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- PDB-3gwm: Crystal structure of the holo-[Acyl-Carrier-Protein] Synthase (AC... -

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Basic information

Entry
Database: PDB / ID: 3gwm
TitleCrystal structure of the holo-[Acyl-Carrier-Protein] Synthase (ACPS) from Mycobacterium smegmatis
ComponentsHolo-[acyl-carrier-protein] synthase
KeywordsTRANSFERASE / Homo-trimer / 9-stand pseudo beta barrel protein / Cytoplasm / Fatty acid biosynthesis / Lipid synthesis / Magnesium / Metal-binding
Function / homology
Function and homology information


holo-[acyl-carrier-protein] synthase / holo-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / magnesium ion binding / cytoplasm
Similarity search - Function
4'-phosphopantetheinyl transferase domain / Holo-[acyl carrier protein] synthase / Phosphopantetheine-protein transferase domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / Ribosomal Protein L22; Chain A / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Holo-[acyl-carrier-protein] synthase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.7 Å
AuthorsPoulsen, C. / Wilmanns, M. / Song, Y.H.
CitationJournal: To be Published
Title: Structure of the holo-[Acyl-Carrier-Protein] Synthase (ACPS) from Mycobacterium
Authors: Poulsen, C. / Wilmanns, M. / Song, Y.H.
History
DepositionApr 1, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Holo-[acyl-carrier-protein] synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3434
Polymers14,0551
Non-polymers2883
Water2,792155
1
A: Holo-[acyl-carrier-protein] synthase
hetero molecules

A: Holo-[acyl-carrier-protein] synthase
hetero molecules

A: Holo-[acyl-carrier-protein] synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,02912
Polymers42,1643
Non-polymers8659
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5740 Å2
ΔGint-155 kcal/mol
Surface area18370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.450, 67.450, 86.060
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-150-

HOH

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Components

#1: Protein Holo-[acyl-carrier-protein] synthase / 4'-phosphopantetheinyl transferase acpS / Holo-ACP synthase


Mass: 14054.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium smegmatis (bacteria) / Strain: MC2 155
References: UniProt: A0R1H6, holo-[acyl-carrier-protein] synthase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.68 Å3/Da / Density % sol: 54.11 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM Bis-Tris pH 6.5, 16% PEG 400, 200mM (NH4)SO4, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionNumber: 32734 / Rmerge(I) obs: 0.094 / D res high: 2.1 Å / Num. obs: 8718 / % possible obs: 99.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
9.392510110010.046
6.649.3917998.910.05
5.426.6422298.710.058
4.75.4228099.610.053
4.24.731599.410.054
3.834.233599.710.06
3.553.8338399.210.062
3.323.5539799.510.067
3.133.3243199.810.07
2.973.1345499.810.087
2.832.9747010010.103
2.712.8348710010.121
2.612.7154410010.145
2.512.6154110010.181
2.432.5156310010.201
2.352.4355710010.231
2.282.3561810010.27
2.212.2860699.810.308
2.152.2161998.610.345
2.12.1561695.210.351
ReflectionResolution: 1.7→25 Å / Num. all: 16195 / Num. obs: 15966 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 26.967 Å2 / Rmerge(I) obs: 0.047
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 2 / Num. measured obs: 2864 / Num. unique all: 1207 / Num. unique obs: 1080 / % possible all: 89.5

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.006data extraction
XDSdata reduction
Auto-Rickshawphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.7→21.851 Å / Occupancy max: 1 / Occupancy min: 0.44 / FOM work R set: 0.862 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.203 798 5 %Random
Rwork0.172 ---
obs0.174 15958 98.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.365 Å2 / ksol: 0.438 e/Å3
Displacement parametersBiso max: 106.41 Å2 / Biso mean: 25.937 Å2 / Biso min: 7.07 Å2
Baniso -1Baniso -2Baniso -3
1-1.412 Å20 Å2-0 Å2
2--1.412 Å20 Å2
3----2.824 Å2
Refinement stepCycle: LAST / Resolution: 1.7→21.851 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1987 0 15 155 2157
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052021
X-RAY DIFFRACTIONf_angle_d0.7433663
X-RAY DIFFRACTIONf_chiral_restr0.063158
X-RAY DIFFRACTIONf_plane_restr0.003306
X-RAY DIFFRACTIONf_dihedral_angle_d13.132502
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.696-1.8030.2891290.242442257195
1.803-1.9420.2891350.2272561269699
1.942-2.1370.2151330.17525372670100
2.137-2.4460.1851340.1692541267599
2.446-3.080.1991340.152540267499
3.08-21.8530.1711330.1582539267299

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