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- PDB-1x1e: Crystal Structure of TT0495 protein from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 1x1e
TitleCrystal Structure of TT0495 protein from Thermus thermophilus HB8
Components2-deoxy-D-gluconate 3-dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI / NPPSFA / National Project on Protein Structural and Functional Analyses
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
2-deoxy-D-gluconate 3-dehydrogenase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsLokanath, N.K. / Terao, Y. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of TT0495 protein from Thermus thermophilus HB8
Authors: Lokanath, N.K. / Terao, Y. / Kunishima, N.
History
DepositionApr 4, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 11, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,7031
Polymers25,7031
Non-polymers00
Water3,261181
1
A: 2-deoxy-D-gluconate 3-dehydrogenase

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

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

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


Theoretical massNumber of molelcules
Total (without water)102,8114
Polymers102,8114
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area13210 Å2
ΔGint-84 kcal/mol
Surface area29480 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)62.712, 62.712, 111.272
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
DetailsBiologically this protein is tetramer

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Components

#1: Protein 2-deoxy-D-gluconate 3-dehydrogenase / dehydrogenase / TT0495 protein


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: pET11a / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.2 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 4.6
Details: Sodium acetate, sodium formate, pH 4.6, microbatch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Mar 23, 2005
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. all: 22764 / Num. obs: 22749 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 15.8
Reflection shellResolution: 1.76→1.82 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VL8

1vl8


Resolution: 1.76→28.45 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1673550.21 / 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
Rfree0.215 1106 4.9 %RANDOM
Rwork0.203 ---
obs0.203 22749 99.9 %-
all-22764 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.1604 Å2 / ksol: 0.369542 e/Å3
Displacement parametersBiso mean: 21.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.2 Å20 Å20 Å2
2--3.2 Å20 Å2
3----6.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.76→28.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1812 0 0 181 1993
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 1.76→1.87 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.28 179 4.8 %
Rwork0.264 3520 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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