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- PDB-1vbk: Crystal structure of PH1313 from Pyrococcus horikoshii Ot3 -

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Basic information

Entry
Database: PDB / ID: 1vbk
TitleCrystal structure of PH1313 from Pyrococcus horikoshii Ot3
Componentshypothetical protein PH1313Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Pyrococcus horikoshii / RIKEN Structural Genomics/Proteomics Initiative / RSGI / NPPSFA / National Project on Protein Structural and Functional Analyses
Function / homology
Function and homology information


CCA tRNA nucleotidyltransferase activity / RNA binding
Similarity search - Function
THUMP domain-like / THUMP superfamily / Thil, AANH domain / Thiamine biosynthesis protein (ThiI) / THUMP fold / THUMP / THUMP domain / THUMP domain / THUMP domain profile. / HUPs ...THUMP domain-like / THUMP superfamily / Thil, AANH domain / Thiamine biosynthesis protein (ThiI) / THUMP fold / THUMP / THUMP domain / THUMP domain / THUMP domain profile. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THUMP domain-containing protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsSugahara, M. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Purification, crystallization and preliminary crystallographic analysis of the putative thiamine-biosynthesis protein PH1313 from Pyrococcus horikoshii OT3
Authors: Sugahara, M. / Murai, S. / Sugahara, M. / Kunishima, N.
History
DepositionFeb 27, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein PH1313
B: hypothetical protein PH1313
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8776
Polymers70,4042
Non-polymers4734
Water11,476637
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.743, 71.164, 141.774
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer in the asymmetric unit.

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Components

#1: Protein hypothetical protein PH1313 / Hypothesis


Mass: 35202.234 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) / References: UniProt: O59053
#2: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 637 / 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: 2.33 Å3/Da / Density % sol: 46.87 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 5.4 / Details: MRD, pH 5.4, MICROBATCH, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL26B111
SYNCHROTRONSPring-8 BL26B120.97906
Detector
TypeIDDetectorDate
RIGAKU RAXIS V1IMAGE PLATENov 30, 2003
RIGAKU RAXIS V2IMAGE PLATEFeb 8, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979061
ReflectionResolution: 1.9→40 Å / Num. all: 57832 / Num. obs: 57832 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 22.27 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.072 / Net I/σ(I): 9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 3.81 / Num. unique all: 5719 / Rsym value: 0.489 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.9→39.47 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2880 -RANDOM
Rwork0.199 ---
all0.203 57762 --
obs0.203 57762 99.5 %-
Displacement parametersBiso mean: 28.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å20 Å20 Å2
2--9.1 Å20 Å2
3----7.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.9→39.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4871 0 32 637 5540
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_bond_d0.005
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.019
RfactorNum. reflection% reflection
Rfree0.299 261 -
Rwork0.256 --
obs-5287 97.3 %

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