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- PDB-3v7i: Germicidin synthase (Gcs) from Streptomyces coelicolor, a type II... -

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Basic information

Entry
Database: PDB / ID: 3v7i
TitleGermicidin synthase (Gcs) from Streptomyces coelicolor, a type III polyketide synthase
ComponentsPutative polyketide synthase
KeywordsTRANSFERASE / LYASE / type III polyketide synthase / acyltransferase
Function / homology
Function and homology information


polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Chalcone/stilbene synthase, N-terminal / Chalcone and stilbene synthases, N-terminal domain / Polyketide synthase, type III / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsAkey, D.L. / Smith, J.L. / Geders, T.W.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Biochemical and Structural Characterization of Germicidin Synthase: Analysis of a Type III Polyketide Synthase That Employs Acyl-ACP as a Starter Unit Donor.
Authors: Chemler, J.A. / Buchholz, T.J. / Geders, T.W. / Akey, D.L. / Rath, C.M. / Chlipala, G.E. / Smith, J.L. / Sherman, D.H.
History
DepositionDec 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative polyketide synthase


Theoretical massNumber of molelcules
Total (without water)44,4891
Polymers44,4891
Non-polymers00
Water43224
1
A: Putative polyketide synthase

A: Putative polyketide synthase


Theoretical massNumber of molelcules
Total (without water)88,9782
Polymers88,9782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation13_455y-1/4,x+1/4,-z+1/41
Buried area4470 Å2
ΔGint-22 kcal/mol
Surface area29040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.703, 182.703, 182.703
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-409-

HOH

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Components

#1: Protein Putative polyketide synthase


Mass: 44488.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: SCO7221 / Plasmid: pDHS100019 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9K464
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 5.71 Å3/Da / Density % sol: 78.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 21-25% isopropanol, 400 mM ammonium acetate, 0.1 M Tris buffer pH 8.5-9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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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: Aug 2, 2007
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: 2.9→50 Å / Num. all: 23726 / Num. obs: 23694 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Biso Wilson estimate: 91.6 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Χ2: 0.93 / Net I/σ(I): 11.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.9-311.10.57823010.8591100
3-3.1211.10.38623040.8651100
3.12-3.27110.27223350.9061100
3.27-3.44110.17923251.0191100
3.44-3.65110.12523361.071100
3.65-3.9410.90.08923350.91100
3.94-4.3310.90.06423740.8541100
4.33-4.9610.80.07523821.3241100
4.96-6.2410.60.05824200.9651100
6.24-509.80.0325820.528199.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→39.869 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7844 / SU ML: 0.34 / σ(F): 1.06 / Phase error: 27.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2528 1203 5.11 %RANDOM
Rwork0.2292 ---
all0.2304 23726 --
obs0.2304 23545 99.51 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.143 Å2 / ksol: 0.303 e/Å3
Displacement parametersBiso max: 509.39 Å2 / Biso mean: 116.7301 Å2 / Biso min: 37.06 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.9→39.869 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2854 0 0 24 2878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032918
X-RAY DIFFRACTIONf_angle_d0.6773998
X-RAY DIFFRACTIONf_chiral_restr0.044460
X-RAY DIFFRACTIONf_plane_restr0.003528
X-RAY DIFFRACTIONf_dihedral_angle_d15.0041020
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-3.01650.38021260.32522405253199
3.0165-3.15370.35571360.3072434257099
3.1537-3.31990.30181350.28642430256599
3.3199-3.52780.2871230.247524332556100
3.5278-3.80.30051310.242624742605100
3.8-4.1820.2651320.215524672599100
4.182-4.78630.22621390.19224822621100
4.7863-6.02690.22721360.198925332669100
6.0269-39.87280.20471450.21512684282999
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)
12.5479-1.4111.24571.6697-0.68881.19681.12890.8147-1.3219-0.6396-0.81970.630.49570.2392-0.36790.58350.3975-0.34340.6569-0.46730.9135-9.298833.9590.732
26.05023.07-1.37212.27130.64692.8515-1.00450.0894-2.27580.2439-0.25290.4650.86430.03081.22341.3452-0.02040.42930.1709-0.17152.6392-25.754511.346124.4426
32.8629-2.40180.49382.8591-0.19040.92290.50170.6742-0.3717-0.2501-0.61980.3390.12650.12350.12910.1990.1863-0.01940.3977-0.10690.45230.210947.143410.7373
42.6472-2.10370.78743.0841-0.63720.34281.0971.6109-0.0005-0.9288-1.19340.15570.1130.59150.06750.62840.5376-0.0261.210.00740.51873.695652.05020.2385
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:65)A1 - 65
2X-RAY DIFFRACTION2(chain A and resid 66:95)A66 - 95
3X-RAY DIFFRACTION3(chain A and resid 96:329)A96 - 329
4X-RAY DIFFRACTION4(chain A and resid 330:389)A330 - 389

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