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- PDB-2db0: Crystal structure of PH0542 -

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Basic information

Entry
Database: PDB / ID: 2db0
TitleCrystal structure of PH0542
Components253aa long hypothetical protein
KeywordsPROTEIN BINDING / HEAT repeats / helical structure / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Repeat of uncharacterized protein PH0542 / Repeat of uncharacterized protein PH0542 / HEAT repeat / HEAT repeat / HEAT repeat profile. / HEAT, type 2 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe ...Repeat of uncharacterized protein PH0542 / Repeat of uncharacterized protein PH0542 / HEAT repeat / HEAT repeat / HEAT repeat profile. / HEAT, type 2 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsNishino, A. / Handa, N. / Kishishita, S. / Murayama, K. / Shirouzu, M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of PH0542
Authors: Handa, N. / Nishino, A. / Kishishita, S. / Murayama, K. / Shirouzu, M. / Yokoyama, S.
History
DepositionDec 14, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 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: 253aa long hypothetical protein
B: 253aa long hypothetical protein


Theoretical massNumber of molelcules
Total (without water)57,4692
Polymers57,4692
Non-polymers00
Water1,820101
1
A: 253aa long hypothetical protein


Theoretical massNumber of molelcules
Total (without water)28,7351
Polymers28,7351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 253aa long hypothetical protein


Theoretical massNumber of molelcules
Total (without water)28,7351
Polymers28,7351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.795, 90.779, 66.451
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein 253aa long hypothetical protein / hypothetical protein / PH0542


Mass: 28734.666 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): B834(DE3)pRARE / References: UniProt: O58277
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 40.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG3350, 0.2M ammonium acetate, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9790, 0.9797, 0.9670
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 20, 2005 / Details: mirrors
RadiationMonochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97971
30.9671
ReflectionResolution: 2.2→50 Å / Num. obs: 24884 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rsym value: 0.075 / Net I/σ(I): 17
Reflection shellResolution: 2.2→2.28 Å / Mean I/σ(I) obs: 4.6 / Rsym value: 0.369 / % possible all: 98.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
REFMAC5.1.24refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.2→50 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: This structure was refined also by CNS 1.1.
RfactorNum. reflection% reflectionSelection details
Rfree0.26801 1252 -RANDOM
Rwork0.20501 ---
obs0.20815 23399 99.2 %-
Displacement parametersBiso mean: 36.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å20 Å2
2---1.67 Å20 Å2
3---0.81 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3807 0 0 101 3908
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.049
X-RAY DIFFRACTIONr_angle_refined_deg2.897
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.638
X-RAY DIFFRACTIONr_chiral_restr0.196
X-RAY DIFFRACTIONr_gen_planes_refined0.014
LS refinement shellResolution: 2.2→2.257 Å
RfactorNum. reflection
Rfree0.341 89
Rwork0.247 -
obs-1675

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