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- PDB-2d0p: Structure of diol dehydratase-reactivating factor in nucleotide f... -

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Basic information

Entry
Database: PDB / ID: 2d0p
TitleStructure of diol dehydratase-reactivating factor in nucleotide free form
Components
  • diol dehydratase-reactivating factor large subunit
  • diol dehydratase-reactivating factor small subunit
KeywordsCHAPERONE
Function / homology
Function and homology information


hydrolase activity / ATP binding / metal ion binding
Similarity search - Function
Swiveling domain of dehydratase reactivase alpha subunit / Coenzyme B12-Dependent Enzyme linker domain / Diol dehydratase-reactivating factor large subunit / Diol/glycerol dehydratase reactivating factor, small subunit / Diol dehydratase-reactivating factor, alpha subunit, swiveling domain superfamily / Diol dehydratase reactivase ATPase-like domain / DD-reactivating factor swiveling domain / Diol dehydratase reactivase ATPase-like domain / DD-reactivating factor swiveling domain / Diol/glycerol dehydratase/dehydratase reactivating factor ...Swiveling domain of dehydratase reactivase alpha subunit / Coenzyme B12-Dependent Enzyme linker domain / Diol dehydratase-reactivating factor large subunit / Diol/glycerol dehydratase reactivating factor, small subunit / Diol dehydratase-reactivating factor, alpha subunit, swiveling domain superfamily / Diol dehydratase reactivase ATPase-like domain / DD-reactivating factor swiveling domain / Diol dehydratase reactivase ATPase-like domain / DD-reactivating factor swiveling domain / Diol/glycerol dehydratase/dehydratase reactivating factor / Dehydratase medium subunit / B12-dependent dehydatase associated subunit / B12-dependent dehydratases, beta subunit / Ribosomal Protein L22; Chain A / Glucose Oxidase; domain 1 / ATPase, nucleotide binding domain / Nucleic acid-binding proteins / 3-Layer(bba) Sandwich / ATPase, nucleotide binding domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleotidyltransferase; domain 5 / Nucleic acid-binding, OB-fold / Alpha-Beta Complex / Beta Barrel / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / : / Diol dehydratase-reactivating factor large subunit / Diol dehydratase-reactivating factor small subunit
Similarity search - Component
Biological speciesKlebsiella oxytoca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsShibata, N. / Mori, K. / Hieda, N. / Higuchi, Y. / Yamanishi, M. / Toraya, T.
CitationJournal: Structure / Year: 2005
Title: Release of a damaged cofactor from a coenzyme B12-dependent enzyme: X-ray structures of diol dehydratase-reactivating factor
Authors: Shibata, N. / Mori, K. / Hieda, N. / Higuchi, Y. / Yamanishi, M. / Toraya, T.
History
DepositionAug 5, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 9, 2020Group: Derived calculations / Structure summary
Category: pdbx_struct_conn_angle / struct ...pdbx_struct_conn_angle / struct / struct_conn / struct_site
Item: _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct.title / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: diol dehydratase-reactivating factor large subunit
B: diol dehydratase-reactivating factor small subunit
C: diol dehydratase-reactivating factor large subunit
D: diol dehydratase-reactivating factor small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,49511
Polymers155,9344
Non-polymers5607
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9570 Å2
ΔGint-131 kcal/mol
Surface area57370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.920, 85.370, 296.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein diol dehydratase-reactivating factor large subunit


Mass: 64329.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Plasmid: pUSI2E / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: GenBank: 3115376, UniProt: O68195*PLUS
#2: Protein diol dehydratase-reactivating factor small subunit


Mass: 13637.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Plasmid: pUSI2E / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: GenBank: 3115377, UniProt: O68196*PLUS
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 3.33 Å3/Da / Density % sol: 63.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG400, ammonium sulfate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 30, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→41 Å / Num. all: 41979 / Num. obs: 41979 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 8.9
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.606 / % possible all: 93.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→40.58 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 216915.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.313 4017 10.1 %RANDOM
Rwork0.238 ---
obs0.238 39661 92.8 %-
all-41911 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.3328 Å2 / ksol: 0.275217 e/Å3
Displacement parametersBiso mean: 84.6 Å2
Baniso -1Baniso -2Baniso -3
1-18.68 Å20 Å20 Å2
2--33.78 Å20 Å2
3----52.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.6 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.99 Å0.85 Å
Refinement stepCycle: LAST / Resolution: 3→40.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10629 0 27 33 10689
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it6.095
X-RAY DIFFRACTIONc_mcangle_it9.458
X-RAY DIFFRACTIONc_scbond_it7.865
X-RAY DIFFRACTIONc_scangle_it11.5710
LS refinement shellResolution: 3→3.11 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.511 319 9.7 %
Rwork0.46 2982 -
obs--78 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4adp.paramadp.top

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