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- PDB-5szz: Novel Structural Insights into GDP-Mediated Regulation of Acyl-Co... -

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Basic information

Entry
Database: PDB / ID: 5szz
TitleNovel Structural Insights into GDP-Mediated Regulation of Acyl-CoA Thioesterases
ComponentsAcyl-CoA hydrolase
KeywordsHYDROLASE / Thioesterase / Nisseria meningitidis / 4HBT / Acyl-CoA thioesterase / Coenzyme A / GDP
Function / homology
Function and homology information


palmitic acid biosynthetic process / acyl-CoA metabolic process / fatty acyl-CoA hydrolase activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / extracellular exosome / cytosol
Similarity search - Function
Hotdog acyl-CoA thioesterase (ACOT)-type domain / Hotdog acyl-CoA thioesterase (ACOT)-type domain profile. / Cytosolic acyl coenzyme A thioester hydrolase / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
COENZYME A / GUANOSINE-5'-DIPHOSPHATE / Acyl-CoA hydrolase
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKhandokar, Y.B. / Srivastava, P. / Forwood, J.K.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural insights into GDP-mediated regulation of a bacterial acyl-CoA thioesterase.
Authors: Khandokar, Y.B. / Srivastava, P. / Cowieson, N. / Sarker, S. / Aragao, D. / Das, S. / Smith, K.M. / Raidal, S.R. / Forwood, J.K.
History
DepositionAug 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_residues
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 27, 2017Group: Advisory / Database references / Category: citation / database_PDB_caveat
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
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: Acyl-CoA hydrolase
D: Acyl-CoA hydrolase
C: Acyl-CoA hydrolase
B: Acyl-CoA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,03516
Polymers72,0504
Non-polymers4,98512
Water6,918384
1
A: Acyl-CoA hydrolase
B: Acyl-CoA hydrolase
hetero molecules

A: Acyl-CoA hydrolase
B: Acyl-CoA hydrolase
hetero molecules

A: Acyl-CoA hydrolase
B: Acyl-CoA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,55324
Polymers108,0766
Non-polymers7,47718
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544-z,x-1/2,-y-1/21
crystal symmetry operation11_545y+1/2,-z-1/2,-x1
Buried area31140 Å2
ΔGint-201 kcal/mol
Surface area33490 Å2
MethodPISA
2
D: Acyl-CoA hydrolase
C: Acyl-CoA hydrolase
hetero molecules

D: Acyl-CoA hydrolase
C: Acyl-CoA hydrolase
hetero molecules

D: Acyl-CoA hydrolase
C: Acyl-CoA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,55324
Polymers108,0766
Non-polymers7,47718
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area31420 Å2
ΔGint-198 kcal/mol
Surface area32930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.620, 152.620, 152.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein
Acyl-CoA hydrolase


Mass: 18012.621 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria)
Gene: ERS514298_01532, ERS514410_00397, ERS514534_01643, ERS514708_01580, ERS514851_00814
Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG
References: UniProt: A0A0Y5D4F5, Hydrolases; Acting on ester bonds; Thioester hydrolases
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 4.11 Å3/Da / Density % sol: 70.09 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100 mM Tris pH 8.5 and 2 M ammonium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9786 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.3→34.12 Å / Num. obs: 52676 / % possible obs: 99.97 % / Redundancy: 22 % / Rmerge(I) obs: 0.013 / Net I/σ(I): 40.43
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 21 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 14.06 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IEN

4ien


Resolution: 2.3→34.12 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.929 / SU B: 0.001 / SU ML: 0 / Cross valid method: FREE R-VALUE / ESU R: 0.145 / ESU R Free: 0.163 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21238 2627 5 %RANDOM
Rwork0.18971 ---
obs0.19085 50049 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.362 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.3→34.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4668 0 308 384 5360
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 205 -
Rwork0.21 3630 -
obs--100 %

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