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- PDB-4gbm: Sulfotransferase Domain from the Curacin Biosynthetic Pathway -

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Basic information

Entry
Database: PDB / ID: 4gbm
TitleSulfotransferase Domain from the Curacin Biosynthetic Pathway
ComponentsCurM Sulfotransferase
KeywordsTRANSFERASE / sulfotransferase / polyketide synthase / curacin / PAP / PAPS
Function / homology
Function and homology information


phosphopantetheine binding / transferase activity / metal ion binding
Similarity search - Function
Sulfotransferase family / : / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain ...Sulfotransferase family / : / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Epoxide hydrolase-like / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / 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 / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Thiolase-like / 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 / CurM
Similarity search - Component
Biological speciesMoorea producta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.62 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
DepositionJul 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: CurM Sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,14219
Polymers36,4081
Non-polymers1,73418
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.856, 67.299, 118.016
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CurM Sulfotransferase


Mass: 36408.340 Da / Num. of mol.: 1 / Fragment: Sulfotransferase domain (UNP residues 1598-1917) / Mutation: Q259A, K260A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moorea producta (bacteria)
Description: The original name of the organism was Lyngbya majuscula which was initially named Moorea producta but has been changed to Moorea producens
Gene: CurM / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F4Y423

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Non-polymers , 6 types, 383 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE / Adenosine 3',5'-bisphosphate


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.5 Å3/Da / Density % sol: 50.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25-31% PEG MME 550, 2.5-12.5 mM ZnSO4, 100 mM MES, pH 6.5, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 1, 2010
Details: K-B PAIR OF BIOMORPH MIRRORS FOR VERTICAL AND HORIZONTAL FOCUSING
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. obs: 46830 / % possible obs: 98.5 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.074 / Χ2: 1.033 / Net I/σ(I): 16.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.62-1.685.90.37541981.007189.6
1.68-1.756.20.27846271.025198.6
1.75-1.826.30.2146211.016198.8
1.82-1.926.40.15646431.031198.9
1.92-2.046.50.11646951.024199.6
2.04-2.26.70.09746961.101199.6
2.2-2.426.80.07947471.046199.8
2.42-2.777.10.06947391.0211100
2.77-3.497.30.06348331.111100
3.49-5070.05250310.944199.7

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.12 Å / D res low: 38.04 Å / FOM : 0.487 / FOM acentric: 0.547 / FOM centric: 0.128 / Reflection: 21605 / Reflection acentric: 18570 / Reflection centric: 2794
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
9.53-13.070.3780.5410.10816810563
7.86-9.530.4420.5740.14820614264
6.85-7.860.5010.6310.15623417064
6.14-6.850.5390.6540.19926519867
5.62-6.140.5360.6450.16729022466
5.21-5.620.5340.6340.1430624462
4.88-5.210.470.5620.12333126269
4.61-4.880.4780.560.10734328162
4.37-4.610.4590.5420.11337930673
4.17-4.370.4790.550.11337631561
4-4.170.480.5520.10840033565
3.84-40.5010.5820.08840133566
3.7-3.840.5060.5840.10443836771
3.58-3.70.5150.5820.10142636759
3.47-3.580.510.5850.10447940574
3.36-3.470.5290.5940.11346840563
3.27-3.360.4990.5590.10147241062
3.18-3.270.5130.5740.14150643571
3.1-3.180.5260.580.13549943960
3.03-3.10.530.5980.10852745471
2.96-3.030.5350.5890.12553847563
2.89-2.960.5430.6030.14753146266
2.83-2.890.5210.5710.16555548669
2.78-2.830.5190.5790.10658751471
2.72-2.780.5320.5830.11354548657
2.67-2.720.540.5970.14260553072
2.63-2.670.5360.5850.12559753460
2.58-2.630.5150.5670.12759352562
2.54-2.580.5050.5560.13762354968
2.5-2.540.4940.5380.16462054965
2.46-2.50.5160.5650.12364657565
2.42-2.460.4980.5440.15361754856
2.38-2.420.4720.5230.12367659178
2.35-2.380.4870.5340.166059059
2.32-2.350.4540.4980.16366157965
2.28-2.320.450.4930.12267359961
2.25-2.280.4290.4730.12570562068
2.23-2.250.420.4610.13469060964
2.2-2.230.4380.4780.1167360354
2.17-2.20.4220.4750.13475364575
2.15-2.170.4170.4620.13171762565
2.12-2.150.4170.4620.13171262457
Phasing dmFOM : 0.77 / FOM acentric: 0.79 / FOM centric: 0.63 / Reflection: 21610 / Reflection acentric: 18816 / Reflection centric: 2794
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.1-38.040.890.930.81033705328
3.8-6.10.910.940.7929602417543
3-3.80.880.90.7336403137503
2.7-30.80.830.5636373213424
2.3-2.70.710.730.4963965751645
2.1-2.30.590.610.439443593351

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RESOLVE2.15phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.62→36.34 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.1997 / WRfactor Rwork: 0.171 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.9065 / SU B: 2.123 / SU ML: 0.043 / SU R Cruickshank DPI: 0.0788 / SU Rfree: 0.0781 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.182 4316 9.2 %RANDOM
Rwork0.1578 ---
obs0.16 46772 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 117.24 Å2 / Biso mean: 19.4813 Å2 / Biso min: 5.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.13 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.62→36.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2275 0 83 365 2723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222468
X-RAY DIFFRACTIONr_angle_refined_deg1.1282.0113327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6935301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20224.602113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7515444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8641516
X-RAY DIFFRACTIONr_chiral_restr0.0710.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211821
X-RAY DIFFRACTIONr_mcbond_it0.7841.51451
X-RAY DIFFRACTIONr_mcangle_it1.44622367
X-RAY DIFFRACTIONr_scbond_it2.59931017
X-RAY DIFFRACTIONr_scangle_it4.0944.5950
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 306 -
Rwork0.213 2899 -
all-3205 -
obs--92.95 %
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)
11.05910.14080.57130.81860.06871.13080.0223-0.07680.06210.1065-0.0482-0.0658-0.00910.0640.02580.0488-0.0033-0.0060.0468-0.01110.075541.28719.00243.317
23.0621.99430.89771.14630.9473.3920.0568-0.38530.03790.0658-0.10640.13320.2097-0.17140.04960.2773-0.0343-0.00970.25940.01430.145936.54918.46456.753
31.04230.23740.67880.63580.27251.08060.035-0.11680.06650.1048-0.0170.0043-0.0116-0.0027-0.01810.0768-0.0011-0.0030.0534-0.00930.097239.44322.82545.186
413.15024.9818-3.533632.4205-4.510311.21220.4061-0.02991.2441.0021-0.04191.7743-0.9605-0.6548-0.36410.26290.07540.12980.2325-0.03230.386717.41926.0842.186
50.7904-0.0950.09050.9671-0.13710.55520.01320.0727-0.0057-0.0786-0.0095-0.04450.03980.0486-0.00360.05920.00070.00160.0546-0.00520.095538.18817.21831.051
60.9367-0.4811-0.02961.7648-0.20470.51140.0366-0.0007-0.0191-0.0794-0.05080.140.0805-0.0310.01420.0531-0.0102-0.02710.0482-0.0250.107826.06115.26532.509
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 68
2X-RAY DIFFRACTION2A69 - 97
3X-RAY DIFFRACTION3A98 - 173
4X-RAY DIFFRACTION4A174 - 184
5X-RAY DIFFRACTION5A185 - 249
6X-RAY DIFFRACTION6A250 - 308

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