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- PDB-3cr8: Hexameric APS kinase from Thiobacillus denitrificans -

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Basic information

Entry
Database: PDB / ID: 3cr8
TitleHexameric APS kinase from Thiobacillus denitrificans
ComponentsSulfate adenylyltransferase, adenylylsulfate kinase
KeywordsTRANSFERASE / APS kinase / Adenylylsulfate kinase / sulfate metabolism / Nucleotide 2 kinase / Nucleotidyltransferase
Function / homology
Function and homology information


adenylyl-sulfate kinase / adenylylsulfate kinase activity / sulfate adenylyltransferase (ATP) activity / sulfate assimilation / hydrogen sulfide biosynthetic process / ATP binding
Similarity search - Function
Sulfate adenylyltransferase / Sulfate adenylyltransferase / Sulphate adenylyltransferase catalytic domain / ATP-sulfurylase PUA-like domain / ATP-sulfurylase / PUA-like domain / Adenylylsulphate kinase / Adenylyl-sulfate kinase / PUA-like superfamily / HUPs ...Sulfate adenylyltransferase / Sulfate 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
Adenylyl-sulfate kinase
Similarity search - Component
Biological speciesThiobacillus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.95 Å
AuthorsGay, S.C. / Segel, I.H. / Fisher, A.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structure of the two-domain hexameric APS kinase from Thiobacillus denitrificans: structural basis for the absence of ATP sulfurylase activity.
Authors: Gay, S.C. / Segel, I.H. / Fisher, A.J.
History
DepositionApr 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sulfate adenylyltransferase, adenylylsulfate kinase
B: Sulfate adenylyltransferase, adenylylsulfate kinase
C: Sulfate adenylyltransferase, adenylylsulfate kinase


Theoretical massNumber of molelcules
Total (without water)184,9153
Polymers184,9153
Non-polymers00
Water1,54986
1
A: Sulfate adenylyltransferase, adenylylsulfate kinase
B: Sulfate adenylyltransferase, adenylylsulfate kinase
C: Sulfate adenylyltransferase, adenylylsulfate kinase

A: Sulfate adenylyltransferase, adenylylsulfate kinase
B: Sulfate adenylyltransferase, adenylylsulfate kinase
C: Sulfate adenylyltransferase, adenylylsulfate kinase


Theoretical massNumber of molelcules
Total (without water)369,8306
Polymers369,8306
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area21000 Å2
ΔGint-75 kcal/mol
Surface area120270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.071, 227.211, 106.766
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-564-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21B
31B
41B
51C
61C
71C
81C

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNASPASPBB4 - 2034 - 203
22GLUGLUALAALABB206 - 263206 - 263
33SERSERSERSERBB288 - 378288 - 378
44GLYGLYTHRTHRBB381 - 477381 - 477
51LEULEUASPASPCC5 - 2035 - 203
62GLUGLUALAALACC206 - 263206 - 263
73SERSERSERSERCC288 - 378288 - 378
84GLYGLYTHRTHRCC381 - 477381 - 477

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Components

#1: Protein Sulfate adenylyltransferase, adenylylsulfate kinase /


Mass: 61638.320 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thiobacillus denitrificans (bacteria) / Strain: ATCC 25259 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q3SM86, sulfate adenylyltransferase, adenylyl-sulfate kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.64 Å3/Da / Density % sol: 53.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: K/Na Tartrate, NaCl, Bis Tris Propane, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 28, 2007 / Details: double crystal monochromator
RadiationMonochromator: Double Si(111) crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. all: 3317 / Num. obs: 38467 / % possible obs: 92.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3 % / Rmerge(I) obs: 0.107 / Χ2: 1.084 / Net I/σ(I): 7.3
Reflection shellResolution: 2.95→3.06 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.357 / Num. unique all: 3925 / Χ2: 0.818 / % possible all: 95.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Translation4 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1I2D

1i2d


Resolution: 2.95→35.028 Å / Isotropic thermal model: isotropic / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1889 4.93 %random
Rwork0.243 ---
all0.246 3925 --
obs0.245 38315 92.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 19.07 Å2 / Biso mean: 60.52 Å2 / Biso min: 139.13 Å2
Baniso -1Baniso -2Baniso -3
1--12.772 Å2-0 Å20 Å2
2---11.034 Å20 Å2
3---23.806 Å2
Refinement stepCycle: LAST / Resolution: 2.95→35.028 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11253 0 0 86 11339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01411358
X-RAY DIFFRACTIONf_angle_d1.86715336
X-RAY DIFFRACTIONf_chiral_restr0.1171775
X-RAY DIFFRACTIONf_plane_restr0.0081967
X-RAY DIFFRACTIONf_dihedral_angle_d20.3324098
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B3636X-RAY DIFFRACTIONPOSITIONAL0.418
15C3589X-RAY DIFFRACTIONPOSITIONAL0.486
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.95-3.030.3961550.3212895305096
3.03-3.1190.3681340.2752863299796
3.119-3.2190.2911470.2612895304296
3.219-3.3340.371350.2622890302596
3.334-3.4680.2961490.2542882303196
3.468-3.6250.3011630.2512829299294
3.625-3.8160.2431580.242869302795
3.816-4.0550.2511430.2242602274587
4.055-4.3680.2631150.2332250236581
4.368-4.8060.231390.1822918305795
4.806-5.4990.2191520.1912893304595
5.499-6.920.2951510.2312923307494
6.92-35.0310.2741480.2572717286585

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