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- PDB-2q1a: 2-keto-3-deoxy-D-arabinonate dehydratase complexed with magnesium... -

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Basic information

Entry
Database: PDB / ID: 2q1a
Title2-keto-3-deoxy-D-arabinonate dehydratase complexed with magnesium and 2-oxobutyrate
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-KETOBUTYRIC ACID / 2-dehydro-3-deoxy-D-arabinonate dehydratase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.5 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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.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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr2_label_atom_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)33,3113
Polymers33,1851
Non-polymers1262
Water1,946108
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)133,24612
Polymers132,7404
Non-polymers5068
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)66,6236
Polymers66,3702
Non-polymers2534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-x,-y,z1
Buried area4700 Å2
ΔGint-20.9 kcal/mol
Surface area23180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.830, 128.830, 224.400
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-296-

HOH

DetailsThe biological unit is a tetramer. A tetramer can be generated with 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-2KT / 2-KETOBUTYRIC ACID / 2-OXOBUTANOIC ACID


Mass: 102.089 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: Jan 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: 2.5→20 Å / Num. all: 31603 / Num. obs: 31603 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.7
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.2 / % possible all: 95.7

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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: 2.5→19.66 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.913 / SU B: 6.58 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25565 1594 5 %RANDOM
Rwork0.23434 ---
obs0.2354 30010 95.99 %-
all-30010 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.579 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20 Å2
2--0.65 Å20 Å2
3----1.3 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2316 0 8 108 2432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222363
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0831.993197
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7365290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.58623.846104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.17815437
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4831520
X-RAY DIFFRACTIONr_chiral_restr0.070.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021757
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1880.2984
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21615
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1591134
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1060.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.23519
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.531.51518
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.93322373
X-RAY DIFFRACTIONr_scbond_it0.83976
X-RAY DIFFRACTIONr_scangle_it1.3644.5824
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 112 -
Rwork0.341 2176 -
obs--96.91 %

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