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- PDB-4jp3: Crystal Structure of TT0495 protein from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 4jp3
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
CITRIC ACID / 2-deoxy-D-gluconate 3-dehydrogenase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 1.2Nov 8, 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)25,8952
Polymers25,7031
Non-polymers1921
Water5,837324
1
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)51,7904
Polymers51,4052
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area3840 Å2
ΔGint-21 kcal/mol
Surface area18030 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)51,7904
Polymers51,4052
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_657-x+1,y,-z+21
Buried area3780 Å2
ΔGint-15 kcal/mol
Surface area18100 Å2
MethodPISA
3
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)103,5798
Polymers102,8114
Non-polymers7684
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 area14900 Å2
ΔGint-77 kcal/mol
Surface area28850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.940, 86.870, 91.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 25702.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q53W82
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.59 Å3/Da / Density % sol: 52.59 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.9
Details: 15% PEG 2000, 1.1M MgCl2, 0.1M NaCl, pH 7.9, EVAPORATION, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9741 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Feb 18, 2013
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9741 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 42860 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 13 Å2
Reflection shellResolution: 1.5→1.55 Å / % possible all: 99.8

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1x1e

1x1e


Resolution: 1.5→34.69 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1792496.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.178 2145 5 %RANDOM
Rwork0.164 ---
obs0.164 42847 99.1 %-
all-43144 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.6891 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 12.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å20 Å2
2--1.28 Å20 Å2
3----0.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.15 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.5→34.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1804 0 13 324 2141
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_d0.79
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.234 348 5.1 %
Rwork0.227 6463 -
obs--95.9 %

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