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- PDB-2d5a: hypothetical protein from Pyrococcus horikoshii OT3 -

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Basic information

Entry
Database: PDB / ID: 2d5a
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
COENZYME A / CoA-binding domain-containing protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 2.0Mar 13, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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: hypothetical protein PH1109
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5152
Polymers16,7471
Non-polymers7681
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.118, 70.118, 141.712
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-1001-

HOH

21A-1037-

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: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 3.09 Å3/Da / Density % sol: 60.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% PEG 4000, 0.1M Tris-HCl, 0.2M Sodium Fluoride, 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: 1.7→50 Å / Num. obs: 23416 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 17.2 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.038 / Rsym value: 0.038 / Net I/σ(I): 31.919
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2041 / Rsym value: 0.639 / % possible all: 88.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→37.48 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 255040.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rwork0.225 ---
Rfree-1088 4.8 %RANDOM
obs-22505 93.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.1413 Å2 / ksol: 0.381238 e/Å3
Displacement parametersBiso mean: 28.8 Å2
Baniso -1Baniso -2Baniso -3
1-5.42 Å20.22 Å20 Å2
2--5.42 Å20 Å2
3----10.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.64 Å
Luzzati d res low-5 Å
Luzzati sigma a0.81 Å0.68 Å
Refinement stepCycle: LAST / Resolution: 1.7→37.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1155 0 48 119 1322
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.035
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d3.22
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.711.5
X-RAY DIFFRACTIONc_mcangle_it3.62
X-RAY DIFFRACTIONc_scbond_it42
X-RAY DIFFRACTIONc_scangle_it5.662.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.532 146 5.1 %
Rwork0.513 2701 -
obs--72.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2coa2end.paramcoa2end.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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