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

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Basic information

Entry
Database: PDB / ID: 5szy
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


long-chain fatty acyl-CoA hydrolase activity / acyl-CoA metabolic process / Hydrolases; Acting on ester bonds; Thioester hydrolases / cytosol
Similarity search - Function
Hotdog acyl-CoA thioesterase (ACOT)-type domain / Cytosolic acyl coenzyme A thioester hydrolase / Hotdog acyl-CoA thioesterase (ACOT)-type domain profile. / 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 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 / database_PDB_caveat / 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

Downloads & links

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Assembly

Deposited unit
A: Acyl-CoA hydrolase
B: Acyl-CoA hydrolase
C: Acyl-CoA hydrolase
D: Acyl-CoA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,86316
Polymers71,8784
Non-polymers4,98512
Water5,945330
1
A: Acyl-CoA hydrolase
C: Acyl-CoA hydrolase
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)115,29524
Polymers107,8186
Non-polymers7,47718
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area30430 Å2
ΔGint-205 kcal/mol
Surface area33850 Å2
MethodPISA
2
B: Acyl-CoA hydrolase
D: Acyl-CoA hydrolase
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)115,29524
Polymers107,8186
Non-polymers7,47718
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Buried area30090 Å2
ΔGint-202 kcal/mol
Surface area34040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.800, 152.800, 152.800
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: 17969.598 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.: 330 / 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: 4.12 Å3/Da / Density % sol: 70.14 %
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: MX2 / Wavelength: 0.9537 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: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→36.02 Å / Num. obs: 80089 / % possible obs: 100 % / Redundancy: 12 % / Rmerge(I) obs: 0.02 / Net I/σ(I): 23.55
Reflection shellResolution: 2→2.07 Å / Redundancy: 12.2 % / Mean I/σ(I) obs: 7.64 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IEN

4ien


Resolution: 2→36.015 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.65
RfactorNum. reflection% reflection
Rfree0.2124 4030 5.03 %
Rwork0.1986 --
obs0.1993 80083 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→36.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4657 0 308 330 5295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085066
X-RAY DIFFRACTIONf_angle_d1.436902
X-RAY DIFFRACTIONf_dihedral_angle_d18.7311952
X-RAY DIFFRACTIONf_chiral_restr0.055770
X-RAY DIFFRACTIONf_plane_restr0.007839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0002-2.02370.23161220.22992594X-RAY DIFFRACTION100
2.0237-2.04840.23471450.22262597X-RAY DIFFRACTION100
2.0484-2.07430.20571360.21762602X-RAY DIFFRACTION100
2.0743-2.10160.26011350.21382610X-RAY DIFFRACTION100
2.1016-2.13040.221410.21132591X-RAY DIFFRACTION100
2.1304-2.16080.22551340.20992631X-RAY DIFFRACTION100
2.1608-2.19310.20971520.20792545X-RAY DIFFRACTION100
2.1931-2.22730.19321280.20432654X-RAY DIFFRACTION100
2.2273-2.26380.21011810.21052520X-RAY DIFFRACTION100
2.2638-2.30290.20951360.20312641X-RAY DIFFRACTION100
2.3029-2.34470.24541290.20192610X-RAY DIFFRACTION100
2.3447-2.38980.21511360.20982612X-RAY DIFFRACTION100
2.3898-2.43860.24581270.21162581X-RAY DIFFRACTION100
2.4386-2.49160.24781420.21832667X-RAY DIFFRACTION100
2.4916-2.54950.25461520.21612586X-RAY DIFFRACTION100
2.5495-2.61330.23981640.21772580X-RAY DIFFRACTION100
2.6133-2.68390.23231420.22982602X-RAY DIFFRACTION100
2.6839-2.76290.27261210.21922644X-RAY DIFFRACTION100
2.7629-2.8520.24131300.22532598X-RAY DIFFRACTION100
2.852-2.95390.22851440.21742623X-RAY DIFFRACTION100
2.9539-3.07210.21261470.21062649X-RAY DIFFRACTION100
3.0721-3.21180.21161330.20842598X-RAY DIFFRACTION100
3.2118-3.38110.22621190.19672664X-RAY DIFFRACTION100
3.3811-3.59270.22521110.1872678X-RAY DIFFRACTION100
3.5927-3.86980.17871550.17732608X-RAY DIFFRACTION100
3.8698-4.25870.1861510.17132642X-RAY DIFFRACTION100
4.2587-4.87360.17361440.1522661X-RAY DIFFRACTION100
4.8736-6.13530.1833990.18822731X-RAY DIFFRACTION100
6.1353-36.02110.1951740.19722734X-RAY DIFFRACTION100

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