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- PDB-2dum: Crystal structure of hypothetical protein, PH0823 -

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Basic information

Entry
Database: PDB / ID: 2dum
TitleCrystal structure of hypothetical protein, PH0823
ComponentsHypothetical protein PH0823
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / conserved hypothetical protein / putative universal protein A / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyUniversal stress protein A family / UspA / Universal stress protein family / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / UspA domain-containing protein
Function and homology information
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.75 Å
AuthorsHosaka, T. / Kishishita, S. / Murayama, K. / Shirouzu, M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of hypothetical protein, PH0823
Authors: Hosaka, T. / Kishishita, S. / Murayama, K. / Shirouzu, M. / Yokoyama, S.
History
DepositionJul 24, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2007Provider: 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 PH0823
B: Hypothetical protein PH0823
C: Hypothetical protein PH0823
D: Hypothetical protein PH0823


Theoretical massNumber of molelcules
Total (without water)78,7444
Polymers78,7444
Non-polymers00
Water50428
1
A: Hypothetical protein PH0823
D: Hypothetical protein PH0823


Theoretical massNumber of molelcules
Total (without water)39,3722
Polymers39,3722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-10 kcal/mol
Surface area14180 Å2
MethodPISA
2
B: Hypothetical protein PH0823
C: Hypothetical protein PH0823


Theoretical massNumber of molelcules
Total (without water)39,3722
Polymers39,3722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-7 kcal/mol
Surface area14350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.786, 120.786, 127.098
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Hypothetical protein PH0823


Mass: 19685.900 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: O58553
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.96 Å3/Da / Density % sol: 58.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 28% Pentaerythritol Ethoxylate (5/4 PO/OH), pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97921, 0.9795, 0.964
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: May 17, 2005
RadiationMonochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979211
20.97951
30.9641
ReflectionResolution: 2.75→45 Å / Num. obs: 20726 / % possible obs: 87.16 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.83957 % / Rsym value: 0.08 / Net I/σ(I): 14.5675
Reflection shellResolution: 2.75→2.88 Å / Mean I/σ(I) obs: 1.86869 / Num. unique all: 559 / Rsym value: 0.345 / % possible all: 30.88

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.75→40 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.893 / SU B: 13.885 / SU ML: 0.266 / Cross valid method: THROUGHOUT / ESU R: 0.985 / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27918 1102 5 %RANDOM
Rwork0.21554 ---
obs0.21867 20723 87.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.737 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20 Å2
2--0.77 Å20 Å2
3----1.54 Å2
Refinement stepCycle: LAST / Resolution: 2.75→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4659 0 0 28 4687
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0350.0224724
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.9931.9986314
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1735558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.4723.843216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg26.093151009
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0181544
X-RAY DIFFRACTIONr_chiral_restr0.1780.2722
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023392
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3230.22680
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3590.23198
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2290.2207
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4240.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.30.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5741.52956
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.72324610
X-RAY DIFFRACTIONr_scbond_it3.62131998
X-RAY DIFFRACTIONr_scangle_it6.0354.51704
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.822 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.512 29 -
Rwork0.374 528 -
obs--30.93 %

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