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- PDB-1vdm: Crystal structure of purine phosphoribosyltransferase from Pyroco... -

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Basic information

Entry
Database: PDB / ID: 1vdm
TitleCrystal structure of purine phosphoribosyltransferase from Pyrococcus horikoshii Ot3
Componentspurine phosphoribosyltransferase
KeywordsTRANSFERASE / purine phosphoribosyltransferase / Pyrococcus horikoshii / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyRossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / glycosyltransferase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / 153aa long hypothetical purine phosphoribosyltransferase
Function and homology information
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å
AuthorsSugahara, M. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of purine phosphoribosyltransferase from Pyrococcus horikoshii Ot3
Authors: Sugahara, M. / Kunishima, N.
History
DepositionMar 23, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: 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: purine phosphoribosyltransferase
B: purine phosphoribosyltransferase
C: purine phosphoribosyltransferase
D: purine phosphoribosyltransferase
E: purine phosphoribosyltransferase
F: purine phosphoribosyltransferase
G: purine phosphoribosyltransferase
H: purine phosphoribosyltransferase
I: purine phosphoribosyltransferase
J: purine phosphoribosyltransferase
K: purine phosphoribosyltransferase
L: purine phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)211,22112
Polymers211,22112
Non-polymers00
Water13,493749
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.603, 157.350, 170.631
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dodecamer in the asymmetric unit.

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Components

#1: Protein
purine phosphoribosyltransferase


Mass: 17601.727 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET11a / Production host: Escherichia coli (E. coli)
References: UniProt: O57827, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 749 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.36 Å3/Da / Density % sol: 63.35 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 4.4 / Details: NaCl, pH 4.4, microbatch, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONSPring-8 BL26B111
SYNCHROTRONSPring-8 BL26B121.0081
ROTATING ANODERIGAKU31.54178
Detector
TypeIDDetectorDate
RIGAKU RAXIS V1IMAGE PLATESep 25, 2003
RIGAKU JUPITER2CCDSep 26, 2003
RIGAKU RAXIS V3IMAGE PLATESep 28, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.00811
31.541781
ReflectionResolution: 2.5→40 Å / Num. all: 99412 / Num. obs: 99412 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 50.611 Å2 / Rmerge(I) obs: 0.129 / Rsym value: 0.123 / Net I/σ(I): 8
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.785 / Mean I/σ(I) obs: 3.23 / Num. unique all: 9841 / Rsym value: 0.731 / % 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: MIR / Resolution: 2.5→39.55 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 4939 -random
Rwork0.209 ---
all0.211 98798 --
obs0.211 98798 100 %-
Displacement parametersBiso mean: 46.4 Å2
Baniso -1Baniso -2Baniso -3
1-8.61 Å20 Å20 Å2
2---6.62 Å20 Å2
3----2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.5→39.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14432 0 0 749 15181
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.008
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.014
RfactorNum. reflection% reflection
Rfree0.313 493 -
Rwork0.298 --
obs-9270 100 %

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