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- PDB-2ree: Crystal structure of the loading GNATL domain of CurA from Lyngby... -

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Basic information

Entry
Database: PDB / ID: 2ree
TitleCrystal structure of the loading GNATL domain of CurA from Lyngbya majuscula
ComponentsCurA
KeywordsTRANSFERASE / LYASE / GNAT / CURACIN / S-ACETYLTRANSFERASE / DECARBOXYLASE / POLYKETIDE SYNTHASE / LOADING / Phosphopantetheine
Function / homology
Function and homology information


DIM/DIP cell wall layer assembly / secondary metabolite biosynthetic process / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / identical protein binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / PKS_PP_betabranch / : / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain ...Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / PKS_PP_betabranch / : / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Acetyltransferase (GNAT) family / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Gcn5-related N-acetyltransferase (GNAT) / 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 / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Thiolase-like / Acyl-CoA N-acyltransferase / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Aminopeptidase / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesLyngbya majuscula (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsGeders, T.W. / Smith, J.L.
CitationJournal: Science / Year: 2007
Title: GNAT-like strategy for polyketide chain initiation.
Authors: Gu, L. / Geders, T.W. / Wang, B. / Gerwick, W.H. / Hakansson, K. / Smith, J.L. / Sherman, D.H.
History
DepositionSep 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 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: CurA
B: CurA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2397
Polymers51,8272
Non-polymers4125
Water8,233457
1
A: CurA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1374
Polymers25,9141
Non-polymers2243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CurA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1023
Polymers25,9141
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.463, 91.463, 138.877
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a monomer and two monomers are present within the asymmetric unit.

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Components

#1: Protein CurA


Mass: 25913.566 Da / Num. of mol.: 2 / Fragment: GNATL loading domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lyngbya majuscula (bacteria) / Strain: 19L / Gene: curA / Plasmid: pMCSG7::GNATL / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q6DNF2, [acyl-carrier-protein] S-acetyltransferase, malonyl-CoA decarboxylase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / 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: 3.24 Å3/Da / Density % sol: 61.98 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: Mother liquor: 100 mM Bis-Tris pH 6.8, 100 mM NaCl, 1.5 M ammonium sulfate, 20% glycerol. Protein buffer: 20 mM Tris pH 7.9, 500 mM NaCl, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97939, 0.97934, 0.97945, 0.96112
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 6, 2006
Details: K-B pair of biomorph mirrors for vertical and horizontal focusing
RadiationMonochromator: double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979391
20.979341
30.979451
40.961121
ReflectionRedundancy: 2.9 % / Av σ(I) over netI: 10.8 / Number: 335880 / Rmerge(I) obs: 0.072 / Χ2: 1.01 / D res high: 2.3 Å / D res low: 50 Å / Num. obs: 114644 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.955099.910.0251.0143
3.934.9510010.0381.023
3.443.9310010.0471.023
3.123.4410010.0721.0112.9
2.93.1210010.1281.0092.9
2.732.910010.1950.9962.9
2.592.7310010.27512.9
2.482.5910010.3681.0132.9
2.382.4810010.4911.0222.9
2.32.3810010.6551.0352.9
ReflectionResolution: 1.95→43.4 Å / Num. all: 49722 / Num. obs: 49722 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 11.2 % / Biso Wilson estimate: 31.6 Å2 / Rmerge(I) obs: 0.069 / Χ2: 1.004 / Net I/σ(I): 13.7
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 4.97 / Num. unique all: 4850 / Χ2: 0.968 / % possible all: 99.2

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Phasing

PhasingMethod: MAD
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se43.020.4770.7040.0421.314
2Se46.6480.2060.7330.1241.146
3Se51.3850.0220.4790.0381.156
4Se600.4480.470.1361.216
5Se600.7530.5550.1561.1
6Se49.0430.7560.5220.0230.793
Phasing dmFOM : 0.66 / FOM acentric: 0.66 / FOM centric: 0.68 / Reflection: 30302 / Reflection acentric: 27116 / Reflection centric: 3186
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.6-43.4960.970.980.9514131038375
4.1-6.60.950.960.941373521616
3.3-4.10.90.90.8450774517560
2.9-3.30.770.770.750914606485
2.5-2.90.520.520.4690278280747
2.3-2.50.310.310.2755575154403

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.1phasing
RESOLVE2.1phasing
REFMACrefinement
PDB_EXTRACT3data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MAD / Resolution: 1.95→43.4 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.867 / SU ML: 0.077 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.211 2491 5 %RANDOM
Rwork0.172 ---
obs0.174 49433 99.64 %-
all-58354 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.329 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å20.78 Å20 Å2
2--1.55 Å20 Å2
3----2.33 Å2
Refinement stepCycle: LAST / Resolution: 1.95→43.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3242 0 23 457 3722
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223548
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.9844847
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5155447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.80225.191183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43415651
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1151522
X-RAY DIFFRACTIONr_chiral_restr0.1030.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022722
X-RAY DIFFRACTIONr_nbd_refined0.2060.21523
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22390
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2350
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.229
X-RAY DIFFRACTIONr_mcbond_it1.01422201
X-RAY DIFFRACTIONr_mcangle_it1.67333458
X-RAY DIFFRACTIONr_scbond_it5.184101540
X-RAY DIFFRACTIONr_scangle_it7.284151372
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 174 -
Rwork0.204 3422 -
all-3596 -
obs--99.39 %

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