PDB-4u6n: Crystal structure of Escherichia coli DiaA

Basic information

• Entry: Database: PDB / ID: 4u6n
• Title: Crystal structure of Escherichia coli DiaA
• Components: DnaA initiator-associating protein DiaA
• Keywords: REPLICATION / DiaA / DnaA initiator-associating protein / DNA replication / SIS family

Function / homology

Function:

DnaA-DiaA complex / positive regulation of DNA-templated DNA replication initiation / carbohydrate derivative metabolic process / carbohydrate derivative binding / DNA replication / protein homodimerization activity / identical protein binding

Domain/homology:

DnaA initiator-associating protein / GmhA/DiaA / : / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta

Component:

DnaA initiator-associating protein DiaA

• Biological species: Escherichia coli (E. coli)
• Method: X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
• Authors: Oakley, A.J. / Lo, T.

Funding support

Australia, 1items

Organization	Grant number	Country
National Health and Medical Research Council (NHMRC, Australia)	APP1021479	Australia

• Citation: Journal: To Be Published; Title: Crystal structure of Escherichia coli DiaA; Authors: Oakley, A.J. / Lo, T. / Lewis, P.J.

History

Deposition	Jul 29, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 6, 2014	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2017	Group: Author supporting evidence / Derived calculations / Other / Source and taxonomy Category: entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Jan 8, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Sep 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / refine_hist Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Revision 1.4	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Assembly

Deposited unit

A: DnaA initiator-associating protein DiaA

hetero molecules

Summary:

• 22.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	22,206	2
Polymers	22,170	1
Non-polymers	35	1
Water	865	48

1

A: DnaA initiator-associating protein DiaA

hetero molecules

A: DnaA initiator-associating protein DiaA

hetero molecules

A: DnaA initiator-associating protein DiaA

hetero molecules

A: DnaA initiator-associating protein DiaA

hetero molecules

Summary:

• defined by author&software
• 88.8 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	88,822	8
Polymers	88,681	4
Non-polymers	142	4
Water	72	4

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_565	-x,-y+1,z	1
crystal symmetry operation	3_555	-x,y,-z	1
crystal symmetry operation	4_565	x,-y+1,-z	1

Calculated values:

Buried area	13730 Å2
ΔGint	-87 kcal/mol
Surface area	24410 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	47.490, 73.820, 106.370
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

Components on special symmetry positions

ID	Model	Components
1	1	A-201- CL
2	1	A-320- HOH
3	1	A-333- HOH

Components

#1: Protein

A DnaA initiator-associating protein DiaA

Details:

Mass: 22170.158 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: diaA, yraO, b3149, JW3118 / Production host: Escherichia coli (E. coli) / Strain (production host): 'BL21-Gold(DE3)pLysS AG' / References: UniProt: P66817

#2: Chemical

A-201 ChemComp-CL / CHLORIDE ION

Details:

Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

#3: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H₂O

• Has protein modification: Y

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

• Crystal: Density Matthews: 2.1 ų/Da / Density % sol: 41.5 %
• Crystal grow: Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.9 ; Details: 0.1 M Tris pH 8.9, 0.25 M MgCl2, and 32-38% PEG3000

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
• Detector: Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 10, 2014
• Radiation: Monochromator: Varimax optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 1.5418 Å / Relative weight: 1
• Reflection: Resolution: 1.91→61 Å / Num. all: 14941 / Num. obs: 14941 / % possible obs: 100 % / Redundancy: 6.9 % / R_merge(I) obs: 0.081 / Net I/σ(I): 13.2
• Reflection shell: Resolution: 1.91→2 Å / Redundancy: 6.8 % / R_merge(I) obs: 0.594 / Mean I/σ(I) obs: 3 / % possible all: 100

Processing

• Software: Name: REFMAC / Version: 5.8.0073 / Classification: refinement

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YVA

2yva

Resolution: 1.91→60.65 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.966 / SU B: 9.425 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.19841	750	5 %	RANDOM
Rwork	0.16489	-	-	-
obs	0.1665	14188	99.86 %	-

• 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: 25.22 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	4.87 Å2	0 Å2	0 Å2
2-	-	-2.1 Å2	0 Å2
3-	-	-	-2.77 Å2

Refinement step

Cycle: 1 / Resolution: 1.91→60.65 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1429	0	1	48	1478

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.019	1469
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1448
X-RAY DIFFRACTION	r_angle_refined_deg	1.887	1.959	2000
X-RAY DIFFRACTION	r_angle_other_deg	0.89	3	3303
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.283	5	198
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.945	23.81	63
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.363	15	247
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.24	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.104	0.2	246
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	1705
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	331
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	1.794	2.329	777
X-RAY DIFFRACTION	r_mcbond_other	1.795	2.326	776
X-RAY DIFFRACTION	r_mcangle_it	2.498	3.479	971
X-RAY DIFFRACTION	r_mcangle_other	2.497	3.482	972
X-RAY DIFFRACTION	r_scbond_it	2.664	2.696	691
X-RAY DIFFRACTION	r_scbond_other	2.663	2.698	692
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.003	3.93	1027
X-RAY DIFFRACTION	r_long_range_B_refined	5.681	18.952	1607
X-RAY DIFFRACTION	r_long_range_B_other	5.683	18.836	1596
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.91→1.957 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.239	62	-
Rwork	0.236	1015	-
obs	-	-	99.81 %

Refinement TLS params.

Method: refined / Origin x: 5.6824 Å / Origin y: 22.8011 Å / Origin z: 9.7287 Å

	11	12	13	21	22	23	31	32	33
T	0.2942 Å2	0.077 Å2	-0.0291 Å2	-	0.0373 Å2	0.0183 Å2	-	-	0.0496 Å2
L	0.9399 °2	-0.4295 °2	-0.2975 °2	-	4.1409 °2	0.815 °2	-	-	5.191 °2
S	-0.0671 Å °	-0.0846 Å °	-0.1431 Å °	0.5445 Å °	0.0241 Å °	-0.2517 Å °	1.0418 Å °	0.4044 Å °	0.043 Å °