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- PDB-5d6j: Crystal structure of a mycobacterial protein -

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Basic information

Entry
Database: PDB / ID: 5d6j
TitleCrystal structure of a mycobacterial protein
Components
  • Acyl-CoA synthase
  • Ubiquitin-like protein SMT3
KeywordsLIGASE/PROTEIN BINDING / Mycobacterium smegmatis / LIGASE-PROTEIN BINDING complex
Function / homology
Function and homology information


long-chain-fatty-acid-[acyl-carrier-protein] ligase / long-chain fatty acid [acyl-carrier-protein] ligase activity / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / SUMOylation of DNA damage response and repair proteins ...long-chain-fatty-acid-[acyl-carrier-protein] ligase / long-chain fatty acid [acyl-carrier-protein] ligase activity / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication proteins / septin ring / SUMOylation of SUMOylation proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / lipid biosynthetic process / ubiquitin-like protein ligase binding / protein sumoylation / fatty acid metabolic process / condensed nuclear chromosome / PML body / protein tag activity / ATP binding / identical protein binding / nucleus
Similarity search - Function
: / Fatty acyl-AMP ligase /fatty acyl-CoA ligase / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / ANL, N-terminal domain / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) ...: / Fatty acyl-AMP ligase /fatty acyl-CoA ligase / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / ANL, N-terminal domain / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Long-chain-fatty-acid--AMP ligase FadD32 / Ubiquitin-like protein SMT3
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsLi, W.J. / Bi, L.J.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: Sci Rep / Year: 2015
Title: Crystal structure of FadD32, an enzyme essential for mycolic acid biosynthesis in mycobacteria.
Authors: Li, W. / Gu, S. / Fleming, J. / Bi, L.
History
DepositionAug 12, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl-CoA synthase
B: Ubiquitin-like protein SMT3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5354
Polymers77,0032
Non-polymers5312
Water8,683482
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.211, 122.211, 142.588
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Acyl-CoA synthase / Fatty-acid-CoA ligase FadD32


Mass: 68306.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: fadD32, MSMEG_6393, MSMEI_6225 / Production host: Escherichia coli (E. coli) / References: UniProt: A0R618
#2: Protein Ubiquitin-like protein SMT3


Mass: 8696.812 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 21-94
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SMT3, YDR510W, D9719.15 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12306
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 482 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.42 %
Crystal growTemperature: 281 K / Method: evaporation / Details: 0.2 M sodium malonate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97928 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / % possible obs: 100 % / Redundancy: 14.3 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 26.5
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 6.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→29.985 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2062 1986 3.84 %
Rwork0.1688 --
obs0.1702 51768 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→29.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5429 0 32 482 5943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055588
X-RAY DIFFRACTIONf_angle_d0.9517610
X-RAY DIFFRACTIONf_dihedral_angle_d13.8442049
X-RAY DIFFRACTIONf_chiral_restr0.037838
X-RAY DIFFRACTIONf_plane_restr0.0041010
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.30630.29411400.21633512X-RAY DIFFRACTION100
2.3063-2.36860.26351400.20623491X-RAY DIFFRACTION100
2.3686-2.43830.27371390.20053500X-RAY DIFFRACTION100
2.4383-2.51690.2781390.20263486X-RAY DIFFRACTION100
2.5169-2.60680.26391420.19033538X-RAY DIFFRACTION100
2.6068-2.71120.22591390.18863500X-RAY DIFFRACTION100
2.7112-2.83450.23471410.19073527X-RAY DIFFRACTION100
2.8345-2.98380.25891410.19413542X-RAY DIFFRACTION100
2.9838-3.17050.22011400.19243517X-RAY DIFFRACTION100
3.1705-3.4150.25231420.18263557X-RAY DIFFRACTION100
3.415-3.75810.20641430.16533575X-RAY DIFFRACTION100
3.7581-4.30050.17351430.14323586X-RAY DIFFRACTION100
4.3005-5.4130.1551440.13573638X-RAY DIFFRACTION100
5.413-29.98780.15511530.15193813X-RAY DIFFRACTION100

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