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- PDB-5cb8: Crystal structure of Adenosine-5'-phosphosulfate kinase in comple... -

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Basic information

Entry
Database: PDB / ID: 5cb8
TitleCrystal structure of Adenosine-5'-phosphosulfate kinase in complex with APS and sulfate
ComponentsProbable adenylyl-sulfate kinase
KeywordsTRANSFERASE / Synechocystis / sulfur metabolism / kinase
Function / homology
Function and homology information


sulfate assimilation via adenylyl sulfate reduction / sulfate assimilation, phosphoadenylyl sulfate reduction by phosphoadenylyl-sulfate reductase (thioredoxin) / adenylyl-sulfate kinase / adenylylsulfate kinase activity / sulfate adenylyltransferase (ATP) activity / hydrogen sulfide biosynthetic process / phosphorylation / ATP binding
Similarity search - Function
Adenylylsulphate kinase / Adenylyl-sulfate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ADENOSINE-5'-PHOSPHOSULFATE / Probable adenylyl-sulfate kinase
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsHerrmann, J. / Jez, J.M.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Recapitulating the Structural Evolution of Redox Regulation in Adenosine 5'-Phosphosulfate Kinase from Cyanobacteria to Plants.
Authors: Herrmann, J. / Nathin, D. / Lee, S.G. / Sun, T. / Jez, J.M.
History
DepositionJun 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable adenylyl-sulfate kinase
B: Probable adenylyl-sulfate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,10310
Polymers43,7462
Non-polymers1,3578
Water10,034557
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-85 kcal/mol
Surface area15700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.756, 140.756, 140.756
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Probable adenylyl-sulfate kinase / APS kinase / ATP adenosine-5'-phosphosulfate 3'-phosphotransferase / Adenosine-5'-phosphosulfate kinase


Mass: 21872.799 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: cysC, slr0676 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P72940, adenylyl-sulfate kinase
#2: Chemical ChemComp-ADX / ADENOSINE-5'-PHOSPHOSULFATE


Type: RNA linking / Mass: 427.284 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O10PS
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 557 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 5 mM APS and 10 mM K2SO4 and mixed with 0.1 M CAPS/KOH, pH 10.5, 2 M ammonium sulfate, and 0.2 M LiSO4
PH range: 10.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.98 Å
DetectorType: SBC-3 / Detector: CCD / Date: Dec 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.88→31.5 Å / Num. all: 810057 / Num. obs: 37779 / % possible obs: 100 % / Redundancy: 21.4 % / Net I/σ(I): 50

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIX1.8.1_1168phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CB6

5cb6


Resolution: 1.88→31.474 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1757 1891 5.01 %
Rwork0.1551 --
obs0.1561 37755 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.88→31.474 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2742 0 82 557 3381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062925
X-RAY DIFFRACTIONf_angle_d1.0383986
X-RAY DIFFRACTIONf_dihedral_angle_d17.5721145
X-RAY DIFFRACTIONf_chiral_restr0.072456
X-RAY DIFFRACTIONf_plane_restr0.005505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8799-1.92690.24981380.19192556X-RAY DIFFRACTION100
1.9269-1.9790.20251230.17782563X-RAY DIFFRACTION100
1.979-2.03720.24871430.1652509X-RAY DIFFRACTION100
2.0372-2.1030.2211280.16392581X-RAY DIFFRACTION100
2.103-2.17810.20281430.16182513X-RAY DIFFRACTION100
2.1781-2.26530.20051530.15352521X-RAY DIFFRACTION100
2.2653-2.36840.19261450.16172527X-RAY DIFFRACTION100
2.3684-2.49320.17171240.15572573X-RAY DIFFRACTION100
2.4932-2.64930.17511270.15822571X-RAY DIFFRACTION100
2.6493-2.85380.18161350.15812543X-RAY DIFFRACTION100
2.8538-3.14070.19191260.15642568X-RAY DIFFRACTION100
3.1407-3.59460.14561370.14772582X-RAY DIFFRACTION100
3.5946-4.52670.13651320.12622592X-RAY DIFFRACTION100
4.5267-31.47840.16751370.17062665X-RAY DIFFRACTION100
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)
12.79671.0651-1.09991.5396-0.2561.8552-0.06070.0071-0.2481-0.10310.0337-0.41760.30080.43970.08630.2430.07460.020.2413-0.01660.192952.833621.84945.137
22.24620.9642-0.4311.199-0.32361.06870.0075-0.00510.1124-0.0056-0.0158-0.05430.04920.08690.02060.1690.017-0.01320.1475-0.01040.142245.88831.589512.4075
31.29240.8226-0.53241.1806-0.30371.7569-0.12210.098-0.0785-0.2340.0659-0.06610.23030.00650.04050.24180.0124-0.00760.1532-0.00810.135440.08818.40625.57
41.8673-0.1009-1.071.38330.69852.8666-0.00090.44650.292-0.40860.0389-0.1604-0.17320.0295-0.11820.1983-0.01970.03530.25710.07930.263765.587448.171317.099
51.2259-0.3292-0.22181.05931.08422.40830.00770.07740.0728-0.05330.0044-0.05630.1271-0.0071-0.01330.1487-0.0058-0.00860.13740.01720.172558.001838.840224.4345
61.6798-0.2486-0.45561.16950.84361.27820.03740.00410.2465-0.06160.0764-0.2441-0.0890.1263-0.07920.1359-0.0155-0.00330.15510.01230.245664.831351.942530.1603
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 3:35
2X-RAY DIFFRACTION2chain A and resid 36:103
3X-RAY DIFFRACTION3chain A and resid 104:176
4X-RAY DIFFRACTION4chain B and resid 2:35
5X-RAY DIFFRACTION5chain B and resid 36:103
6X-RAY DIFFRACTION6chain B and resid 104:177

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