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- PDB-1nbw: Glycerol dehydratase reactivase -

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Basic information

Entry
Database: PDB / ID: 1nbw
TitleGlycerol dehydratase reactivase
Components
  • GLYCEROL DEHYDRATASE REACTIVASE ALPHA SUBUNIT
  • GLYCEROL DEHYDRATASE REACTIVASE BETA SUBUNIT
KeywordsHYDROLASE / Glycerol dehydratase / Reactivase / Molecular chaperone / Actin-like ATPase domain / beta/beta/alpha swiveling domain
Function / homology
Function and homology information


glycerol dehydratase / glycerol dehydratase 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
Glycerol dehydratase reactivation factor small subunit / Dha2 protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.4 Å
AuthorsLiao, D.-I. / Reiss, L. / Turner Jr., I. / Dotson, G.
CitationJournal: Structure / Year: 2003
Title: Structure of glycerol dehydratase reactivase: A new type of molecular chaperone
Authors: Liao, D.-I. / Reiss, L. / Turner Jr., I. / Dotson, G.
History
DepositionDec 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLYCEROL DEHYDRATASE REACTIVASE ALPHA SUBUNIT
B: GLYCEROL DEHYDRATASE REACTIVASE BETA SUBUNIT
C: GLYCEROL DEHYDRATASE REACTIVASE ALPHA SUBUNIT
D: GLYCEROL DEHYDRATASE REACTIVASE BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,3916
Polymers151,3114
Non-polymers802
Water10,070559
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9090 Å2
ΔGint-66 kcal/mol
Surface area57410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.000, 110.000, 332.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe biological assembly of glycerol dehydratase reactivase is a heterotetramer. The asymmetric unit of the crystal contains an entire heterotetramer. It consists of two copies of alpha-beta heterodimers related by a non-crystallographic two fold symmetry. Chain names for the two alpha subunits are A and C, those for the beta subunits are B and D.

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Components

#1: Protein GLYCEROL DEHYDRATASE REACTIVASE ALPHA SUBUNIT


Mass: 63650.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: dhaB4 / Plasmid: pET23a(+) / Production host: Escherichia coli (E. coli) / References: UniProt: Q59474
#2: Protein GLYCEROL DEHYDRATASE REACTIVASE BETA SUBUNIT


Mass: 12005.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: orf2b / Plasmid: pET23a(+) / Production host: Escherichia coli (E. coli) / References: UniProt: Q48423
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 559 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.32 Å3/Da / Density % sol: 62.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Na Acetate, Imidazole, CaCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
PH range low: 6.6 / PH range high: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.55 Msodium acetate1reservoir
20.1 Mimidazole1reservoirpH6.5-6.6
30.05 M1reservoirCaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 79404 / Num. obs: 79404 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 29.3
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 4.4 / % possible all: 82.4
Reflection
*PLUS
Num. measured all: 534068
Reflection shell
*PLUS
% possible obs: 82.4 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
CNSrefinement
RefinementMethod to determine structure: SIRAS / Resolution: 2.4→30 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.271 3975 random
Rwork0.232 --
all-79404 -
obs-78659 -
Displacement parametersBiso mean: 39.4 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10518 0 2 559 11079
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.34
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d24.18
X-RAY DIFFRACTIONc_improper_angle_d0.909
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.18
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.909

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