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- PDB-4i5v: Crystal structure of yeast Ap4A phosphorylase Apa2 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4i5v
TitleCrystal structure of yeast Ap4A phosphorylase Apa2 in complex with Ap4A
Components5',5'''-P-1,P-4-tetraphosphate phosphorylase 2
KeywordsTRANSFERASE / alpha/beta fold / Ap4A phosphorylase / Ap4A
Function / homology
Function and homology information


sulfate adenylyltransferase (ADP) / sulfate adenylyltransferase (ADP) activity / ATP adenylyltransferase / bis(5'-nucleosyl)-tetraphosphatase activity / ATP:ADP adenylyltransferase activity / nucleotide biosynthetic process / nucleoside catabolic process / ATP binding / nucleus / cytoplasm
Similarity search - Function
ATP adenylyltransferase / Ap4A phosphorylase 1/2 / ATP adenylyltransferase, C-terminal / Ap4A phosphorylase 1/2-like / Ap4A phosphorylase 1/2, N-terminal domain / ATP adenylyltransferase C-terminal domain / Ap4A phosphorylase N-terminal domain / HIT family, subunit A / HIT-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BIS(ADENOSINE)-5'-TETRAPHOSPHATE / Diadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.696 Å
AuthorsJiang, Y.L. / Hou, W.T. / Chen, Y. / Zhou, C.Z.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Structures of yeast Apa2 reveal catalytic insights into a canonical AP4A phosphorylase of the histidine triad superfamily
Authors: Hou, W.T. / Li, W.Z. / Chen, Y. / Jiang, Y.L. / Zhou, C.Z.
History
DepositionNov 29, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5',5'''-P-1,P-4-tetraphosphate phosphorylase 2
B: 5',5'''-P-1,P-4-tetraphosphate phosphorylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3444
Polymers75,6722
Non-polymers1,6732
Water93752
1
A: 5',5'''-P-1,P-4-tetraphosphate phosphorylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6722
Polymers37,8361
Non-polymers8361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 5',5'''-P-1,P-4-tetraphosphate phosphorylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6722
Polymers37,8361
Non-polymers8361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-17 kcal/mol
Surface area26070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.353, 52.781, 70.764
Angle α, β, γ (deg.)90.00, 99.92, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 5',5'''-P-1,P-4-tetraphosphate phosphorylase 2 / ATP adenylyltransferase / Ap4A phosphorylase II / AP / A phosphorylase / Diadenosine 5' / 5'''-P1 / ...ATP adenylyltransferase / Ap4A phosphorylase II / AP / A phosphorylase / Diadenosine 5' / 5'''-P1 / P4-tetraphosphate phosphorylase / AP-4-A phosphorylase


Mass: 37835.789 Da / Num. of mol.: 2 / Mutation: H161A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: APA2, YDR530C, D9719.33 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P22108, ATP adenylyltransferase
#2: Chemical ChemComp-B4P / BIS(ADENOSINE)-5'-TETRAPHOSPHATE


Mass: 836.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28N10O19P4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 23% PEG 2K, 0.1M Tris-HCl, pH 8.0, 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.696→50 Å / Num. obs: 19447 / % possible obs: 93.9 % / Redundancy: 2.2 % / Biso Wilson estimate: 69.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.4
Reflection shellResolution: 2.7→2.79 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 1.9 / Num. unique all: 1801 / % possible all: 96.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.696→42.07 Å / SU ML: 0.79 / σ(F): 1.36 / Phase error: 30.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2608 988 5.08 %
Rwork0.1806 --
obs0.185 19436 93.66 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.005 Å2 / ksol: 0.316 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-14.4379 Å2-0 Å2-8.9332 Å2
2--7.5843 Å2-0 Å2
3----13.5841 Å2
Refinement stepCycle: LAST / Resolution: 2.696→42.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4685 0 106 52 4843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084910
X-RAY DIFFRACTIONf_angle_d1.336680
X-RAY DIFFRACTIONf_dihedral_angle_d15.5171800
X-RAY DIFFRACTIONf_chiral_restr0.085757
X-RAY DIFFRACTIONf_plane_restr0.006844
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6964-2.83850.41421280.2959267895
2.8385-3.01630.32731220.2296267596
3.0163-3.24920.29551530.2104267596
3.2492-3.5760.28781530.2044266896
3.576-4.0930.27431350.1728267395
4.093-5.15530.21631540.1428258592
5.1553-42.0750.24281430.1722249486
Refinement TLS params.Method: refined / Origin x: 20.0455 Å / Origin y: 2.0837 Å / Origin z: 35.5139 Å
111213212223313233
T0.1977 Å2-0.0603 Å2-0.0758 Å2-0.1444 Å20.0341 Å2--0.1674 Å2
L3.2536 °2-1.227 °2-0.5537 °2-2.1457 °2-0.0928 °2--1.1118 °2
S0.0905 Å °0.0895 Å °-0.2601 Å °-0.0523 Å °0.0831 Å °0.2327 Å °0.0716 Å °-0.28 Å °0.0888 Å °
Refinement TLS groupSelection details: ALL

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