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- PDB-2d59: hypothetical protein from Pyrococcus horikoshii OT3 -

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Basic information

Entry
Database: PDB / ID: 2d59
Titlehypothetical protein from Pyrococcus horikoshii OT3
Componentshypothetical protein PH1109
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / coa binding / hypothetical protein / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


CoA binding domain / CoA binding domain / CoA-binding / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CoA-binding domain-containing protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsHiyama, T.B. / Sekine, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.STRUCT.FUNCT.GENOM. / Year: 2006
Title: Structural basis of CoA recognition by the Pyrococcus single-domain CoA-binding proteins.
Authors: Hiyama, T.B. / Zhao, M. / Kitago, Y. / Yao, M. / Sekine, S. / Terada, T. / Kuroishi, C. / Liu, Z.J. / Rose, J.P. / Kuramitsu, S. / Shirouzu, M. / Watanabe, N. / Yokoyama, S. / Tanaka, I. / Wang, B.C.
History
DepositionOct 31, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: hypothetical protein PH1109


Theoretical massNumber of molelcules
Total (without water)16,7471
Polymers16,7471
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.758, 61.758, 61.389
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1007-

HOH

21A-1073-

HOH

31A-1120-

HOH

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Components

#1: Protein hypothetical protein PH1109


Mass: 16747.432 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: ph1109 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O58836
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.02 Å3/Da / Density % sol: 39.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% PEG 4000, 0.1M Tris-HCl, 1M di-ammonium hydrogen citrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 25, 2005
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 16631 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 40.861
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 3.6 / Num. unique all: 1564 / Rsym value: 0.614 / % possible all: 96.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→40.33 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 915614.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.239 817 4.9 %RANDOM
Rwork0.212 ---
obs0.212 16264 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.4352 Å2 / ksol: 0.396119 e/Å3
Displacement parametersBiso mean: 28.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.33 Å22.01 Å20 Å2
2--2.33 Å20 Å2
3----4.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.65→40.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1148 0 0 123 1271
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_mcbond_it2.311.5
X-RAY DIFFRACTIONc_mcangle_it3.112
X-RAY DIFFRACTIONc_scbond_it4.032
X-RAY DIFFRACTIONc_scangle_it5.622.5
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.298 123 4.5 %
Rwork0.261 2584 -
obs--99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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