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

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Basic information

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


phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / identical protein binding
Similarity search - Function
Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / PKS_PP_betabranch / 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. ...Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / PKS_PP_betabranch / 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 / Acetyltransferase (GNAT) family / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Gcn5-related N-acetyltransferase (GNAT) / 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 / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Thiolase-like / Acyl-CoA N-acyltransferase / Phosphopantetheine attachment site / Aminopeptidase / 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
ACETYL COENZYME *A / CurA
Similarity search - Component
Biological speciesLyngbya majuscula (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.75 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CurA
B: CurA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4464
Polymers51,8272
Non-polymers1,6192
Water724
1
A: CurA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7232
Polymers25,9141
Non-polymers8101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CurA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7232
Polymers25,9141
Non-polymers8101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.886, 91.886, 139.486
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 4 / Auth seq-ID: 222 - 424 / Label seq-ID: 7 - 209

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
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-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.28 Å3/Da / Density % sol: 62.5 %
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 Å
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: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 2.75→46.5 Å / Num. all: 18214 / Num. obs: 18214 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.7 % / Biso Wilson estimate: 60.3 Å2 / Rmerge(I) obs: 0.094 / Χ2: 1.003 / Net I/σ(I): 10.6
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 4.9 / Num. unique all: 1800 / Χ2: 1.003 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
Blu-Icedata collection
PHASERphasing
RefinementStarting model: Apo CurA GNATL domain

Resolution: 2.75→46.5 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.891 / SU B: 23.383 / SU ML: 0.224 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.605 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 914 5 %RANDOM
Rwork0.207 ---
obs0.21 18190 99.8 %-
all-18193 --
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: 39.054 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20.07 Å20 Å2
2--0.13 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.75→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3310 0 102 4 3416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223591
X-RAY DIFFRACTIONr_angle_refined_deg1.3512.0234911
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.595421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38125.169178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.64515620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2161520
X-RAY DIFFRACTIONr_chiral_restr0.0930.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022699
X-RAY DIFFRACTIONr_nbd_refined0.2130.21376
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22448
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2103
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0980.23
X-RAY DIFFRACTIONr_mcbond_it0.3041.52138
X-RAY DIFFRACTIONr_mcangle_it0.56223368
X-RAY DIFFRACTIONr_scbond_it0.91531658
X-RAY DIFFRACTIONr_scangle_it1.5614.51534
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1612 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.340.5
MEDIUM THERMAL0.272
LS refinement shellResolution: 2.752→2.823 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 63 -
Rwork0.274 1244 -
all-1307 -
obs--98.49 %

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