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- PDB-4jp2: Crystal Structure of TT0495 protein from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 4jp2
TitleCrystal Structure of TT0495 protein from Thermus thermophilus HB8
Components2-deoxy-D-gluconate 3-dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann fold
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsPampa, K.J. / Lokanath, N.K. / Kunishima, N. / Ravishnkar Rai, V.
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. / Ravishnkar Rai, V.
History
DepositionMar 19, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Oct 30, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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)25,8431
Polymers25,8431
Non-polymers00
Water6,035335
1
A: 2-deoxy-D-gluconate 3-dehydrogenase

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


Theoretical massNumber of molelcules
Total (without water)51,6872
Polymers51,6872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area2970 Å2
ΔGint-23 kcal/mol
Surface area18490 Å2
MethodPISA
2
A: 2-deoxy-D-gluconate 3-dehydrogenase

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


Theoretical massNumber of molelcules
Total (without water)51,6872
Polymers51,6872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2920 Å2
ΔGint-19 kcal/mol
Surface area18540 Å2
MethodPISA
3
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)103,3744
Polymers103,3744
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 area13130 Å2
ΔGint-84 kcal/mol
Surface area29770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.944, 62.944, 111.434
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-469-

HOH

21A-510-

HOH

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Components

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


Mass: 25843.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q53W82
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.14 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.1
Details: 15% PEG 4000, 0.1M potassium phosphate, 0.1M magnesium chloride, pH 7.1, EVAPORATION, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Feb 18, 2013
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.15→50 Å / Num. obs: 79896 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 6.3 Å2
Reflection shellHighest resolution: 1.15 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→22.44 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1854654.01 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.199 4024 5 %RANDOM
Rwork0.189 ---
obs0.189 79854 99.5 %-
all-80142 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.1272 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 13.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20 Å20 Å2
2--0.76 Å20 Å2
3----1.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.12 Å0.12 Å
Luzzati d res low-5 Å
Luzzati sigma a--0.03 Å
Refinement stepCycle: LAST / Resolution: 1.15→22.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1812 0 0 335 2147
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 1.15→1.22 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.182 660 5.1 %
Rwork0.183 12309 -
obs--98.7 %

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