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- PDB-3uie: Crystal structure of adenosine 5'-phosphosulfate kinase from Arab... -

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Basic information

Entry
Database: PDB / ID: 3uie
TitleCrystal structure of adenosine 5'-phosphosulfate kinase from Arabidopsis Thaliana in Complex with AMPPNP and APS
ComponentsAdenylyl-sulfate kinase 1, chloroplastic
Keywordstransferase/transferase inhibitor / Rossmann fold / Kinase / chloroplast / transferase-transferase inhibitor complex
Function / homology
Function and homology information


adenylyl-sulfate kinase / adenylylsulfate kinase activity / sulfate assimilation / hydrogen sulfide biosynthetic process / L-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 / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Adenylyl-sulfate kinase 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.794 Å
AuthorsRavilious, G.E. / Jez, J.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural basis and evolution of redox regulation in plant adenosine-5'-phosphosulfate kinase.
Authors: Ravilious, G.E. / Nguyen, A. / Francois, J.A. / Jez, J.M.
History
DepositionNov 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

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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)69,18612
Polymers66,3133
Non-polymers2,8739
Water8,629479
1
A: Adenylyl-sulfate kinase 1, chloroplastic
hetero molecules

A: Adenylyl-sulfate kinase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1248
Polymers44,2092
Non-polymers1,9166
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6450 Å2
ΔGint-63 kcal/mol
Surface area15870 Å2
MethodPISA
2
B: Adenylyl-sulfate kinase 1, chloroplastic
C: Adenylyl-sulfate kinase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1248
Polymers44,2092
Non-polymers1,9166
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-71 kcal/mol
Surface area15700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.137, 95.313, 73.327
Angle α, β, γ (deg.)90.00, 114.08, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-252-

GLU

21B-532-

HOH

DetailsChain A and symmetry mate form crystallographic dimer Chain B and C form non-crystallographic dimer

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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-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / 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: 2.91 Å3/Da / Density % sol: 57.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES pH 7.5, 200 mM magnesium chloride, 17.5 % PEG 2000, 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 315r / Detector: CCD / Date: Jun 27, 2010
RadiationMonochromator: high resolution double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.794→30.5 Å / Num. all: 70893 / Num. obs: 69476 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.8→1.83 Å / % possible all: 98.4

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.794→30.5 Å / SU ML: 0.21 / σ(F): 0 / Phase error: 22.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2013 3160 5.1 %
Rwork0.1728 --
obs0.1742 61929 87.11 %
all-70893 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.739 Å2 / ksol: 0.416 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.7831 Å20 Å21.7431 Å2
2--13.0313 Å20 Å2
3----12.2482 Å2
Refinement stepCycle: LAST / Resolution: 1.794→30.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4428 0 177 479 5084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064803
X-RAY DIFFRACTIONf_angle_d1.0766534
X-RAY DIFFRACTIONf_dihedral_angle_d22.1631993
X-RAY DIFFRACTIONf_chiral_restr0.061723
X-RAY DIFFRACTIONf_plane_restr0.004827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7936-1.85770.29092430.27723962X-RAY DIFFRACTION60
1.8577-1.93210.27522480.23464666X-RAY DIFFRACTION69
1.9321-2.020.24593100.19895674X-RAY DIFFRACTION84
2.02-2.12650.22743110.18796353X-RAY DIFFRACTION94
2.1265-2.25960.21413350.17346279X-RAY DIFFRACTION93
2.2596-2.4340.23873360.17556119X-RAY DIFFRACTION91
2.434-2.67890.20793120.17976327X-RAY DIFFRACTION94
2.6789-3.06620.20943410.17636498X-RAY DIFFRACTION96
3.0662-3.86180.18123850.15956607X-RAY DIFFRACTION98
3.8618-30.54030.17683390.16016284X-RAY DIFFRACTION92
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)
10.4986-0.2067-0.4680.79420.01071.7133-0.00680.0335-0.0188-0.0639-0.02740.00140.08060.07370.03570.18450.0226-0.00560.25480.00540.2055.4967-0.3418-13.0846
21.8995-0.4888-0.21440.4261-0.05971.122-0.0344-0.1139-0.02140.04440.09730.0237-0.2-0.0663-0.03990.2820.08990.02140.21680.05970.2346-11.205124.5241-34.9406
31.6938-0.2874-0.88550.6762-0.07471.40880.13180.53260.0013-0.1431-0.11840.0135-0.218-0.2982-0.02760.25840.09130.00470.34650.03020.1905-2.647922.557-60.7723
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C

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