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- PDB-7clu: PigF with SAH -

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Basic information

Entry
Database: PDB / ID: 7clu
TitlePigF with SAH
ComponentsMethyltransferase domain-containing protein
KeywordsTRANSFERASE / prodigiosin / PigF / methyl-transferase / induce-fit
Function / homology
Function and homology information


O-methyltransferase activity / methylation
Similarity search - Function
Acetylserotonin O-methyltransferase, dimerisation domain / Dimerisation domain / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
ACETATE ION / Methyltransferase domain-containing protein
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsQiu, S. / Xu, D. / Han, N. / Sun, B. / Ran, T. / Wang, W.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770074 China
National Natural Science Foundation of China (NSFC)31770050 China
Citation
Journal: Iucrj / Year: 2022
Title: Crystal structures of PigF, an O-methyltransferase involved in the prodigiosin synthetic pathway, reveal an induced-fit substrate-recognition mechanism.
Authors: Qiu, S. / Xu, D. / Xu, M. / Zhou, H. / Sun, N. / Zhang, L. / Zhao, M. / He, J. / Ran, T. / Sun, B. / Wang, W.
#1: Journal: To Be Published
Title: structure of PigF at 1.9 A
Authors: Qiu, S. / Ran, T. / Xu, D. / Wang, W.
History
DepositionJul 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 29, 2024Group: Data collection / Derived calculations / Category: atom_type / chem_comp_atom / chem_comp_bond / Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyltransferase domain-containing protein
B: Methyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5734
Polymers77,4222
Non-polymers1512
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7430 Å2
ΔGint-60 kcal/mol
Surface area26640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.095, 52.358, 92.835
Angle α, β, γ (deg.)90.000, 97.352, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Methyltransferase domain-containing protein / Putative O-methyl transferase / SAM-dependent methyltransferase


Mass: 38710.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: pigF, AR325_07835, E4655_02280, FOT62_11605 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5W249
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.15 Å3/Da / Density % sol: 42.82 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→19.574 Å / Num. obs: 48615 / % possible obs: 93.6 % / Redundancy: 2.2 % / CC1/2: 0.996 / Rpim(I) all: 0.052 / Net I/σ(I): 7.9
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 2.1 % / Num. unique obs: 3366 / CC1/2: 0.506 / Rpim(I) all: 0.624

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→19.57 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / Cross valid method: FREE R-VALUE / ESU R: 0.184 / ESU R Free: 0.167
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.248 2408 4.955 %
Rwork0.2004 46194 -
all0.203 --
obs-48602 93.038 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 30.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.824 Å2-0 Å2-0.024 Å2
2--3.04 Å2-0 Å2
3----1.171 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4991 0 10 334 5335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0135114
X-RAY DIFFRACTIONr_bond_other_d0.0350.0174774
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.6356930
X-RAY DIFFRACTIONr_angle_other_deg2.2951.57411004
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5515637
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.45721.277282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.03315824
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4461542
X-RAY DIFFRACTIONr_chiral_restr0.1040.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025803
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021151
X-RAY DIFFRACTIONr_nbd_refined0.2170.21196
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2260.24669
X-RAY DIFFRACTIONr_nbtor_refined0.1880.22576
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.22504
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2220.2292
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.10.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1840.219
X-RAY DIFFRACTIONr_nbd_other0.2630.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1630.211
X-RAY DIFFRACTIONr_mcbond_it2.8723.2012558
X-RAY DIFFRACTIONr_mcbond_other2.873.22556
X-RAY DIFFRACTIONr_mcangle_it3.4374.7823191
X-RAY DIFFRACTIONr_mcangle_other3.4394.7823192
X-RAY DIFFRACTIONr_scbond_it3.4673.4162556
X-RAY DIFFRACTIONr_scbond_other3.4663.4162557
X-RAY DIFFRACTIONr_scangle_it4.3715.0223739
X-RAY DIFFRACTIONr_scangle_other4.375.0223740
X-RAY DIFFRACTIONr_lrange_it4.76538.3925988
X-RAY DIFFRACTIONr_lrange_other4.76538.395989
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.3271770.33499X-RAY DIFFRACTION96.2556
1.949-2.0030.3231950.2823415X-RAY DIFFRACTION96.2153
2.003-2.0610.3171750.2723302X-RAY DIFFRACTION95.8379
2.061-2.1240.3011680.253215X-RAY DIFFRACTION95.619
2.124-2.1940.3011410.2363097X-RAY DIFFRACTION94.9004
2.194-2.2710.2811800.2282988X-RAY DIFFRACTION94.7085
2.271-2.3560.3191130.232900X-RAY DIFFRACTION94.4218
2.356-2.4530.2821580.2342739X-RAY DIFFRACTION94.3034
2.453-2.5620.2721400.222662X-RAY DIFFRACTION94.2165
2.562-2.6860.2711340.212481X-RAY DIFFRACTION93.3929
2.686-2.8320.2571270.2042384X-RAY DIFFRACTION92.8624
2.832-3.0030.2241260.2022256X-RAY DIFFRACTION92.3256
3.003-3.210.2381140.1852086X-RAY DIFFRACTION91.6667
3.21-3.4670.263970.1881962X-RAY DIFFRACTION91.6741
3.467-3.7980.21880.1821763X-RAY DIFFRACTION89.1189
3.798-4.2450.212890.1541551X-RAY DIFFRACTION88.267
4.245-4.90.185700.151372X-RAY DIFFRACTION86.141
4.9-5.9970.185600.1881181X-RAY DIFFRACTION88.2646
5.997-8.4630.196380.184902X-RAY DIFFRACTION84.3049
8-100.318180.163439X-RAY DIFFRACTION70.5247

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