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- PDB-2d1y: Crystal structure of TT0321 from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 2d1y
TitleCrystal structure of TT0321 from Thermus thermophilus HB8
Componentshypothetical protein TT0321
KeywordsOXIDOREDUCTASE / strucrtural genomics / Thermus thermophilus HB8 / 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 / nucleotide binding
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / 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 / Oxidoreductase, short-chain dehydrogenase/reductase family
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsAsada, Y. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Chem.Biol.Interact. / Year: 2009
Title: Biochemical and structural characterization of a short-chain dehydrogenase/reductase of Thermus thermophilus HB8: a hyperthermostable aldose-1-dehydrogenase with broad substrate specificity.
Authors: Asada, Y. / Endo, S. / Inoue, Y. / Mamiya, H. / Hara, A. / Kunishima, N. / Matsunaga, T.
History
DepositionSep 2, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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
Revision 1.4Oct 25, 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

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Assembly

Deposited unit
A: hypothetical protein TT0321
B: hypothetical protein TT0321
C: hypothetical protein TT0321
D: hypothetical protein TT0321
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,6188
Polymers107,9644
Non-polymers2,6544
Water14,898827
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17810 Å2
ΔGint-132 kcal/mol
Surface area32620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.391, 95.334, 71.409
Angle α, β, γ (deg.)90.00, 108.254, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is tetramer

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Components

#1: Protein
hypothetical protein TT0321


Mass: 26991.070 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SLC4
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 827 / 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 Å3/Da / Density % sol: 38.12 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 8.5
Details: 0.2M Magnesium Chloride hexahydrate, 0.1M Tris-HCl, 30% w/v PEG 4000, pH 8.5, MICROBATCH, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Feb 7, 2005 / Details: mirrors
RadiationMonochromator: Bending Magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. all: 108794 / Num. obs: 108794 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 16.761 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 12.7
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 4.29 / Num. unique all: 10829 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IPE.pdb

1ipe


Resolution: 1.65→28.93 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.194 5439 -RAMDOM
Rwork0.175 ---
all0.176 108767 --
obs0.176 108767 99.7 %-
Displacement parametersBiso mean: 21.7 Å2
Baniso -1Baniso -2Baniso -3
1--6.37 Å20 Å2-0.67 Å2
2--6.99 Å20 Å2
3----0.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.65→28.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7183 0 176 827 8186
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellResolution: 1.65→1.73 Å / Rfactor Rfree error: 0.009
RfactorNum. reflection% reflection
Rfree0.231 665 -
Rwork0.221 --
obs--98.8 %

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