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- PDB-4maf: Soybean ATP Sulfurylase -

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Basic information

Entry
Database: PDB / ID: 4maf
TitleSoybean ATP Sulfurylase
ComponentsATP sulfurylaseSulfate adenylyltransferase
KeywordsTRANSFERASE / ATP sulfurylase / sulfur metabolism
Function / homology
Function and homology information


sulfate adenylyltransferase / sulfate adenylyltransferase (ATP) activity / sulfate assimilation / ATP binding
Similarity search - Function
Sulfate adenylyltransferase / Sulfate adenylyltransferase / Sulphate adenylyltransferase / Sulphate adenylyltransferase catalytic domain / ATP-sulfurylase PUA-like domain / ATP-sulfurylase / PUA-like domain / PUA-like superfamily / HUPs / Rossmann-like alpha/beta/alpha sandwich fold ...Sulfate adenylyltransferase / Sulfate adenylyltransferase / Sulphate adenylyltransferase / Sulphate adenylyltransferase catalytic domain / ATP-sulfurylase PUA-like domain / ATP-sulfurylase / PUA-like domain / PUA-like superfamily / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-PHOSPHOSULFATE / Sulfate adenylyltransferase
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsHerrmann, J. / Ravilious, G.E. / McKinney, S.E. / Westfall, C.S. / Lee, S.G. / Krishnan, H.B. / Jez, J.M.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structure and mechanism of soybean ATP sulfurylase and the committed step in plant sulfur assimilation.
Authors: Herrmann, J. / Ravilious, G.E. / McKinney, S.E. / Westfall, C.S. / Lee, S.G. / Baraniecka, P. / Giovannetti, M. / Kopriva, S. / Krishnan, H.B. / Jez, J.M.
History
DepositionAug 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Apr 30, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: ATP sulfurylase
B: ATP sulfurylase
C: ATP sulfurylase
D: ATP sulfurylase
E: ATP sulfurylase
F: ATP sulfurylase
G: ATP sulfurylase
H: ATP sulfurylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)368,15616
Polymers364,7388
Non-polymers3,4188
Water14,862825
1
A: ATP sulfurylase
H: ATP sulfurylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0394
Polymers91,1842
Non-polymers8552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-16 kcal/mol
Surface area32220 Å2
MethodPISA
2
B: ATP sulfurylase
C: ATP sulfurylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0394
Polymers91,1842
Non-polymers8552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-16 kcal/mol
Surface area33150 Å2
MethodPISA
3
D: ATP sulfurylase
E: ATP sulfurylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0394
Polymers91,1842
Non-polymers8552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-16 kcal/mol
Surface area32850 Å2
MethodPISA
4
F: ATP sulfurylase
G: ATP sulfurylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0394
Polymers91,1842
Non-polymers8552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-18 kcal/mol
Surface area33000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.268, 230.751, 159.197
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11B-1097-

HOH

21E-1087-

HOH

31G-1045-

HOH

41G-1051-

HOH

51G-1059-

HOH

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Components

#1: Protein
ATP sulfurylase / Sulfate adenylyltransferase


Mass: 45592.191 Da / Num. of mol.: 8 / Fragment: UNP residues 49-449
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q8SAG1, sulfate adenylyltransferase
#2: Chemical
ChemComp-ADX / ADENOSINE-5'-PHOSPHOSULFATE / 3'-Phosphoadenosine-5'-phosphosulfate


Type: RNA linking / Mass: 427.284 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H14N5O10PS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 825 / 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: 2.57 Å3/Da / Density % sol: 52.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 0.1 M HEPES, pH 7.3, 18% PEG-8000, 0.2 M NaCl, 5 mM APS, 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: Nov 28, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.48→48.211 Å / Num. obs: 123420 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 33.69 Å2 / Rsym value: 0.094 / Net I/σ(I): 18

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1XNJ

1xnj


Resolution: 2.48→48.21 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 22.66 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2215 6234 5.05 %random
Rwork0.1726 ---
obs0.1751 123420 93.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.48→48.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25446 0 216 825 26487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00826334
X-RAY DIFFRACTIONf_angle_d1.14935774
X-RAY DIFFRACTIONf_dihedral_angle_d16.27310047
X-RAY DIFFRACTIONf_chiral_restr0.0753878
X-RAY DIFFRACTIONf_plane_restr0.0054626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.51120.28452120.23313830X-RAY DIFFRACTION93
2.5112-2.54080.31242050.22463866X-RAY DIFFRACTION94
2.5408-2.57180.28962400.21743956X-RAY DIFFRACTION95
2.5718-2.60430.26592200.20993938X-RAY DIFFRACTION95
2.6043-2.63860.27722120.20683959X-RAY DIFFRACTION96
2.6386-2.67470.27022300.20263939X-RAY DIFFRACTION96
2.6747-2.71290.26212280.2013943X-RAY DIFFRACTION95
2.7129-2.75340.25022130.19953992X-RAY DIFFRACTION96
2.7534-2.79650.29472260.19163914X-RAY DIFFRACTION95
2.7965-2.84230.24462270.19543962X-RAY DIFFRACTION95
2.8423-2.89130.2562020.1993935X-RAY DIFFRACTION95
2.8913-2.94390.27812080.20563942X-RAY DIFFRACTION95
2.9439-3.00050.26891990.21113941X-RAY DIFFRACTION95
3.0005-3.06170.26152010.2043940X-RAY DIFFRACTION95
3.0617-3.12830.25581900.20813954X-RAY DIFFRACTION95
3.1283-3.2010.28021990.21333941X-RAY DIFFRACTION94
3.201-3.28110.26642150.21243931X-RAY DIFFRACTION94
3.2811-3.36980.24412180.19813901X-RAY DIFFRACTION94
3.3698-3.46890.26581960.1923925X-RAY DIFFRACTION94
3.4689-3.58080.26321950.18393914X-RAY DIFFRACTION94
3.5808-3.70880.19082020.17063896X-RAY DIFFRACTION93
3.7088-3.85720.18222090.15723902X-RAY DIFFRACTION93
3.8572-4.03270.18391910.14423893X-RAY DIFFRACTION93
4.0327-4.24520.18511750.13433913X-RAY DIFFRACTION92
4.2452-4.51090.1691930.13093870X-RAY DIFFRACTION92
4.5109-4.85890.17012070.13223854X-RAY DIFFRACTION92
4.8589-5.34730.17882140.13813828X-RAY DIFFRACTION91
5.3473-6.11980.21032160.15313817X-RAY DIFFRACTION90
6.1198-7.70520.17811900.15913828X-RAY DIFFRACTION89
7.7052-48.21980.16862010.14573762X-RAY DIFFRACTION85
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)
12.03381.1070.32752.4396-0.00320.51890.0841-0.3487-0.3987-0.05790.10380.00390.0749-0.1331-0.14990.35-0.002-0.01140.32950.13730.459513.3887-85.3747-27.4386
20.94750.0572-0.55971.30990.50761.2394-0.086-0.1468-0.21620.3813-0.13450.35290.2586-0.270.10090.281-0.0580.10770.32020.00620.2727-13.3492-25.9165-23.5926
30.862-0.386-0.11391.38170.36720.57380.00990.1517-0.1284-0.06740.0391-0.04420.04320.0486-0.02620.12-0.00940.01570.2028-0.00920.190813.3464-32.1516-52.2135
41.34650.70990.71931.39760.70450.93720.316-0.4743-0.20510.5118-0.1901-0.16180.4223-0.2902-0.06440.4703-0.1017-0.09590.35990.03050.2523-32.2661-27.0318-67.4289
50.9974-0.606-0.40841.40680.7690.878-0.02490.1851-0.3591-0.0349-0.20660.54270.1197-0.31060.15420.20420.00450.01330.2885-0.08060.4264-61.15-29.945-94.197
61.05990.0807-0.06651.41090.08510.7391-0.04750.4268-0.0999-0.38530.1114-0.3559-0.00970.1419-0.03890.4526-0.13770.19680.5464-0.12760.4985-36.1388-88.265-12.1305
71.3061-0.17610.29210.94520.56921.2349-0.1424-0.05910.197-0.0363-0.01680.187-0.288-0.15860.13030.26050.0759-0.07240.3041-0.00860.3338-63.249-84.23916.095
81.74950.29050.12941.83510.01590.632-0.44730.429-0.1395-1.12470.52540.9597-0.068-0.1134-0.11130.9952-0.2149-0.65570.54980.31571.1132-14.3826-88.4809-54.5023
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H

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