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- PDB-1jq5: Bacillus Stearothermophilus Glycerol dehydrogenase complex with NAD+ -

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Basic information

Entry
Database: PDB / ID: 1jq5
TitleBacillus Stearothermophilus Glycerol dehydrogenase complex with NAD+
ComponentsGlycerol dehydrogenase
KeywordsOXIDOREDUCTASE / NAD / glycerol metabolism
Function / homology
Function and homology information


anaerobic glycerol catabolic process / glycerol dehydrogenase / glycerol dehydrogenase (NAD+) activity / metal ion binding / cytosol
Similarity search - Function
Glycerol dehydrogenase / Iron-containing alcohol dehydrogenases signature 2. / Iron-containing alcohol dehydrogenases signature 1. / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Alcohol dehydrogenase, iron-type, conserved site / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Rossmann fold - #1970 / Up-down Bundle ...Glycerol dehydrogenase / Iron-containing alcohol dehydrogenases signature 2. / Iron-containing alcohol dehydrogenases signature 1. / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Alcohol dehydrogenase, iron-type, conserved site / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Rossmann fold - #1970 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glycerol dehydrogenase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsRuzheinikov, S.N. / Burke, J. / Sedelnikova, S. / Baker, P.J. / Taylor, R. / Bullough, P.A. / Muir, N.M. / Gore, M.G. / Rice, D.W.
Citation
Journal: Structure / Year: 2001
Title: Glycerol dehydrogenase. structure, specificity, and mechanism of a family III polyol dehydrogenase.
Authors: Ruzheinikov, S.N. / Burke, J. / Sedelnikova, S. / Baker, P.J. / Taylor, R. / Bullough, P.A. / Muir, N.M. / Gore, M.G. / Rice, D.W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Purification, crystallization and quaternary structure analysis of a glycerol dehydrogenase S305C mutant from Bacillus stearothemophilus
Authors: Burke, J. / Ruzheinikov, S.N. / Sedelnikova, S. / Baker, P.J. / Holmes, D. / Muir, N.M. / Gore, M.G. / Rice, D.W.
History
DepositionAug 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycerol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3594
Polymers39,5651
Non-polymers7943
Water4,882271
1
A: Glycerol dehydrogenase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)322,87432
Polymers316,5208
Non-polymers6,35424
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area32570 Å2
ΔGint-491 kcal/mol
Surface area97190 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)104.66, 104.66, 148.51
Angle α, β, γ (deg.)90, 90, 90
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-372-

ZN

DetailsThe biological assembly is an octamer generated from the monomer in the asymmetric unit by the operations: y, -x, z; -x, y, -z; x, -y, -z; y, x, -z; -x, -y, -z; -y, x, z; -y, -x, -z;

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Components

#1: Protein Glycerol dehydrogenase


Mass: 39564.996 Da / Num. of mol.: 1 / Mutation: S305C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: GLDA or GLD / Plasmid: pKK233-2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM103 / References: UniProt: P32816, glycerol dehydrogenase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: Ammonium Sulfate, PEG 400, ZnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Details: Burke, J., (2001) Acta Crystallogr., Sect.D, 57, 165.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
20.5-2.0 Mammonium sulfate1reservoir
32-6 %PEG4001reservoir
40.020 mM1reservoirZnCl2

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 29, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→10 Å / Num. all: 42016 / Num. obs: 42016 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 19.9
Reflection shellResolution: 1.7→1.74 Å / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 2.7 / % possible all: 78.6
Reflection
*PLUS
Num. measured all: 196167
Reflection shell
*PLUS
% possible obs: 78.6 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JPU

1jpu


Resolution: 1.7→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.1903 2095 RANDOM
Rwork0.1514 --
all-42016 -
obs-41600 -
Displacement parametersBiso mean: 30.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2748 0 46 271 3065
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.59
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_dihedral_angle_d21.267
X-RAY DIFFRACTIONc_improper_angle_d1.03
X-RAY DIFFRACTIONc_mcbond_it3.88
X-RAY DIFFRACTIONc_mcangle_it6.05
X-RAY DIFFRACTIONc_scbond_it5.33
X-RAY DIFFRACTIONc_scangle_it8.58
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / σ(F): 1 / % reflection Rfree: 5 % / Rfactor obs: 0.151
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.267
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.03

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