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- PDB-2hun: Crystal structure of hypothetical protein PH0414 from Pyrococcus ... -

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Basic information

Entry
Database: PDB / ID: 2hun
TitleCrystal structure of hypothetical protein PH0414 from Pyrococcus horikoshii OT3
Components336aa long hypothetical dTDP-glucose 4,6-dehydratase
KeywordsLYASE / ROSSMANN FOLD / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


dTDP-glucose 4,6-dehydratase activity / nucleotide-sugar metabolic process / nucleotide binding
Similarity search - Function
dTDP-glucose 4,6-dehydratase / GDP-mannose 4,6 dehydratase / NAD(P)-binding domain / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 336aa long hypothetical dTDP-glucose 4,6-dehydratase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsYamamoto, H. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of hypothetical protein PH0414 from Pyrococcus horikoshii OT3
Authors: Yamamoto, H. / Kunishima, N.
History
DepositionJul 26, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 26, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
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

Downloads & links

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Assembly

Deposited unit
A: 336aa long hypothetical dTDP-glucose 4,6-dehydratase
B: 336aa long hypothetical dTDP-glucose 4,6-dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2924
Polymers77,9652
Non-polymers1,3272
Water8,719484
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-44 kcal/mol
Surface area25770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.892, 73.677, 100.222
Angle α, β, γ (deg.)90.00, 128.995, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 336aa long hypothetical dTDP-glucose 4,6-dehydratase


Mass: 38982.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O58151, dTDP-glucose 4,6-dehydratase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 2.63 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 8.2
Details: 0.2M tri-Sodium Citrate, 20% (w/v) PEG3350, pH 8.2, 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 JUPITER 210 / Detector: CCD / Date: Apr 17, 2006 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→40 Å / Num. all: 51052 / Num. obs: 49776 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.078 / Net I/σ(I): 10.6
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 3.8 / Num. unique all: 4293 / Rsym value: 0.212

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code: 1R66

1r66


Resolution: 2.07→8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2930363.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 2382 5 %RANDOM
Rwork0.204 ---
obs0.204 47574 97.9 %-
all-48594 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 70.9159 Å2 / ksol: 0.433331 e/Å3
Displacement parametersBiso mean: 34.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å21.5 Å2
2--1.47 Å20 Å2
3----0.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.07→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5339 0 88 484 5911
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.84
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3 316 5 %
Rwork0.253 5943 -
obs-6256 74.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3NAD.paramNAD.top

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