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- PDB-4i5t: Crystal structure of yeast Ap4A phosphorylase Apa2 -

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Basic information

Entry
Database: PDB / ID: 4i5t
TitleCrystal structure of yeast Ap4A phosphorylase Apa2
Components5',5'''-P-1,P-4-tetraphosphate phosphorylase 2
KeywordsTRANSFERASE / Ap4A phosphorylase / Ap4A
Function / homology
Function and homology information


sulfate adenylyltransferase (ADP) / sulfate adenylyltransferase (ADP) activity / ATP adenylyltransferase / ATP:ADP adenylyltransferase activity / bis(5'-nucleosyl)-tetraphosphatase 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 ...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
Diadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 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
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)75,8062
Polymers75,8062
Non-polymers00
Water4,035224
1
A: 5',5'''-P-1,P-4-tetraphosphate phosphorylase 2


Theoretical massNumber of molelcules
Total (without water)37,9031
Polymers37,9031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 5',5'''-P-1,P-4-tetraphosphate phosphorylase 2


Theoretical massNumber of molelcules
Total (without water)37,9031
Polymers37,9031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: 5',5'''-P-1,P-4-tetraphosphate phosphorylase 2

B: 5',5'''-P-1,P-4-tetraphosphate phosphorylase 2


Theoretical massNumber of molelcules
Total (without water)75,8062
Polymers75,8062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x+1/2,-y-1/2,-z1
Buried area2030 Å2
ΔGint-8 kcal/mol
Surface area27100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.760, 74.460, 112.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 37902.859 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.03 Å3/Da / Density % sol: 39.56 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 18% PEG 2K, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97917 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 2.3→47.49 Å / Num. obs: 27391 / % possible obs: 97.4 % / Redundancy: 5.7 % / Biso Wilson estimate: 37.3 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 10.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→44.844 Å / SU ML: 0.74 / σ(F): 1.35 / Phase error: 29.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2777 1374 5.03 %
Rwork0.2029 --
obs0.2067 27333 97.02 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.629 Å2 / ksol: 0.326 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.4013 Å2-0 Å20 Å2
2---4.5689 Å20 Å2
3---1.1676 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.844 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4870 0 0 224 5094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084989
X-RAY DIFFRACTIONf_angle_d1.2516771
X-RAY DIFFRACTIONf_dihedral_angle_d15.2041861
X-RAY DIFFRACTIONf_chiral_restr0.085755
X-RAY DIFFRACTIONf_plane_restr0.005878
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.38220.37511080.2646219183
2.3822-2.47760.35641380.2638238791
2.4776-2.59040.3511270.2547260699
2.5904-2.72690.28391510.23432629100
2.7269-2.89770.34071390.22662652100
2.8977-3.12140.32191150.20942683100
3.1214-3.43540.28031720.20132623100
3.4354-3.93230.26911530.19672676100
3.9323-4.95330.22051420.15962713100
4.9533-44.85290.24741290.1973279998

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