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- PDB-2ekp: Structure of TT0495 protein from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 2ekp
TitleStructure of TT0495 protein from Thermus thermophilus
Components2-deoxy-D-gluconate 3-dehydrogenase
KeywordsOXIDOREDUCTASE / gluconate dehydrogenase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / nucleotide binding
Similarity search - Function
PKS_KR / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 2-deoxy-D-gluconate 3-dehydrogenase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsLokanath, N.K. / Pampa, K.J. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: The first crystal structure of NAD-dependent 3-dehydro-2-deoxy-D-gluconate dehydrogenase from Thermus thermophilus HB8
Authors: Pampa, K.J. / Lokanath, N.K. / Kunishima, N. / Rai, R.V.
History
DepositionMar 23, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Apr 16, 2014Group: Database references
Revision 1.3Oct 25, 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

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Assembly

Deposited unit
A: 2-deoxy-D-gluconate 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5504
Polymers25,7031
Non-polymers8483
Water7,116395
1
A: 2-deoxy-D-gluconate 3-dehydrogenase
hetero molecules

A: 2-deoxy-D-gluconate 3-dehydrogenase
hetero molecules

A: 2-deoxy-D-gluconate 3-dehydrogenase
hetero molecules

A: 2-deoxy-D-gluconate 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,20116
Polymers102,8114
Non-polymers3,39012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_657-x+1,y,-z+21
crystal symmetry operation4_557x,-y,-z+21
Buried area19780 Å2
ΔGint-118.3 kcal/mol
Surface area28220 Å2
MethodPISA
2
A: 2-deoxy-D-gluconate 3-dehydrogenase
hetero molecules

A: 2-deoxy-D-gluconate 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1018
Polymers51,4052
Non-polymers1,6956
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area5930 Å2
ΔGint-43.8 kcal/mol
Surface area18070 Å2
MethodPISA
3
A: 2-deoxy-D-gluconate 3-dehydrogenase
hetero molecules

A: 2-deoxy-D-gluconate 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1018
Polymers51,4052
Non-polymers1,6956
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_657-x+1,y,-z+21
Buried area6230 Å2
ΔGint-36.4 kcal/mol
Surface area17770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.873, 87.233, 92.093
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1643-

HOH

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Components

#1: Protein 2-deoxy-D-gluconate 3-dehydrogenase / gluconate dehydrogenase


Mass: 25702.729 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET-11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q53W82, 2-deoxy-D-gluconate 3-dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 28% PEG 1000, 0.2M NH2SO4, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.9 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Dec 13, 2006 / Details: graphite
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. all: 94622 / Num. obs: 94728 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 7.3 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 10.1
Reflection shellResolution: 1.15→1.19 Å / % possible all: 99.8

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Processing

Software
NameClassification
HKL-2000data collection
EPMRphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X1E

1x1e


Resolution: 1.15→23.5 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.169 4743 -random
Rwork0.168 ---
all-94622 --
obs-94728 99.9 %-
Refinement stepCycle: LAST / Resolution: 1.15→23.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1804 0 56 395 2255
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
LS refinement shellResolution: 1.15→1.19 Å

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