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- PDB-2q1d: 2-keto-3-deoxy-D-arabinonate dehydratase complexed with magnesium... -

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Basic information

Entry
Database: PDB / ID: 2q1d
Title2-keto-3-deoxy-D-arabinonate dehydratase complexed with magnesium and 2,5-dioxopentanoate
Components2-keto-3-deoxy-D-arabinonate dehydratase
KeywordsLYASE / FAH-family fold
Function / homology
Function and homology information


2-dehydro-3-deoxy-D-arabinonate dehydratase / D-arabinose catabolic process / hydro-lyase activity / protein homotetramerization / magnesium ion binding
Similarity search - Function
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
Similarity search - Domain/homology
2,5-DIOXOPENTANOIC ACID / 2-dehydro-3-deoxy-D-arabinonate dehydratase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.7 Å
AuthorsBarends, T. / Brouns, S. / Worm, P. / Akerboom, J. / Turnbull, A. / Salmon, L.
CitationJournal: 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
DepositionMay 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: 2-keto-3-deoxy-D-arabinonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3393
Polymers33,1851
Non-polymers1542
Water93752
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


Theoretical massNumber of molelcules
Total (without water)133,35812
Polymers132,7404
Non-polymers6188
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
2
X: 2-keto-3-deoxy-D-arabinonate dehydratase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)66,6796
Polymers66,3702
Non-polymers3094
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-x,-y,z1
Buried area4130 Å2
ΔGint-30.5 kcal/mol
Surface area22170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.280, 128.280, 223.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11X-935-

HOH

DetailsThe biological assembly is a tetramer. A tetramer can be generated by the crystallographic symmetry operators.

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Components

#1: Protein 2-keto-3-deoxy-D-arabinonate dehydratase


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: kdaD / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: Q97UA0
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-DO4 / 2,5-DIOXOPENTANOIC ACID


Mass: 130.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 1, 2006 / Details: osmic mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 25301 / Num. obs: 25301 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 11.4
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 4.1 / % possible all: 93.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
XFITdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2Q18

2q18


Resolution: 2.7→19.58 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.902 / SU B: 9.281 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26077 1284 5 %RANDOM
Rwork0.22638 ---
obs0.22809 24400 99.1 %-
all-24400 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.816 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å20 Å20 Å2
2--1.58 Å20 Å2
3----3.17 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2227 0 10 52 2289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222274
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3221.9913077
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9985279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61623.91897
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.46315418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5321518
X-RAY DIFFRACTIONr_chiral_restr0.0820.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021680
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.2988
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21565
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.161102
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0530.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.122111
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.61.51448
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.08422291
X-RAY DIFFRACTIONr_scbond_it1.2393938
X-RAY DIFFRACTIONr_scangle_it2.1624.5786
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 86 -
Rwork0.383 1666 -
obs--94.45 %

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