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- PDB-1zun: Crystal Structure of a GTP-Regulated ATP Sulfurylase Heterodimer ... -

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Basic information

Entry
Database: PDB / ID: 1zun
TitleCrystal Structure of a GTP-Regulated ATP Sulfurylase Heterodimer from Pseudomonas syringae
Components
  • Sulfate adenylyltransferase subunit 2
  • sulfate adenylate transferase, subunit 1/adenylylsulfate kinase
KeywordsTRANSFERASE / beta barrel / switch domain / heterodimer / pyrophosphate / G protein / GTPase
Function / homology
Function and homology information


sulfate adenylyltransferase / adenylylsulfate kinase activity / sulfate adenylyltransferase (ATP) activity / sulfate assimilation / hydrogen sulfide biosynthetic process / guanosine tetraphosphate binding / small molecule binding / GTPase activity / GTP binding / ATP binding
Similarity search - Function
Sulphate adenylyltransferase, small subunit / : / Sulphate adenylyltransferase, large subunit / Sulfate adenylyltransferase subunit CysN, GTP-binding domain / Sulfate adenylyltransferase subunit CysN, Domain II / Sulfate adenylyltransferase subunit CysN, Domain III / Phosphoadenosine phosphosulphate reductase / Phosphoadenosine phosphosulfate reductase family / Adenylyl-sulfate kinase / Adenylylsulphate kinase ...Sulphate adenylyltransferase, small subunit / : / Sulphate adenylyltransferase, large subunit / Sulfate adenylyltransferase subunit CysN, GTP-binding domain / Sulfate adenylyltransferase subunit CysN, Domain II / Sulfate adenylyltransferase subunit CysN, Domain III / Phosphoadenosine phosphosulphate reductase / Phosphoadenosine phosphosulfate reductase family / Adenylyl-sulfate kinase / Adenylylsulphate kinase / GTP-eEF1A C-terminal domain-like / : / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / HUPs / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Elongation Factor Tu (Ef-tu); domain 3 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Rossmann-like alpha/beta/alpha sandwich fold / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / : / Sulfate adenylyltransferase subunit 2 / Sulfate adenylyltransferase subunit 1
Similarity search - Component
Biological speciesPseudomonas syringae (bacteria)
Pseudomonas syringae pv. tomato str. DC3000 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsMougous, J.D. / Lee, D.H. / Hubbard, S.C. / Schelle, M.W. / Vocadlo, D.J. / Berger, J.M. / Bertozzi, C.R.
CitationJournal: Mol.Cell / Year: 2006
Title: Molecular basis for g protein control of the prokaryotic ATP sulfurylase.
Authors: Mougous, J.D. / Lee, D.H. / Hubbard, S.C. / Schelle, M.W. / Vocadlo, D.J. / Berger, J.M. / Bertozzi, C.R.
History
DepositionMay 31, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sulfate adenylyltransferase subunit 2
B: sulfate adenylate transferase, subunit 1/adenylylsulfate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2326
Polymers86,2192
Non-polymers1,0144
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7210 Å2
ΔGint-54 kcal/mol
Surface area25560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.072, 110.072, 171.002
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Sulfate adenylyltransferase subunit 2 / Sulfate adenylate transferase / SAT / ATP-sulfurylase small subunit / ATP sulfurylase catalytic subunit (CysD)


Mass: 37913.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae (bacteria) / Gene: cysD / Plasmid: pET28B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q87WW0, sulfate adenylyltransferase
#2: Protein sulfate adenylate transferase, subunit 1/adenylylsulfate kinase / GTPase domain of ATP sulfurylase regulatory subunit (CysN)


Mass: 48304.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato str. DC3000 (bacteria)
Species: Pseudomonas syringae group genomosp. 3 / Gene: cysNC / Plasmid: pET21A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 28871567, UniProt: Q87WW1*PLUS

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Non-polymers , 5 types, 91 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#6: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, tris hydrochloric acid, sodium acetate, guanosine diphosphate, 5'-adenyly-diphosphate-monothiophosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1951
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.110.9184, 0.9793
SYNCHROTRONALS 8.2.120.9794
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 29, 2004 / Details: MIRRORS
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI(111)MADMx-ray1
2SI(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.91841
20.97931
30.97941
ReflectionResolution: 2.7→50 Å / Num. obs: 21160 / % possible obs: 0.154 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 55.835 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 16.07
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 2.84 / Num. unique all: 4101 / Rsym value: 0.346 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.872 / SU B: 27.792 / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 1.629 / ESU R Free: 0.373 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27617 1091 5.2 %RANDOM
Rwork0.22162 ---
obs0.22439 20020 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.103 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20.64 Å20 Å2
2--1.29 Å20 Å2
3----1.93 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4688 0 61 87 4836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0224842
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0591.9746558
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2855592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05623.687217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.28115833
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3361535
X-RAY DIFFRACTIONr_chiral_restr0.0710.2733
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023616
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.22202
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.23250
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2212
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1580.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2451.52966
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.46324775
X-RAY DIFFRACTIONr_scbond_it0.57931938
X-RAY DIFFRACTIONr_scangle_it0.9814.51783
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 59 -
Rwork0.274 1432 -
obs--100 %

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