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- PDB-5xum: Crystal structure of Thermotoga maritima holo-[acyl-carrier-prote... -

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Basic information

Entry
Database: PDB / ID: 5xum
TitleCrystal structure of Thermotoga maritima holo-[acyl-carrier-protein] synthase (AcpS)
ComponentsHolo-[acyl-carrier-protein] synthase
KeywordsTRANSFERASE / Gram-negative bacteria / phosphopantetheinyl transferase / homotrimer
Function / homology
Function and homology information


holo-[acyl-carrier-protein] synthase / L-lysine biosynthetic process via aminoadipic acid / holo-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / magnesium ion binding / cytosol
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 speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLiao, Y.P. / Wang, D.L. / Yin, D.P. / Zhang, Q.Y. / Wang, Y.M. / Wang, D.Q. / Zhu, H.X. / Chen, S.
CitationJournal: To Be Published
Title: Crystal structures of acyl carrier protein synthases (AcpS) from three Gram-negative bacteria
Authors: Liao, Y.P. / Wang, D.L. / Yin, D.P. / Zhang, Q.Y. / Wang, Y.M. / Wang, D.Q. / Zhu, H.X. / Chen, S.
History
DepositionJun 23, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
A: Holo-[acyl-carrier-protein] synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4142
Polymers19,3221
Non-polymers921
Water1,13563
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)58,2436
Polymers57,9673
Non-polymers2763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area5250 Å2
ΔGint-17 kcal/mol
Surface area23020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.960, 72.960, 84.220
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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


Mass: 19322.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: acpS, TM_0692 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WZF6, holo-[acyl-carrier-protein] synthase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 3.35 Å3/Da / Density % sol: 63.27 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 8 / Details: 10mM Tris-HCl pH 8.0, 100mM NaCl, 10mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2014
RadiationMonochromator: DOUBLE CRYSTAL Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→63.185 Å / Num. obs: 14645 / % possible obs: 98.2 % / Redundancy: 5.4 % / Biso Wilson estimate: 37.39 Å2 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.038 / Net I/σ(I): 11
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2146 / Rpim(I) all: 0.272 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F80

1f80


Resolution: 2.1→63.18 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.946 / SU B: 8.112 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.422 / ESU R Free: 0.152 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22136 739 5 %RANDOM
Rwork0.16915 ---
obs0.17167 13905 98.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 52.678 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.05 Å20 Å2
2---0.09 Å20 Å2
3---0.14 Å2
Refinement stepCycle: 1 / Resolution: 2.1→63.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1354 0 6 63 1423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191390
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8741.9731864
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0615169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.64922.12166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82715258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.3371515
X-RAY DIFFRACTIONr_chiral_restr0.060.2206
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021034
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.49431389
X-RAY DIFFRACTIONr_sphericity_free27.582539
X-RAY DIFFRACTIONr_sphericity_bonded18.60351388
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 54 -
Rwork0.208 1019 -
obs--98.53 %

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