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- PDB-7w58: Crystal structure of acyl-carrier protein synthase from Mycobacte... -

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Basic information

Entry
Database: PDB / ID: 7w58
TitleCrystal structure of acyl-carrier protein synthase from Mycobacterium smegmatis
Components4'-phosphopantetheinyl transferase
KeywordsTRANSFERASE / AcpS / Mycobacterium smegmatis
Function / homology
Function and homology information


holo-[acyl-carrier-protein] synthase / holo-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / magnesium ion binding
Similarity search - Function
Holo-[acyl carrier protein] synthase / Phosphopantetheine-protein transferase domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily
Similarity search - Domain/homology
NICKEL (II) ION / Holo-[acyl-carrier-protein] synthase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.27 Å
AuthorsYadav, S. / Bhatia, I. / Biswal, B.K.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2022
Title: Identification, structure determination and analysis of Mycobacterium smegmatis acyl-carrier protein synthase (AcpS) crystallized serendipitously.
Authors: Bhatia, I. / Yadav, S. / Biswal, B.K.
History
DepositionNov 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4'-phosphopantetheinyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3694
Polymers14,1861
Non-polymers1833
Water1,74797
1
A: 4'-phosphopantetheinyl transferase
hetero molecules

A: 4'-phosphopantetheinyl transferase
hetero molecules

A: 4'-phosphopantetheinyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,10712
Polymers42,5583
Non-polymers5489
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 area5060 Å2
ΔGint-45 kcal/mol
Surface area18500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.640, 67.640, 85.779
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-379-

HOH

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Components

#1: Protein 4'-phosphopantetheinyl transferase


Mass: 14186.021 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: acpS, NCTC7017_04197 / Production host: Mycolicibacterium smegmatis (bacteria)
References: UniProt: A0A8B4R1L0, holo-[acyl-carrier-protein] synthase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 53.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Sodium acetate trihydrate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5417 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 6746 / % possible obs: 97.5 % / Redundancy: 8.3 % / CC1/2: 0.99 / Net I/σ(I): 21.44
Reflection shellResolution: 2.25→2.29 Å / Num. unique obs: 180 / CC1/2: 0.81

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GWM

3gwm


Resolution: 2.27→34.63 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.128 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.282 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2033 321 4.8 %RANDOM
Rwork0.1671 ---
obs0.1691 6425 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.61 Å2 / Biso mean: 34.874 Å2 / Biso min: 16.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0.04 Å20 Å2
2---0.08 Å20 Å2
3---0.27 Å2
Refinement stepCycle: final / Resolution: 2.27→34.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms985 0 9 97 1091
Biso mean--39.79 40.85 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0121017
X-RAY DIFFRACTIONr_angle_refined_deg1.1251.6391382
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1185130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.17220.76952
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.75415163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.242159
X-RAY DIFFRACTIONr_chiral_restr0.0890.2141
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02773
LS refinement shellResolution: 2.271→2.33 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 11 -
Rwork0.303 481 -
all-492 -
obs--98.01 %

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