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- PDB-7wa9: Crystal structure of MSMEG_5634 from Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 7wa9
TitleCrystal structure of MSMEG_5634 from Mycobacterium smegmatis
ComponentsMSMEG_5634
KeywordsLIPID BINDING PROTEIN / MSMEG_5634 / acyl-AcpM / FAS-II inhibitor / Mycobacterium smegmatis
Function / homologyPolyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta / Toxin
Function and homology information
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsWang, Z. / Zhang, W.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81972604 China
National Natural Science Foundation of China (NSFC)32171138 China
National Natural Science Foundation of China (NSFC)31870725 China
National Natural Science Foundation of China (NSFC)32071204 China
CitationJournal: Front Microbiol / Year: 2022
Title: A Novel Acyl-AcpM-Binding Protein Confers Intrinsic Sensitivity to Fatty Acid Synthase Type II Inhibitors in Mycobacterium smegmatis
Authors: Li, M. / Huang, Q. / Zhang, W. / Cao, Y. / Wang, Z. / Zhao, Z. / Zhang, X. / Zhang, J.
History
DepositionDec 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MSMEG_5634


Theoretical massNumber of molelcules
Total (without water)16,4071
Polymers16,4071
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8050 Å2
Unit cell
Length a, b, c (Å)71.072, 55.011, 40.733
Angle α, β, γ (deg.)90.000, 112.754, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein MSMEG_5634


Mass: 16407.494 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_5634 / Production host: Escherichia coli (E. coli) / References: UniProt: A0R3Y0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.24 Å3/Da / Density % sol: 45.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 0.2 M Calcium acetate hydrate, 20% w/v Polyethylene Glycol 3350, pH 7.5

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 21971 / % possible obs: 98.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 18.33 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 33.3
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.596 / Num. unique obs: 1149

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→22.19 Å / SU ML: 0.2789 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 32.8413
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2821 542 4.78 %
Rwork0.2333 10797 -
obs0.2357 11339 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.19 Å2
Refinement stepCycle: LAST / Resolution: 1.9→22.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1121 0 0 52 1173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081148
X-RAY DIFFRACTIONf_angle_d1.09541557
X-RAY DIFFRACTIONf_chiral_restr0.0634174
X-RAY DIFFRACTIONf_plane_restr0.0062196
X-RAY DIFFRACTIONf_dihedral_angle_d15.2655426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.090.32221400.22892662X-RAY DIFFRACTION98.04
2.09-2.40.29021310.23172695X-RAY DIFFRACTION98.91
2.4-3.020.30761260.26112723X-RAY DIFFRACTION99.62
3.02-22.190.25741450.22212717X-RAY DIFFRACTION98.25

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