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- PDB-4fxp: Crystal structure of adenosine 5'-phosphosulfate kinase from Arab... -

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Basic information

Entry
Database: PDB / ID: 4fxp
TitleCrystal structure of adenosine 5'-phosphosulfate kinase from Arabidopsis thaliana in Complex with Sulfate and APS
ComponentsAdenylyl-sulfate kinase 1, chloroplastic
KeywordsTRANSFERASE / Rossmann fold / Nucleotide kinase / Chloroplast
Function / homology
Function and homology information


adenylyl-sulfate kinase / adenylylsulfate kinase activity / sulfate assimilation / hydrogen sulfide biosynthetic process / cysteine biosynthetic process / phosphorylation / plastid / chloroplast / ATP binding / identical protein binding
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
ADENOSINE-5'-PHOSPHOSULFATE / Adenylyl-sulfate kinase 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.954 Å
AuthorsRavilious, G.E. / Jez, J.M.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Nucleotide binding site communication in Arabidopsis thaliana adenosine 5'-phosphosulfate kinase.
Authors: Ravilious, G.E. / Jez, J.M.
History
DepositionJul 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: Adenylyl-sulfate kinase 1, chloroplastic
B: Adenylyl-sulfate kinase 1, chloroplastic
C: Adenylyl-sulfate kinase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8839
Polymers66,3133
Non-polymers1,5706
Water7,044391
1
A: Adenylyl-sulfate kinase 1, chloroplastic
hetero molecules

A: Adenylyl-sulfate kinase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2556
Polymers44,2092
Non-polymers1,0474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5000 Å2
ΔGint-79 kcal/mol
Surface area16690 Å2
MethodPISA
2
B: Adenylyl-sulfate kinase 1, chloroplastic
C: Adenylyl-sulfate kinase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2556
Polymers44,2092
Non-polymers1,0474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-79 kcal/mol
Surface area16260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.948, 92.348, 73.183
Angle α, β, γ (deg.)90.00, 113.52, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Adenylyl-sulfate kinase 1, chloroplastic / ATP adenosine-5'-phosphosulfate 3'-phosphotransferase / Adenosine-5'-phosphosulfate kinase / APS kinase


Mass: 22104.318 Da / Num. of mol.: 3 / Fragment: UNP residues 77-276
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AKN1, At2g14750, F26C24.11, T6B13.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q43295, adenylyl-sulfate kinase
#2: Chemical ChemComp-ADX / ADENOSINE-5'-PHOSPHOSULFATE


Type: RNA linking / Mass: 427.284 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O10PS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.83 Å3/Da / Density % sol: 56.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.25
Details: 0.1 M hepes, 200 mM magnesium chloride, 15 % PEG 2000, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 27, 2010
RadiationMonochromator: Sagittal focusing Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→33.9 Å / Num. obs: 52723 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.954→33.857 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 22.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1891 2675 5.07 %
Rwork0.1658 --
obs0.167 52723 98.6 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.782 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.1221 Å20 Å25.553 Å2
2--15.7705 Å20 Å2
3----15.6484 Å2
Refinement stepCycle: LAST / Resolution: 1.954→33.857 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4488 0 96 391 4975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064849
X-RAY DIFFRACTIONf_angle_d0.996595
X-RAY DIFFRACTIONf_dihedral_angle_d16.7761929
X-RAY DIFFRACTIONf_chiral_restr0.061723
X-RAY DIFFRACTIONf_plane_restr0.004862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9537-2.02350.24772650.19424834X-RAY DIFFRACTION96
2.0235-2.10450.20622510.16925055X-RAY DIFFRACTION100
2.1045-2.20030.18962320.16075032X-RAY DIFFRACTION100
2.2003-2.31630.19732600.16635084X-RAY DIFFRACTION100
2.3163-2.46140.21722630.17355061X-RAY DIFFRACTION100
2.4614-2.65130.20672790.18075022X-RAY DIFFRACTION100
2.6513-2.9180.21862790.18245058X-RAY DIFFRACTION100
2.918-3.33990.19932940.1725037X-RAY DIFFRACTION100
3.3399-4.20670.16812760.14935064X-RAY DIFFRACTION99
4.2067-33.86190.16672760.16024801X-RAY DIFFRACTION93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.54140.1599-0.39960.79990.2781.7234-0.0024-0.04860.00290.1065-0.0456-0.01420.1891-0.0248-00.192-0.0283-0.02430.22210.00080.2146-5.29510.786712.9676
21.86050.27970.03510.56760.25081.5029-0.08130.0662-0.099-0.09470.1359-0.0428-0.2960.2112-0.00010.3012-0.12740.01740.1941-0.03050.240711.943324.12735.465
31.06640.0484-0.58210.67450.03821.39260.1167-0.35560.01460.1148-0.0825-0.0081-0.21120.241-00.2708-0.0912-0.0010.3143-0.02290.25952.791923.019961.1345
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C

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