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- PDB-2yvu: Crystal structure of APE1195 -

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Basic information

Entry
Database: PDB / ID: 2yvu
TitleCrystal structure of APE1195
ComponentsProbable adenylyl-sulfate kinase
KeywordsTRANSFERASE / KINASE / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


sulfate assimilation via adenylyl sulfate reduction / sulfate assimilation, phosphoadenylyl sulfate reduction by phosphoadenylyl-sulfate reductase (thioredoxin) / adenylyl-sulfate kinase / adenylylsulfate kinase activity / sulfate adenylyltransferase (ATP) activity / hydrogen sulfide biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
: / Adenylyl-sulfate kinase / Adenylylsulphate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable adenylyl-sulfate kinase
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsIshii, R. / Bessho, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be published
Title: Crystal structure of APE1195
Authors: Ishii, R. / Bessho, Y. / Yokoyama, S.
History
DepositionApr 15, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE UNIPROT Q9YCR6 was updated on 2007-06-26. The author constructed the plasmid following the ...SEQUENCE UNIPROT Q9YCR6 was updated on 2007-06-26. The author constructed the plasmid following the old database Q9YCR6 including the first 4 residues MET GLN ALA LEU.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable adenylyl-sulfate kinase
B: Probable adenylyl-sulfate kinase


Theoretical massNumber of molelcules
Total (without water)42,2472
Polymers42,2472
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.010, 102.820, 45.580
Angle α, β, γ (deg.)90.00, 96.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Probable adenylyl-sulfate kinase / APE1195 / APS kinase / Adenosine-5'-phosphosulfate kinase / ATP adenosine-5'-phosphosulfate 3'- ...APE1195 / APS kinase / Adenosine-5'-phosphosulfate kinase / ATP adenosine-5'-phosphosulfate 3'-phosphotransferase


Mass: 21123.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Strain: K1 / Gene: cysC / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q9YCR6, adenylyl-sulfate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 49.25 %
Crystal growTemperature: 293 K / Method: oil batch / pH: 7.6
Details: 15% (v/v) MPD, 0.1M HEPES-NaOH, 0.2M tri-Na Citr, pH 7.6, oil batch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 28, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 23374 / Num. obs: 23213 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 31.2
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.159 / Mean I/σ(I) obs: 5.4 / Num. unique all: 2117 / % possible all: 91.3

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GKS

2gks


Resolution: 2.1→45.27 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1283584.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1160 5 %RANDOM
Rwork0.202 ---
obs0.202 23094 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.8713 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 38.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å2-0.77 Å2
2---8.35 Å20 Å2
3---9.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.1→45.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2807 0 0 131 2938
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it3.451.5
X-RAY DIFFRACTIONc_mcangle_it4.552
X-RAY DIFFRACTIONc_scbond_it5.252
X-RAY DIFFRACTIONc_scangle_it6.782.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.29 211 5.8 %
Rwork0.229 3407 -
obs--93.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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