFFRACTION	100
2.5722-2.6143	0.2953	143	0.242	2702	X-RAY DIFFRACTION	100
2.6143-2.6594	0.2916	139	0.2285	2718	X-RAY DIFFRACTION	100
2.6594-2.7078	0.2952	143	0.2305	2722	X-RAY DIFFRACTION	100
2.7078-2.7599	0.3091	143	0.2219	2726	X-RAY DIFFRACTION	100
2.7599-2.8162	0.3008	136	0.221	2713	X-RAY DIFFRACTION	100
2.8162-2.8775	0.3102	138	0.2059	2718	X-RAY DIFFRACTION	100
2.8775-2.9444	0.2869	144	0.2037	2701	X-RAY DIFFRACTION	100
2.9444-3.018	0.2607	147	0.1928	2710	X-RAY DIFFRACTION	100
3.018-3.0996	0.3105	140	0.2054	2726	X-RAY DIFFRACTION	100
3.0996-3.1909	0.2689	144	0.1911	2721	X-RAY DIFFRACTION	100
3.1909-3.2939	0.226	143	0.1831	2725	X-RAY DIFFRACTION	100
3.2939-3.4116	0.2546	145	0.1745	2691	X-RAY DIFFRACTION	100
3.4116-3.5482	0.2312	141	0.1572	2748	X-RAY DIFFRACTION	100
3.5482-3.7097	0.2027	144	0.1499	2717	X-RAY DIFFRACTION	100
3.7097-3.9053	0.2027	148	0.1399	2695	X-RAY DIFFRACTION	100
3.9053-4.15	0.1589	143	0.132	2719	X-RAY DIFFRACTION	100
4.15-4.4704	0.1466	141	0.1209	2739	X-RAY DIFFRACTION	100
4.4704-4.9203	0.1538	143	0.1253	2701	X-RAY DIFFRACTION	100
4.9203-5.6324	0.2279	143	0.1537	2713	X-RAY DIFFRACTION	100
5.6324-7.0962	0.2181	140	0.1787	2717	X-RAY DIFFRACTION	100
7.0962-169.1774	0.1676	140	0.1245	2741	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Origin x: 13.1059 Å / Origin y: -36.6604 Å / Origin z: 43.8695 Å

	11	12	13	21	22	23	31	32	33
T	0.4052 Å2	-0.0764 Å2	-0.0125 Å2	-	0.3924 Å2	0.0089 Å2	-	-	0.4765 Å2
L	0.1055 °2	-0.0167 °2	-0.0412 °2	-	0.1074 °2	-0.0761 °2	-	-	1.9188 °2
S	-0.017 Å °	-0.0226 Å °	0.0412 Å °	0.0125 Å °	-0.0377 Å °	-0.0331 Å °	-0.23 Å °	0.2335 Å °	0.0001 Å °

• Refinement TLS group: Selection details: all