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- PDB-2gks: Crystal Structure of the Bi-functional ATP Sulfurylase-APS Kinase... -

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Basic information

Entry
Database: PDB / ID: 2gks
TitleCrystal Structure of the Bi-functional ATP Sulfurylase-APS Kinase from Aquifex aeolicus, a Chemolithotrophic Thermophile
ComponentsBifunctional SAT/APS kinase
KeywordsTRANSFERASE / Kinase / Sulfurylase
Function / homology
Function and homology information


sulfur amino acid metabolic process / sulfate assimilation via adenylyl sulfate reduction / sulfate assimilation, phosphoadenylyl sulfate reduction by phosphoadenylyl-sulfate reductase (thioredoxin) / adenylyl-sulfate kinase / sulfate adenylyltransferase / adenylylsulfate kinase activity / sulfate adenylyltransferase (ATP) activity / sulfate assimilation / hydrogen sulfide biosynthetic process / ATP binding
Similarity search - Function
Sulphate adenylyltransferase, prokaryotic-type / Sulfate adenylyltransferase / Sulfate adenylyltransferase / Sulphate adenylyltransferase / Sulphate adenylyltransferase catalytic domain / ATP-sulfurylase PUA-like domain / ATP-sulfurylase / PUA-like domain / Adenylylsulphate kinase / Adenylyl-sulfate kinase ...Sulphate adenylyltransferase, prokaryotic-type / Sulfate adenylyltransferase / Sulfate adenylyltransferase / Sulphate adenylyltransferase / Sulphate adenylyltransferase catalytic domain / ATP-sulfurylase PUA-like domain / ATP-sulfurylase / PUA-like domain / Adenylylsulphate kinase / Adenylyl-sulfate kinase / PUA-like superfamily / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / P-loop containing nucleotide triphosphate hydrolases / Roll / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Probable bifunctional SAT/APS kinase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsYu, Z. / MacRea, I.J. / Lansdon, E.B. / Segel, I.H. / Fisher, A.J.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal structure of the bifunctional ATP sulfurylase-APS kinase from the chemolithotrophic thermophile Aquifex aeolicus.
Authors: Yu, Z. / Lansdon, E.B. / Segel, I.H. / Fisher, A.J.
History
DepositionApr 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 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_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
Remark 999SEQUENCE Authors indicate that position 21 is a Glu. Sequence in the database could be a variant

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional SAT/APS kinase
B: Bifunctional SAT/APS kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,4796
Polymers125,7702
Non-polymers1,7094
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-30 kcal/mol
Surface area46760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.228, 67.283, 108.728
Angle α, β, γ (deg.)90.00, 105.43, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer in the asymmetric

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Components

#1: Protein Bifunctional SAT/APS kinase


Mass: 62885.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: sat/cysC / Plasmid: pET23a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O67174, sulfate adenylyltransferase, adenylyl-sulfate kinase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.3 Å3/Da / Density % sol: 46.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 40% ethanol, 1.0% PEG 6000, 50 mM NaAc, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 50214 / Num. obs: 49813 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.056
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 4.01 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I2D

1i2d


Resolution: 2.31→19.62 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 14.548 / SU ML: 0.183 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.4 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23979 2475 5 %RANDOM
Rwork0.196 ---
all0.19821 47281 --
obs0.19821 47281 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.798 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20.12 Å2
2---0.07 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.31→19.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8446 0 108 299 8853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0228755
X-RAY DIFFRACTIONr_angle_refined_deg1.235211859
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.37851046
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16923.483379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.629151582
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8681563
X-RAY DIFFRACTIONr_chiral_restr0.0750.21301
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026495
X-RAY DIFFRACTIONr_nbd_refined0.1880.23995
X-RAY DIFFRACTIONr_nbtor_refined0.3030.25870
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2439
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.214
X-RAY DIFFRACTIONr_mcbond_it0.431.55445
X-RAY DIFFRACTIONr_mcangle_it0.71228507
X-RAY DIFFRACTIONr_scbond_it1.1933830
X-RAY DIFFRACTIONr_scangle_it1.8764.53352
LS refinement shellResolution: 2.31→2.37 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 154 -
Rwork0.218 3244 -
obs--93.15 %
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)
13.5171-0.0059-1.31333.27580.31312.5248-0.08620.2074-0.1995-0.3734-0.07920.32610.0736-0.00080.1654-0.14240.0778-0.0733-0.2073-0.0766-0.165819.3240.16468.957
22.6847-0.8577-0.30453.75440.64452.5058-0.3265-0.7132-0.42860.65030.12660.56560.30730.12950.1999-0.04790.15450.08920.03240.046-0.178213.1473.86993.732
325.3483-7.471716.80753.2006-7.073515.64370.3341-1.7708-1.90740.27820.89711.09330.5866-1.0787-1.23110.08250.15430.05990.144-0.00230.0806-4.63415.77494.62
46.95840.4053-1.06112.54580.59582.0378-0.31790.7222-0.1495-0.29450.09990.40450.1987-0.40620.218-0.0528-0.0597-0.0396-0.1338-0.0591-0.0227-20.2121.60267.47
53.3372-1.02232.1773.1314-1.20714.4967-0.2487-0.08140.2808-0.14250.0712-0.1781-0.3891-0.20540.1774-0.15190.0326-0.0377-0.1927-0.0462-0.2558-35.02456.89571.664
63.6269-0.93022.02653.9588-0.71754.3868-0.3644-1.05440.19450.73450.2-0.0851-0.3929-0.62430.1644-0.02650.1484-0.00660.1862-0.0555-0.3048-29.30549.54295.726
718.1283-2.9092-9.48767.15528.21421.46360.6898-0.4920.31040.12040.542-1.2704-0.45411.93-1.23180.00760.0628-0.09380.1684-0.0338-0.0273-9.61939.01596.362
84.14170.191-1.85011.0338-0.59352.67540.1441-0.01870.8794-0.05120.17270.1068-0.27160.1374-0.3168-0.0824-0.0059-0.032-0.2502-0.08270.03318.28734.76268.049
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 1404 - 140
2X-RAY DIFFRACTION2AA141 - 321141 - 321
3X-RAY DIFFRACTION3AA337 - 370337 - 370
4X-RAY DIFFRACTION4AA371 - 546371 - 546
5X-RAY DIFFRACTION5BB3 - 1403 - 140
6X-RAY DIFFRACTION6BB141 - 321141 - 321
7X-RAY DIFFRACTION7BB337 - 370337 - 370
8X-RAY DIFFRACTION8BB371 - 546371 - 546

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