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- PDB-1m8p: Crystal Structure of P. chrysogenum ATP Sulfurylase in the T-state -

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Basic information

Entry
Database: PDB / ID: 1m8p
TitleCrystal Structure of P. chrysogenum ATP Sulfurylase in the T-state
Componentssulfate adenylyltransferase
KeywordsTRANSFERASE / Rossmann fold / phosphosulfate binding / T-state
Function / homology
Function and homology information


sulfate assimilation via adenylyl sulfate reduction / sulfate assimilation, phosphoadenylyl sulfate reduction by phosphoadenylyl-sulfate reductase (thioredoxin) / sulfate adenylyltransferase / adenylylsulfate kinase activity / sulfate adenylyltransferase (ATP) activity / hydrogen sulfide biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Sulfate adenylyltransferase / : / Sulfate adenylyltransferase / Sulfate adenylyltransferase / Sulphate adenylyltransferase / Sulphate adenylyltransferase catalytic domain / ATP-sulfurylase PUA-like domain / ATP-sulfurylase / PUA-like domain / Adenylyl-sulfate kinase ...Sulfate adenylyltransferase / : / Sulfate adenylyltransferase / Sulfate adenylyltransferase / Sulphate adenylyltransferase / Sulphate adenylyltransferase catalytic domain / ATP-sulfurylase PUA-like domain / ATP-sulfurylase / PUA-like domain / Adenylyl-sulfate kinase / Adenylylsulphate kinase / PUA-like superfamily / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / P-loop containing nucleotide triphosphate hydrolases / Roll / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE / Sulfate adenylyltransferase
Similarity search - Component
Biological speciesPenicillium chrysogenum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMacRae, I.J. / Segel, I.H. / Fisher, A.J.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Allosteric Inhibition via R-State Destabilization in ATP Sulfurylase from Penicillium chrysogenum
Authors: MacRae, I.J. / Segel, I.H. / Fisher, A.J.
History
DepositionJul 25, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: 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 state THAT Gly 369 is not an insertion into their sequence and that the original ...SEQUENCE AUTHORS state THAT Gly 369 is not an insertion into their sequence and that the original published sequence was missing this residue.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: sulfate adenylyltransferase
B: sulfate adenylyltransferase
C: sulfate adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,7096
Polymers192,1873
Non-polymers1,5223
Water8,251458
1
A: sulfate adenylyltransferase
B: sulfate adenylyltransferase
C: sulfate adenylyltransferase
hetero molecules

A: sulfate adenylyltransferase
B: sulfate adenylyltransferase
C: sulfate adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)387,41912
Polymers384,3756
Non-polymers3,0446
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
MethodPQS
2
A: sulfate adenylyltransferase
hetero molecules

B: sulfate adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,1404
Polymers128,1252
Non-polymers1,0152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area5480 Å2
ΔGint-29 kcal/mol
Surface area47830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.449, 135.449, 234.587
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe second part of the biological assembly is generated by the two fold axis:

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Components

#1: Protein sulfate adenylyltransferase / atp-sulfurylase / sulfate adenylate transferase / SAT


Mass: 64062.492 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium chrysogenum (fungus) / Plasmid: pET-23a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q12650, sulfate adenylyltransferase
#2: Chemical ChemComp-PPS / 3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE


Mass: 507.264 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O13P2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 3.23 Å3/Da / Density % sol: 61.93 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 8000, magnesium chloride, tris(hydroxymethyl)aminomethane, 3'-phosphoadenosine-5'-phosphosulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal
*PLUS
Density % sol: 67 %
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlATP sulfurylase1drop
25 mMPAPS1drop
30.2 mMEDTA1drop
410 mMTris1droppH8.0
510-14 %(w/v)PEG80001reservoir
6150-250 mM1reservoirMgCl2
7100 mMTris-HCl1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 77547 / Num. obs: 77547 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 63.2 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 3.6 / Num. unique all: 8436 / % possible all: 98.5
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 391636
Reflection shell
*PLUS
% possible obs: 98.5 % / Redundancy: 3.2 % / Num. unique obs: 8436 / Num. measured obs: 26754

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I2D

1i2d


Resolution: 2.6→29.33 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 186973.94 / Data cutoff high rms absF: 3186973.94 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 3968 5.2 %RANDOM
Rwork0.218 ---
all0.221 76621 --
obs0.218 76621 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.5433 Å2 / ksol: 0.318152 e/Å3
Displacement parametersBiso mean: 67 Å2
Baniso -1Baniso -2Baniso -3
1--14.53 Å20.77 Å20 Å2
2---14.53 Å20 Å2
3---29.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.6→29.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13503 0 93 458 14054
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d1.05
X-RAY DIFFRACTIONc_mcbond_it3.821.5
X-RAY DIFFRACTIONc_mcangle_it5.632
X-RAY DIFFRACTIONc_scbond_it5.812
X-RAY DIFFRACTIONc_scangle_it7.622.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.385 626 5 %
Rwork0.316 11960 -
obs--98.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_TOP
X-RAY DIFFRACTION3PAPS.PARPAPS.TOP
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.67
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.05

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