PDB-2q18: 2-keto-3-deoxy-D-arabinonate dehydratase

Basic information

• Entry: Database: PDB / ID: 2q18
• Title: 2-keto-3-deoxy-D-arabinonate dehydratase
• Components: 2-keto-3-deoxy-D-arabinonate dehydratase
• Keywords: LYASE / FAH-family fold

Function / homology

Function:

2-dehydro-3-deoxy-D-arabinonate dehydratase / D-arabinose catabolic process / hydro-lyase activity / protein homotetramerization / magnesium ion binding

Domain/homology:

Vcp-like ATPase; Chain A, domain 2 - #40 / : / Fumarylacetoacetate hydrolase; domain 2 / Fumarylacetoacetase-like, C-terminal domain / Fumarylacetoacetase-like, C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily / Fumarylacetoacetate (FAA) hydrolase family / Vcp-like ATPase; Chain A, domain 2 / Roll / Alpha-Beta Complex / Alpha Beta

Component:

PHOSPHATE ION / 2-dehydro-3-deoxy-D-arabinonate dehydratase

• Biological species: Sulfolobus solfataricus (archaea)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
• Authors: Barends, T. / Brouns, S. / Worm, P. / Akerboom, J. / Turnbull, A. / Salmon, L.
• Citation: Journal: J.Mol.Biol. / Year: 2008; Title: Structural insight into substrate binding and catalysis of a novel 2-keto-3-deoxy-D-arabinonate dehydratase illustrates common mechanistic features of the FAH superfamily.; Authors: Brouns, S.J. / Barends, T.R. / Worm, P. / Akerboom, J. / Turnbull, A.P. / Salmon, L. / van der Oost, J.

History

Deposition	May 24, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 8, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Source and taxonomy / Version format compliance
Revision 1.2	Oct 18, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Jan 24, 2018	Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4	Feb 21, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond / database_2 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Assembly

Deposited unit

X: 2-keto-3-deoxy-D-arabinonate dehydratase

hetero molecules

Summary:

• 33.3 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	33,280	2
Polymers	33,185	1
Non-polymers	95	1
Water	5,116	284

1

X: 2-keto-3-deoxy-D-arabinonate dehydratase

hetero molecules

X: 2-keto-3-deoxy-D-arabinonate dehydratase

hetero molecules

X: 2-keto-3-deoxy-D-arabinonate dehydratase

hetero molecules

X: 2-keto-3-deoxy-D-arabinonate dehydratase

hetero molecules

Summary:

• defined by author
• 133 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	133,120	8
Polymers	132,740	4
Non-polymers	380	4
Water	72	4

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	8_555	-y,-x,-z	1
crystal symmetry operation	10_555	-x,-y,z	1
crystal symmetry operation	15_555	y,x,-z	1

2

X: 2-keto-3-deoxy-D-arabinonate dehydratase

hetero molecules

X: 2-keto-3-deoxy-D-arabinonate dehydratase

hetero molecules

Summary:

• defined by software
• 66.6 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	66,560	4
Polymers	66,370	2
Non-polymers	190	2
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	10_555	-x,-y,z	1

Calculated values:

Buried area	4320 Å2
ΔGint	-24.1 kcal/mol
Surface area	22070 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	127.815, 127.815, 222.366
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	98
Space group name H-M	I4122

Components on special symmetry positions

ID	Model	Components
1	1	X-4304- HOH
2	1	X-4313- HOH

• Details: The biological assembly is a tetramer. A tetramer can be generated by the crystallographic symmetry.

Components

#1: Protein

X 2-keto-3-deoxy-D-arabinonate dehydratase

Details:

Mass: 33185.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: dkaD / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: Q97UA0

#2: Chemical

X-4285 ChemComp-PO4 / PHOSPHATE ION

Details:

Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄

#3: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION

Sample preparation

• Crystal grow: Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 ; Details: Na/K phosphate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9795 Å
• Detector: Type: MARRESEARCH / Detector: CCD / Date: Jan 1, 2005; Details: Rh-coated silicon mirror, silicon 111 monochromator, Rh-coated glass mirror
• Radiation: Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.9795 Å / Relative weight: 1
• Reflection: Resolution: 2.1→111.11 Å / Num. all: 53699 / Num. obs: 53699 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / R_merge(I) obs: 0.094 / Net I/σ(I): 23.1
• Reflection shell: Resolution: 2.1→2.18 Å / R_merge(I) obs: 0.582 / Mean I/σ(I) obs: 3.4 / % possible all: 98.7

Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
MAR345	software	data collection
DENZO		data reduction
SCALEPACK		data scaling
SHELXDE		phasing

Refinement

Method to determine structure: SAD / Resolution: 2.1→111.11 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.942 / SU B: 2.721 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.21882	2732	5.1 %	RANDOM
Rwork	0.20128	-	-	-
obs	0.20216	50918	99.31 %	-
all	-	50918	-	-

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 34.851 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	0.72 Å2	0 Å2	0 Å2
2-	-	0.72 Å2	0 Å2
3-	-	-	-1.43 Å2

Refinement step

Cycle: LAST / Resolution: 2.1→111.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2236	0	5	284	2525

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	2279
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.067	1.99	3086
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.876	5	280
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.677	23.98	98
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.482	15	420
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.068	15	18
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	355
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	1681
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.179	0.2	1052
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.304	0.2	1588
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.161	1	249
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	0.146	0.2	54
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.218	1	25
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	0.986	1.5	1471
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.581	2	2299
X-RAY DIFFRACTION	r_scbond_it	2.504	3	931
X-RAY DIFFRACTION	r_scangle_it	3.997	4.5	787
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.1→2.153 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.301	194	-
Rwork	0.267	3653	-
obs	-	-	97.66 %