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- PDB-3ne3: Mycobacterium tuberculosis Acyl Carrier Protein Synthase Apo structure -

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Basic information

Entry
Database: PDB / ID: 3ne3
TitleMycobacterium tuberculosis Acyl Carrier Protein Synthase Apo structure
ComponentsHolo-[acyl-carrier-protein] synthase
KeywordsTRANSFERASE / acyl carrier protein synthase / acyl carrier protein / fatty acid synthase / ACPS / Mycobacterium Tuberculosis Structural Proteomics Project / Structural Genomics / XMTB
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 / Holo-[acyl-carrier-protein] synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsGokulan, K. / Mycobacterium Tuberculosis Structural Proteomics Project (XMTB)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Mycobacterium tuberculosis acyl carrier protein synthase adopts two different pH-dependent structural conformations.
Authors: Gokulan, K. / Aggarwal, A. / Shipman, L. / Besra, G.S. / Sacchettini, J.C.
History
DepositionJun 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 25, 2012Group: Database references / Structure summary
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Holo-[acyl-carrier-protein] synthase


Theoretical massNumber of molelcules
Total (without water)14,0201
Polymers14,0201
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Holo-[acyl-carrier-protein] synthase

B: Holo-[acyl-carrier-protein] synthase

B: Holo-[acyl-carrier-protein] synthase


Theoretical massNumber of molelcules
Total (without water)42,0593
Polymers42,0593
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area3710 Å2
ΔGint-21 kcal/mol
Surface area17860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.933, 67.933, 83.982
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 14019.756 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: acpS, MT2599, MTV009.08c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3
References: UniProt: P0A4W8, UniProt: P9WQD3*PLUS, holo-[acyl-carrier-protein] synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.66 Å3/Da / Density % sol: 53.76 %
Crystal growMethod: evaporation
Details: 5.6% PEG 4K, 0.07 M sodium acetate pH 4.6 to 5.5, 30% glycerol, EVAPORATION
PH range: 4 to 6

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→48.19 Å / Num. obs: 10843 / % possible obs: 100 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 54

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
CNSrefinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 1.9→48.19 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.891 / SU B: 5.149 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.274 544 4.8 %RANDOM
Rwork0.248 ---
obs0.249 10843 100 %-
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: 43.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20.15 Å20 Å2
2--0.3 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms979 0 0 23 1002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0360.0211001
X-RAY DIFFRACTIONr_bond_other_d0.0030.02927
X-RAY DIFFRACTIONr_angle_refined_deg2.6491.9311365
X-RAY DIFFRACTIONr_angle_other_deg1.61732135
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2265128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.3640.2157
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021135
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02208
X-RAY DIFFRACTIONr_nbd_refined0.2480.2225
X-RAY DIFFRACTIONr_nbd_other0.2640.21069
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1090.2659
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.212
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2740.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.060.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9541.5643
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.42421034
X-RAY DIFFRACTIONr_scbond_it4.2183358
X-RAY DIFFRACTIONr_scangle_it6.6624.5331
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.435 33
Rwork0.355 804

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