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- PDB-4gox: Sulfotransferase Domain from the Synechococcus PCC 7002 Olefin Sy... -

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Basic information

Entry
Database: PDB / ID: 4gox
TitleSulfotransferase Domain from the Synechococcus PCC 7002 Olefin Synthase
ComponentsPolyketide synthase
KeywordsTRANSFERASE / olefin synthase / polyketide synthase / hydrocarbon / sulfotransferase / PAPS / PAP / 3'phosphoadenosine-5'phosphosulfate
Function / homology
Function and homology information


: / DIM/DIP cell wall layer assembly / fatty acid synthase activity / secondary metabolite biosynthetic process / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / nucleotide binding / plasma membrane / cytoplasm
Similarity search - Function
Sulfotransferase family / Fatty acyl-AMP ligase /fatty acyl-CoA ligase / PKS_PP_betabranch / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / ANL, N-terminal domain / PKS_KR / Acyl transferase domain superfamily ...Sulfotransferase family / Fatty acyl-AMP ligase /fatty acyl-CoA ligase / PKS_PP_betabranch / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / ANL, N-terminal domain / PKS_KR / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / AMP-binding, conserved site / Putative AMP-binding domain signature. / Epoxide hydrolase-like / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold / P-loop containing nucleotide triphosphate hydrolases / NAD(P)-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-3'-5'-DIPHOSPHATE / Polyketide synthase
Similarity search - Component
Biological speciesSynechococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMcCarthy, J.G. / Smith, J.L.
CitationJournal: Acs Chem.Biol. / Year: 2012
Title: Structural basis of functional group activation by sulfotransferases in complex metabolic pathways.
Authors: McCarthy, J.G. / Eisman, E.B. / Kulkarni, S. / Gerwick, L. / Gerwick, W.H. / Wipf, P. / Sherman, D.H. / Smith, J.L.
History
DepositionAug 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8622
Polymers35,4351
Non-polymers4271
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)131.440, 131.440, 47.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Polyketide synthase / OLS Sulfotransferase


Mass: 35435.004 Da / Num. of mol.: 1 / Fragment: sulfotransferase domain (UNP residues 2121-2430)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. (bacteria) / Strain: ATCC 27264 / PCC 7002 / PR-6 / Gene: SYNPCC7002_A1173 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1XKC6
#2: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.87 Å3/Da / Density % sol: 57.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 27-30% PEG1500, 100 mM MMT buffer (DL-malic acid, MES, Tris), pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 15, 2010
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 23099 / Num. obs: 23099 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 46.6 Å2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allDiffraction-ID% possible all
2.15-2.237.50.63322481100
2.23-2.327.60.45222641100
2.32-2.427.70.31422571100
2.42-2.557.80.21522901100
2.55-2.7180.15822821100
2.71-2.928.10.12522981100
2.92-3.218.40.09623011100
3.21-3.688.70.05823391100
3.68-4.638.70.05323431100
4.63-5080.0352477198.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
BUSTER2.10.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→33.07 Å / Cor.coef. Fo:Fc: 0.9593 / Cor.coef. Fo:Fc free: 0.9469 / SU R Cruickshank DPI: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2197 1190 5.18 %RANDOM
Rwork0.1882 ---
all0.1898 22991 --
obs0.1898 22991 99.85 %-
Displacement parametersBiso mean: 61.51 Å2
Baniso -1Baniso -2Baniso -3
1--1.8601 Å20 Å20 Å2
2---1.8601 Å20 Å2
3---3.7203 Å2
Refine analyzeLuzzati coordinate error obs: 0.391 Å
Refinement stepCycle: LAST / Resolution: 2.15→33.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2211 0 27 96 2334
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d791SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes61HARMONIC2
X-RAY DIFFRACTIONt_gen_planes324HARMONIC5
X-RAY DIFFRACTIONt_it2293HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion295SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2720SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2293HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3125HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion18.12
LS refinement shellResolution: 2.15→2.25 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2392 145 5.27 %
Rwork0.2196 2605 -
all0.2207 2750 -
obs--99.85 %
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)
13.0945-1.3625-0.67913.056-0.1682.9468-0.2626-0.24990.23690.1950.1730.179-0.0509-0.54420.0896-0.0960.152-0.02880.08540.0119-0.2038-49.849-17.9881-0.5456
22.6225-2.9104-2.9092.5782.91040.33260.05710.04890.27370.16850.0603-0.1664-0.3677-0.0257-0.11740.03020.152-0.01060.01820.03240.1089-47.3532-5.54364.1241
35.6464-2.9104-2.91047.42942.91042.99420.0429-0.03990.50540.28480.30830.508-0.4269-0.5442-0.3512-0.20040.1520.05210.22150.0517-0.1743-58.8472-8.9074.4186
43.6282-0.8356-0.892.7535-0.34125.3264-0.2003-0.1270.0064-0.03610.14720.16220.3779-0.54420.0531-0.09590.1386-0.01240.03810.0282-0.2043-47.5225-22.3052-2.5286
50.08772.91040.78841.8465-2.91040.3204-0.00970.04790.2439-0.0058-0.013-0.2037-0.1240.26230.02270.00130.0729-0.03390.01660.1520.2182-26.9587-10.9835-7.4865
64.521-1.62291.21722.9899-1.23425.564-0.04880.54420.2581-0.4719-0.1332-0.31030.18790.00440.182-0.04580.1520.0364-0.08780.0363-0.2535-38.5761-20.2532-13.9634
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|18 - 73}A18 - 73
2X-RAY DIFFRACTION2{A|74 - 87}A74 - 87
3X-RAY DIFFRACTION3{A|88 - 123}A88 - 123
4X-RAY DIFFRACTION4{A|124 - 163}A124 - 163
5X-RAY DIFFRACTION5{A|164 - 188}A164 - 188
6X-RAY DIFFRACTION6{A|189 - 308}A189 - 308

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