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- PDB-1yli: Crystal structure of HI0827, a hexameric broad specificity acyl-c... -

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Basic information

Entry
Database: PDB / ID: 1yli
TitleCrystal structure of HI0827, a hexameric broad specificity acyl-coenzyme A thioesterase
ComponentsPutative acyl-CoA thioester hydrolase HI0827
KeywordsHYDROLASE / Structural Genomics / HI0827 / YCIA_HAEIN / thioesterase / coenzyme A / Structure 2 Function Project / S2F
Function / homology
Function and homology information


long-chain fatty acyl-CoA hydrolase activity / acyl-CoA metabolic process / fatty acid catabolic process / Hydrolases; Acting on ester bonds; Thioester hydrolases / cytosol / cytoplasm
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 / Uncharacterized acyl-CoA thioester hydrolase HI_0827
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsStructure 2 Function Project (S2F)
CitationJournal: To be Published
Title: STRUCTURE OF HI0827, A THIOESTERASE ACTING ON SHORT-CHAIN ACYL-COA COMPOUNDS
Authors: Willis, M.A. / Zhuang, Z. / Song, F. / Howard, A. / Dunaway-Mariano, D. / Herzberg, O.
History
DepositionJan 19, 2005Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 1, 2005ID: 1NNG
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 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 / struct_conn / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative acyl-CoA thioester hydrolase HI0827
B: Putative acyl-CoA thioester hydrolase HI0827
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,18210
Polymers33,3022
Non-polymers1,8808
Water3,873215
1
A: Putative acyl-CoA thioester hydrolase HI0827
B: Putative acyl-CoA thioester hydrolase HI0827
hetero molecules

A: Putative acyl-CoA thioester hydrolase HI0827
B: Putative acyl-CoA thioester hydrolase HI0827
hetero molecules

A: Putative acyl-CoA thioester hydrolase HI0827
B: Putative acyl-CoA thioester hydrolase HI0827
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,54630
Polymers99,9076
Non-polymers5,63924
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area13490 Å2
ΔGint-150 kcal/mol
Surface area37200 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)163.676, 163.676, 163.676
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11B-1-

CA

21B-257-

HOH

31B-262-

HOH

DetailsThe biological assembly is a hexamer generated from the dimer in the asymmetric unit by the operations: z,x,y and y,z,x.

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Components

#1: Protein Putative acyl-CoA thioester hydrolase HI0827


Mass: 16651.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: YCIA-HAEIN / Plasmid: pET23b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P44886, Hydrolases; Acting on ester bonds; Thioester hydrolases
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 54.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, bicine, calcium acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 17-ID11.5545
SYNCHROTRONAPS 17-ID21.0720, 1.0723, 1.0543
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDMar 17, 2002
ADSC QUANTUM 2102CCDMar 17, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si (111)SINGLE WAVELENGTHMx-ray1
2Si (111)MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.55451
21.0721
31.07231
41.05431
ReflectionResolution: 1.9→30 Å / Num. all: 29132 / Num. obs: 29132 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 19.8 % / Biso Wilson estimate: 19 Å2 / Rsym value: 0.075 / Χ2: 1.045 / Net I/σ(I): 17
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 2433 / Rsym value: 0.65 / Χ2: 0.819 / % possible all: 83.4

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
1111.07214.98-22.85
1121.072313.48-17.83
1131.054312.79-7.85
Phasing dmFOM : 0.52 / FOM acentric: 0.52 / FOM centric: 0.51 / Reflection: 25370 / Reflection acentric: 22300 / Reflection centric: 3070
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.7-24.6950.950.950.841204839365
3.6-5.70.920.940.8534322847585
2.9-3.60.840.860.742753729546
2.5-2.90.650.680.4542883816472
2.1-2.50.290.290.1974856784701
2-2.10.080.080.0746864285401

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.02phasing
RESOLVE2.02phasing
REFMACrefinement
PDB_EXTRACT1.501data extraction
RefinementMethod to determine structure: MAD / Resolution: 1.95→24.68 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 7.368 / SU ML: 0.11 / SU R Cruickshank DPI: 0.153 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.148 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2123 8 %RANDOM
Rwork0.18 ---
all0.184 26684 --
obs0.184 26684 97.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.164 Å2
Refinement stepCycle: LAST / Resolution: 1.95→24.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2195 0 112 215 2522
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.01723490.022
X-RAY DIFFRACTIONr_angle_refined_deg1.61931802.011
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.812885
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2099024.111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.06141615
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1041715
X-RAY DIFFRACTIONr_chiral_restr0.1123620.2
X-RAY DIFFRACTIONr_gen_planes_refined0.00616660.02
X-RAY DIFFRACTIONr_nbd_refined0.21710080.2
X-RAY DIFFRACTIONr_nbtor_refined0.29816030.2
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1471830.2
X-RAY DIFFRACTIONPOTENTIAL METAL-ION REFINED ATOMS (A)0.03720.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.222400.2
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.18120.2
X-RAY DIFFRACTIONSYMMETRY METAL-ION REFINED ATOMS (A)0.04920.2
X-RAY DIFFRACTIONr_mcbond_it1.00814771.5
X-RAY DIFFRACTIONr_mcangle_it1.45223122
X-RAY DIFFRACTIONr_scbond_it2.429843
X-RAY DIFFRACTIONr_scangle_it3.568684.5
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 136 -
Rwork0.245 1457 -
obs--79.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.41121.5581-0.0183.02630.2881.74750.0012-0.2863-0.32520.2980.0201-0.1910.17170.0163-0.0213-0.0920.07680.0611-0.10880.0822-0.1528-7.7965-19.507311.2036
21.3023-0.046-0.09022.73751.0253.157-0.0045-0.11670.13130.1825-0.03410.2003-0.0773-0.1480.0387-0.11520.04150.0835-0.11670.0427-0.1338-18.96950.091112.4064
38.5725-0.64523.1992.2763-4.19718.2199-0.1043-0.2659-0.3777-0.1860.20030.3335-0.1438-0.3262-0.096-0.0590.06640.1509-0.02420.0478-0.0741-25.8422-20.9688.248
424.0982-7.956-15.33195.9338.844214.0815-0.1415-1.5414-0.23450.70430.1985-0.33320.47681.2693-0.057-0.03090.09540.03670.03920.0863-0.1115-7.3166-2.901327.0061
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA11 - 15210 - 151
22BB5 - 1524 - 151
33AC - D155 - 1561
44BE - F1 - 1551

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