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- PDB-2z0t: Crystal structure of hypothetical protein PH0355 -

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Basic information

Entry
Database: PDB / ID: 2z0t
TitleCrystal structure of hypothetical protein PH0355
ComponentsPutative uncharacterized protein PH0355
KeywordsRNA BINDING PROTEIN / alpha/beta protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Uncharacterised conserved protein UCP016134 / Hypothetical protein. / ASCH / ASCH domain / ASCH domain / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / PUA-like superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
ASCH domain-containing protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsMurayama, K. / Takemoto, C. / Kato-Murayama, M. / Kawazoe, M. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of hypothetical protein PH0355
Authors: Murayama, K. / Takemoto, C. / Kato-Murayma, M. / Kawazoe, M. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionMay 7, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 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

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein PH0355
B: Putative uncharacterized protein PH0355
C: Putative uncharacterized protein PH0355
D: Putative uncharacterized protein PH0355


Theoretical massNumber of molelcules
Total (without water)51,2764
Polymers51,2764
Non-polymers00
Water10,917606
1
A: Putative uncharacterized protein PH0355


Theoretical massNumber of molelcules
Total (without water)12,8191
Polymers12,8191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative uncharacterized protein PH0355


Theoretical massNumber of molelcules
Total (without water)12,8191
Polymers12,8191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative uncharacterized protein PH0355


Theoretical massNumber of molelcules
Total (without water)12,8191
Polymers12,8191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Putative uncharacterized protein PH0355


Theoretical massNumber of molelcules
Total (without water)12,8191
Polymers12,8191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.082, 51.336, 66.233
Angle α, β, γ (deg.)108.09, 90.02, 109.31
Int Tables number1
Space group name H-MP1
DetailsAUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN

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Components

#1: Protein
Putative uncharacterized protein PH0355


Mass: 12818.990 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: O58093
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 606 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.07 %

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-5A10.97926, 0.97947, 0.9600
ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT21.5418
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJun 15, 2006
RIGAKU RAXIS IV2IMAGE PLATEMar 12, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979261
20.979471
30.961
41.54181
ReflectionResolution: 1.8→50 Å / Num. obs: 41140 / % possible obs: 94 % / Observed criterion σ(F): -3 / Redundancy: 4 % / Biso Wilson estimate: 17 Å2 / Rsym value: 0.031 / Net I/σ(I): 33.8
Reflection shellResolution: 1.8→1.86 Å / Rsym value: 0.092 / % possible all: 90.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→25.66 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 418886.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2052 5 %RANDOM
Rwork0.178 ---
obs0.178 41003 94.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.1191 Å2 / ksol: 0.32389 e/Å3
Displacement parametersBiso mean: 21.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å21.01 Å20.4 Å2
2--0.54 Å20.18 Å2
3----1.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.8→25.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3584 0 0 606 4190
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.63
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.711.5
X-RAY DIFFRACTIONc_mcangle_it2.392
X-RAY DIFFRACTIONc_scbond_it3.242
X-RAY DIFFRACTIONc_scangle_it4.932.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.255 367 5.6 %
Rwork0.216 6216 -
obs--90.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top

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