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- PDB-2d13: Crystal Structure of PH1257 from Pyrococcus horikoshii OT3 -

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Basic information

Entry
Database: PDB / ID: 2d13
TitleCrystal Structure of PH1257 from Pyrococcus horikoshii OT3
Componentshypothetical protein PH1257Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Hypothetical / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


putative n-type atp pyrophosphatase, domain 2 / putative n-type atp pyrophosphatase, domain 2 / Diphthamide synthase domain / Uncharacterised protein MJ0570 / Uncharacterised protein MJ0570, ATP-binding / Diphthine--ammonia ligase/Uncharacterised protein MJ0570 / Diphthamide synthase / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Alpha-Beta Complex ...putative n-type atp pyrophosphatase, domain 2 / putative n-type atp pyrophosphatase, domain 2 / Diphthamide synthase domain / Uncharacterised protein MJ0570 / Uncharacterised protein MJ0570, ATP-binding / Diphthine--ammonia ligase/Uncharacterised protein MJ0570 / Diphthamide synthase / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Diphthami_syn_2 domain-containing protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLokanath, N.K. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of PH1257 from Pyrococcus horikoshii OT3
Authors: Lokanath, N.K. / Kunishima, N.
History
DepositionAug 12, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: hypothetical protein PH1257
B: hypothetical protein PH1257
C: hypothetical protein PH1257
D: hypothetical protein PH1257


Theoretical massNumber of molelcules
Total (without water)103,2314
Polymers103,2314
Non-polymers00
Water3,837213
1
A: hypothetical protein PH1257
C: hypothetical protein PH1257


Theoretical massNumber of molelcules
Total (without water)51,6162
Polymers51,6162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-6 kcal/mol
Surface area19880 Å2
MethodPISA
2
B: hypothetical protein PH1257
D: hypothetical protein PH1257


Theoretical massNumber of molelcules
Total (without water)51,6162
Polymers51,6162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-6 kcal/mol
Surface area19410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.974, 96.696, 84.921
Angle α, β, γ (deg.)90.00, 93.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
hypothetical protein PH1257 / Hypothesis


Mass: 25807.781 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) / Strain (production host): BL21_cododnPlus(DE3)-RIL / References: GenBank: 14591076, UniProt: O58996*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.2 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 8.2
Details: Tris-HCl, CaCl2, PEG4000, pH 8.2, microbatch, temperature 295.0K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jul 20, 2005 / Details: Graphite
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 32752 / Num. obs: 32935 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 7.5
Reflection shellResolution: 2.4→2.49 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.1.27refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RU8

1ru8
PDB Unreleased entry


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.912 / SU B: 8.206 / SU ML: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.79 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1624 5 %RANDOM
Rwork0.229 ---
all0.229 32935 --
obs0.229 32752 99.61 %-
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: 33.699 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20.39 Å2
2--0.5 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6656 0 0 213 6869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226786
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.9739126
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.4695820
X-RAY DIFFRACTIONr_chiral_restr0.10.2999
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024975
X-RAY DIFFRACTIONr_nbd_refined0.2540.22970
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2269
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.29
X-RAY DIFFRACTIONr_mcbond_it1.1651.54096
X-RAY DIFFRACTIONr_mcangle_it2.18526519
X-RAY DIFFRACTIONr_scbond_it3.15632690
X-RAY DIFFRACTIONr_scangle_it5.0324.52607
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.296 127
Rwork0.258 2475

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