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- PDB-3bqb: Hexagonal kristal form of 2-keto-3-deoxyarabinonate dehydratase -

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Basic information

Entry
Database: PDB / ID: 3bqb
TitleHexagonal kristal form of 2-keto-3-deoxyarabinonate dehydratase
ComponentsPutative uncharacterized protein
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-dehydro-3-deoxy-D-arabinonate dehydratase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBarends, T.M. / 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.J. / Barends, T.R.M. / Worm, P. / Akerboom, J. / Turnbull, A.P. / Salmon, L. / van der Oost, J.
History
DepositionDec 20, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 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

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
X: Putative uncharacterized protein
Z: Putative uncharacterized protein
Y: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,8388
Polymers132,7404
Non-polymers974
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Putative uncharacterized protein
X: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4194
Polymers66,3702
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-28 kcal/mol
Surface area23220 Å2
MethodPISA
3
Z: Putative uncharacterized protein
Y: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4194
Polymers66,3702
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-26 kcal/mol
Surface area22100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.092, 157.092, 131.921
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
Putative uncharacterized protein / 2-keto-3-deoxyarabinonate dehydratase


Mass: 33185.078 Da / Num. of mol.: 4 / Fragment: UNP residues 6-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: DKAD / Plasmid: pET24 / 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.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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

CrystalDensity Matthews: 3.54 Å3/Da / Density % sol: 65.25 %
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: Dec 7, 2005 / Details: Osmic mirrors
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→99.9 Å / Num. all: 50804 / Num. obs: 50804 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 81.7 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 30.7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 3.4 / Num. unique all: 5043 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Q18

2q18


Resolution: 2.7→33.74 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.909 / SU B: 13.219 / SU ML: 0.255 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.578 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28355 2562 5.1 %RANDOM
Rwork0.23808 ---
all0.24031 48004 --
obs0.24031 48004 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 63.124 Å2
Baniso -1Baniso -2Baniso -3
1-1.89 Å20.95 Å20 Å2
2--1.89 Å20 Å2
3----2.84 Å2
Refinement stepCycle: LAST / Resolution: 2.7→33.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9024 0 4 56 9084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0229182
X-RAY DIFFRACTIONr_bond_other_d0.0010.028662
X-RAY DIFFRACTIONr_angle_refined_deg0.9961.98812430
X-RAY DIFFRACTIONr_angle_other_deg0.709320182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7951130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.12823.945398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.195151697
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9881574
X-RAY DIFFRACTIONr_chiral_restr0.0580.21429
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.029992
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021762
X-RAY DIFFRACTIONr_nbd_refined0.180.21671
X-RAY DIFFRACTIONr_nbd_other0.1620.29265
X-RAY DIFFRACTIONr_nbtor_refined0.1650.24534
X-RAY DIFFRACTIONr_nbtor_other0.0750.25543
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2227
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1280.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1730.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0430.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5151.57484
X-RAY DIFFRACTIONr_mcbond_other0.0351.52294
X-RAY DIFFRACTIONr_mcangle_it0.54629270
X-RAY DIFFRACTIONr_scbond_it0.45134095
X-RAY DIFFRACTIONr_scangle_it0.7084.53160
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.696→2.766 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 197 -
Rwork0.389 3377 -
obs--95.51 %

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