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- PDB-6lcn: Crystal structure of Serine Acetyltransferase from Planctomyces l... -

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Basic information

Entry
Database: PDB / ID: 6lcn
TitleCrystal structure of Serine Acetyltransferase from Planctomyces limnophilus at 2.15A
ComponentsSerine O-acetyltransferase
KeywordsTRANSFERASE / PSI-Biology / IFN / Structural Genomics
Function / homologySerine acetyltransferase, N-terminal domain superfamily / Serine acetyltransferase, LbH domain / serine O-acetyltransferase / serine O-acetyltransferase activity / Trimeric LpxA-like superfamily / DI(HYDROXYETHYL)ETHER / Serine O-acetyltransferase
Function and homology information
Biological speciesPlanctopirus limnophila DSM 3776 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsKumar, N. / Singh, R.P. / Singh, A.K. / Kumaran, S.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Health & Human Services (HHS)No.3/1/3/JRF-2015/HRD-LS/48/30922/131 India
Council of Scientific & Industrial Research India
CitationJournal: To Be Published
Title: Understanding Mechanics of competitive-allostery Using Engineered Cysteine Synthase Assembly
Authors: Kumar, N. / Singh, R.P. / Kumaran, S.
History
DepositionNov 19, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.2Nov 22, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine O-acetyltransferase
B: Serine O-acetyltransferase
C: Serine O-acetyltransferase
D: Serine O-acetyltransferase
E: Serine O-acetyltransferase
F: Serine O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,24119
Polymers221,1586
Non-polymers1,08313
Water13,799766
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39100 Å2
ΔGint-198 kcal/mol
Surface area63880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.719, 113.165, 230.133
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Serine O-acetyltransferase


Mass: 36859.645 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Planctopirus limnophila DSM 3776 (bacteria)
Strain: DSM 3776 / Gene: Plim_1307 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D5SUT9, serine O-acetyltransferase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 766 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.71 Å3/Da / Density % sol: 54.56 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M MES pH=6.5, 12% w/v PEG 20,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5417 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2.15→47.596 Å / Num. obs: 120745 / % possible obs: 99.64 % / Redundancy: 4.7 % / Biso Wilson estimate: 32.4 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.09531 / Rpim(I) all: 0.04956 / Rrim(I) all: 0.1078 / Net I/σ(I): 14.44
Reflection shellResolution: 2.15→2.227 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.742 / Num. unique obs: 11863 / CC1/2: 0.658 / Rpim(I) all: 0.3909 / Rrim(I) all: 0.8414 / % possible all: 99.23

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PHENIX1.17.1-366refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F1X

3f1x


Resolution: 2.15→47.596 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.78 / SU ML: 0.143 / Cross valid method: FREE R-VALUE / ESU R: 0.204 / ESU R Free: 0.172
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.223 1990 1.652 %
Rwork0.1866 --
all0.187 --
obs-120491 99.694 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.87 Å2
Baniso -1Baniso -2Baniso -3
1-1.514 Å20 Å20 Å2
2--0.095 Å20 Å2
3----1.609 Å2
Refinement stepCycle: LAST / Resolution: 2.15→47.596 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14076 0 67 766 14909
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01214539
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.63519791
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5251794
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.36720.844794
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.521152292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.61915118
X-RAY DIFFRACTIONr_chiral_restr0.1070.21939
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211190
X-RAY DIFFRACTIONr_nbd_refined0.2120.27155
X-RAY DIFFRACTIONr_nbtor_refined0.3090.29869
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2822
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2090.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.150.29
X-RAY DIFFRACTIONr_mcbond_it3.1483.6547191
X-RAY DIFFRACTIONr_mcangle_it4.6365.4478968
X-RAY DIFFRACTIONr_scbond_it4.3914.0737348
X-RAY DIFFRACTIONr_scangle_it6.2485.92910819
X-RAY DIFFRACTIONr_lrange_it9.10968.32761064
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.15-2.2060.3011430.28285870.28388050.7910.899.14820.273
2.206-2.2660.2891440.25884780.25886240.8230.83599.97680.244
2.266-2.3320.2661380.24782130.24883550.8510.85399.95210.228
2.332-2.4040.2661340.22580120.22681480.8930.89199.97550.204
2.404-2.4820.2371310.21377640.21478950.9150.9051000.188
2.482-2.5690.2271270.21975280.2276580.9080.89999.96080.192
2.569-2.6660.2681220.2172330.21173580.9030.9199.95920.181
2.666-2.7740.2541180.20469960.20571160.9080.91999.97190.175
2.774-2.8970.2341120.18766980.18868150.9210.93499.92660.158
2.897-3.0380.2141080.17664460.17765620.9460.94999.87810.147
3.038-3.2020.2071030.17160980.17162040.9380.95599.95160.147
3.202-3.3950.209980.17358190.17459250.9450.95399.8650.153
3.395-3.6280.217920.16854570.16955570.9460.9699.8560.153
3.628-3.9170.218840.17251040.17352080.9480.95999.6160.158
3.917-4.2880.178790.14946940.14947990.9620.9799.45820.138
4.288-4.7890.216710.14742430.14943440.9530.97199.30940.142
4.789-5.520.181640.16438120.16538930.9620.96399.56330.159
5.52-6.7380.221530.21732710.21733300.9480.95499.81980.2
6.738-9.4350.204430.16125810.16226380.9660.97299.46930.163
9.435-47.5960.198260.1814570.18115840.9420.96593.62370.205

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