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- PDB-1d6j: CRYSTAL STRUCTURE OF ADENOSINE 5'-PHOSPHOSULFATE (APS) KINASE FRO... -

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Basic information

Entry
Database: PDB / ID: 1d6j
TitleCRYSTAL STRUCTURE OF ADENOSINE 5'-PHOSPHOSULFATE (APS) KINASE FROM PENICILLIUM CHRYSOGENUM
ComponentsADENOSINE-5'PHOSPHOSULFATE KINASE
KeywordsTRANSFERASE / APS KINASE / ADENYLYLSULFATE KINASE / SULFATE / NUCLEOTIDE KINASE
Function / homology
Function and homology information


adenylyl-sulfate kinase / adenylylsulfate kinase activity / sulfate assimilation / hydrogen sulfide biosynthetic process / cysteine biosynthetic process / methionine biosynthetic process / phosphorylation / ATP binding / cytosol
Similarity search - Function
Adenylylsulphate kinase / Adenylyl-sulfate kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
L(+)-TARTARIC ACID / Adenylyl-sulfate kinase
Similarity search - Component
Biological speciesPenicillium chrysogenum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsMacRae, I.J. / Segel, I.H. / Fisher, A.J.
CitationJournal: Biochemistry / Year: 2000
Title: Crystal structure of adenosine 5'-phosphosulfate kinase from Penicillium chrysogenum.
Authors: MacRae, I.J. / Segel, I.H. / Fisher, A.J.
History
DepositionOct 13, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADENOSINE-5'PHOSPHOSULFATE KINASE
B: ADENOSINE-5'PHOSPHOSULFATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7603
Polymers47,6102
Non-polymers1501
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-12 kcal/mol
Surface area15610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.862, 83.484, 141.951
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 ADENOSINE-5'PHOSPHOSULFATE KINASE / APS KINASE


Mass: 23804.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium chrysogenum (fungus) / Plasmid: PET23A / Production host: Escherichia coli (E. coli) / References: UniProt: Q12657, adenylyl-sulfate kinase
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 298 K / Method: batch / pH: 6
Details: 1.0 M NA/K TARTRATE, O.1 M MES, PH 6.0, 0.5% POLYETHYLINIMINE, BATCH, temperature 298K
Crystal
*PLUS
Density % sol: 59 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: or batch
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
20.8-1.2 MNa+/K+ tartrate1reservoir
30.1 MNa MES1reservoir
40.5 %polyethylinimine1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 8, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 31625 / Num. obs: 31625 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 34.2 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 30.9
Reflection shellResolution: 2→2.13 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.25 / % possible all: 96.4
Reflection
*PLUS
Num. measured all: 109188
Reflection shell
*PLUS
% possible obs: 96.4 %

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Processing

Software
NameVersionClassification
PHASESphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2→36.49 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2297291.57 / Data cutoff high rms absF: 2297291.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1537 4.9 %RANDOM
Rwork0.207 ---
obs0.207 31625 98.6 %-
all-31625 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.96 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 45.8 Å2
Baniso -1Baniso -2Baniso -3
1-6.24 Å20 Å20 Å2
2---11.66 Å20 Å2
3---5.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2→36.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2798 0 10 198 3006
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
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_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.28
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.411.5
X-RAY DIFFRACTIONc_mcangle_it5.652
X-RAY DIFFRACTIONc_scbond_it5.982
X-RAY DIFFRACTIONc_scangle_it7.442.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.319 266 5.2 %
Rwork0.265 4842 -
obs--96.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMTAR.TOP
X-RAY DIFFRACTION3TAR.PARWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.28

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