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- PDB-2zau: Crystal structure of an N-terminally truncated selenophosphate sy... -

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Basic information

Entry
Database: PDB / ID: 2zau
TitleCrystal structure of an N-terminally truncated selenophosphate synthetase from Aquifex aeolicus
ComponentsSelenide, water dikinase
KeywordsTRANSFERASE / INTRAMOLECULAR S-S BOND / TRIMER OF DIMERS / ATP-binding / Kinase / Magnesium / Nucleotide-binding / Selenium / Selenocysteine / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


selenide, water dikinase / selenide, water dikinase activity / selenocysteine biosynthetic process / phosphorylation / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Selenophosphate synthetase, class I / Selenophosphate synthetase / Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal domain / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily ...Selenophosphate synthetase, class I / Selenophosphate synthetase / Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal domain / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain / 60s Ribosomal Protein L30; Chain: A; / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Selenide, water dikinase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsSekine, S. / Matsumoto, E. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Structure of an N-terminally truncated selenophosphate synthetase from Aquifex aeolicus
Authors: Matsumoto, E. / Sekine, S. / Akasaka, R. / Otta, Y. / Katsura, K. / Inoue, M. / Kaminishi, T. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionOct 10, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Selenide, water dikinase
B: Selenide, water dikinase
C: Selenide, water dikinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,0756
Polymers102,7903
Non-polymers2853
Water7,945441
1
A: Selenide, water dikinase
B: Selenide, water dikinase
C: Selenide, water dikinase
hetero molecules

A: Selenide, water dikinase
B: Selenide, water dikinase
C: Selenide, water dikinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,15012
Polymers205,5806
Non-polymers5706
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area11760 Å2
ΔGint-71 kcal/mol
Surface area76440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.161, 165.198, 167.684
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Selenide, water dikinase / / Selenophosphate synthetase / Selenium donor protein


Mass: 34263.375 Da / Num. of mol.: 3
Fragment: N-terminally truncated form, residues 2-311 (27-336)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: selD / Plasmid: pET25b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codonplus-RIL / References: UniProt: O67139, selenide, water dikinase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 3.14 Å3/Da / Density % sol: 60.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: MPD, AMMONIUM PHOSPHATE, NA-HEPES, pH 7.10, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 25, 2005
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 82314 / % possible obs: 93.9 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 18.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 3.66 / Rsym value: 0.429 / % possible all: 94.7

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2→46.29 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3740376.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.239 4140 5 %RANDOM
Rwork0.212 ---
obs0.212 82004 93.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.36 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 39.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.52 Å20 Å20 Å2
2---4.73 Å20 Å2
3---2.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2→46.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7077 0 15 441 7533
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.154
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.33
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.861.5
X-RAY DIFFRACTIONc_mcangle_it2.852
X-RAY DIFFRACTIONc_scbond_it2.562
X-RAY DIFFRACTIONc_scangle_it3.872.5
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.285 510 5 %
Rwork0.247 9709 -
obs--94.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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