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- PDB-2dt4: Crystal structure of Pyrococcus horikoshii a plant- and prokaryot... -

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Basic information

Entry
Database: PDB / ID: 2dt4
TitleCrystal structure of Pyrococcus horikoshii a plant- and prokaryote-conserved (PPC) protein at 1.60 resolution
ComponentsHypothetical protein PH0802
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PPC domain
Function / homologyPredicted DNA-binding protein with PD1-like DNA-binding motif / PPC domain / Plants and Prokaryotes Conserved (PCC) domain / PPC domain profile profile. / Hypothetical protein, similar to alpha- acetolactate decarboxylase; domain 2 / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta / PPC domain-containing protein
Function and homology information
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsLin, L. / Nakano, H. / Uchiyama, S. / Fujimoto, S. / Matsunaga, S. / Nakamura, S.
CitationJournal: Proteins / Year: 2007
Title: Crystal structure of Pyrococcus horikoshii PPC protein at 1.60 A resolution
Authors: Lin, L. / Nakano, H. / Nakamura, S. / Uchiyama, S. / Fujimoto, S. / Matsunaga, S. / Kobayashi, Y. / Ohkubo, T. / Fukui, K.
History
DepositionJul 10, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Hypothetical protein PH0802
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2062
Polymers16,1141
Non-polymers921
Water3,135174
1
A: Hypothetical protein PH0802
hetero molecules

A: Hypothetical protein PH0802
hetero molecules

A: Hypothetical protein PH0802
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6186
Polymers48,3413
Non-polymers2763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area10730 Å2
ΔGint-64 kcal/mol
Surface area16460 Å2
MethodPISA
2
A: Hypothetical protein PH0802
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)97,23512
Polymers96,6826
Non-polymers5536
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_555-x+y,y,-z+1/21
crystal symmetry operation12_565x,x-y+1,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)53.922, 53.922, 159.181
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-1271-

HOH

21A-1273-

HOH

31A-1275-

HOH

41A-1295-

HOH

51A-1301-

HOH

61A-1314-

HOH

DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: 1-Y,1-Y+X,Z and Y-X,1-X,Z.

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Components

#1: Protein Hypothetical protein PH0802 / plant- and prokaryote-conserved protein / PPC protein


Mass: 16113.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O58532
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.07 Å3/Da / Density % sol: 40.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 1.8M ammonium sulphate, 0.2M potassium sodium tartrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9794, 0.9796, 0.9744, 0.9843
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 17, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97961
30.97441
40.98431
ReflectionResolution: 1.6→18.83 Å / Num. all: 17768 / Num. obs: 17768 / % possible obs: 95.67 % / Biso Wilson estimate: 15.3 Å2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→10 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.394 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1932 925 5.1 %RANDOM
Rwork0.16379 ---
all0.16531 17247 --
obs0.16531 17247 95.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.736 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1137 0 6 174 1317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221165
X-RAY DIFFRACTIONr_bond_other_d0.0020.021095
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.9971563
X-RAY DIFFRACTIONr_angle_other_deg0.79232566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.315142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1090.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021258
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02224
X-RAY DIFFRACTIONr_nbd_refined0.2020.2177
X-RAY DIFFRACTIONr_nbd_other0.2550.21196
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.2717
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2110
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.140.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3150.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.2 67
Rwork0.155 1087

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