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- PDB-6he0: Crystal structure of 2-Hydroxyisobutyryl-CoA Ligase (HCL) in comp... -

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Basic information

Entry
Database: PDB / ID: 6he0
TitleCrystal structure of 2-Hydroxyisobutyryl-CoA Ligase (HCL) in complex with 2-HIB-AMP and CoA in the thioesterfication state
Components2-hydroxyisobutyryl-CoA synthetase
KeywordsLIGASE / 2-hydroxyisobutyrate CoA
Function / homology
Function and homology information


Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases / ligase activity / nucleotide binding
Similarity search - Function
AMP-dependent ligase, C-terminal / AMP-binding enzyme C-terminal domain / ANL, C-terminal domain / ANL, N-terminal domain / AMP-dependent synthetase/ligase / AMP-binding enzyme / GMP Synthetase; Chain A, domain 3 / AMP-binding enzyme, C-terminal domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-8LE / ADENOSINE MONOPHOSPHATE / COENZYME A / 2-hydroxyisobutyryl-CoA synthetase
Similarity search - Component
Biological speciesAquincola tertiaricarbonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsZahn, M. / Rohwerder, T. / Strater, N.
CitationJournal: J.Mol.Biol. / Year: 2019
Title: Structures of 2-Hydroxyisobutyric Acid-CoA Ligase Reveal Determinants of Substrate Specificity and Describe a Multi-Conformational Catalytic Cycle.
Authors: Zahn, M. / Kurteva-Yaneva, N. / Schuster, J. / Krug, U. / Georgi, T. / Muller, R.H. / Rohwerder, T. / Strater, N.
History
DepositionAug 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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
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: 2-hydroxyisobutyryl-CoA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4914
Polymers55,9431
Non-polymers1,5483
Water2,954164
1
A: 2-hydroxyisobutyryl-CoA synthetase
hetero molecules

A: 2-hydroxyisobutyryl-CoA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,9828
Polymers111,8862
Non-polymers3,0966
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area7540 Å2
ΔGint-36 kcal/mol
Surface area33660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.054, 95.054, 100.742
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein 2-hydroxyisobutyryl-CoA synthetase


Mass: 55943.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquincola tertiaricarbonis (bacteria) / Gene: hcl / Production host: Escherichia coli (E. coli)
References: UniProt: I3VE75, Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases
#2: Chemical ChemComp-8LE / [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] 2-methyl-2-oxidanyl-propanoate


Mass: 433.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N5O9P
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.35 Å3/Da / Density % sol: 47.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M TRIS PH 8.0, 24% PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.31→40 Å / Num. obs: 23659 / % possible obs: 99.8 % / Redundancy: 8.2 % / Biso Wilson estimate: 42.39 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 16.2
Reflection shellResolution: 2.31→2.43 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 5 / Num. unique obs: 3391 / % possible all: 99

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
BUSTER2.10.3refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Y4O

2y4o


Resolution: 2.31→38.1 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.908 / SU R Cruickshank DPI: 0.282 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.296 / SU Rfree Blow DPI: 0.212 / SU Rfree Cruickshank DPI: 0.212
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1206 5.13 %RANDOM
Rwork0.166 ---
obs0.169 23493 99.9 %-
Displacement parametersBiso mean: 39.65 Å2
Baniso -1Baniso -2Baniso -3
1--3.3281 Å20 Å20 Å2
2---3.3281 Å20 Å2
3---6.6563 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 2.31→38.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3748 0 100 164 4012
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013968HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.065401HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1367SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes91HARMONIC2
X-RAY DIFFRACTIONt_gen_planes610HARMONIC5
X-RAY DIFFRACTIONt_it3968HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.5
X-RAY DIFFRACTIONt_other_torsion18.52
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion494SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies18HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4723SEMIHARMONIC4
LS refinement shellResolution: 2.31→2.41 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2757 162 5.73 %
Rwork0.1804 2664 -
all0.1854 2826 -
obs--100 %
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)
10.6598-0.19-0.23781.01280.00071.215-0.0469-0.0264-0.11390.27590.04640.18840.2022-0.16880.0005-0.02280.02560.0381-0.07780.0318-0.078310.411232.78315.7895
22.4282-0.7648-0.6321.73430.25972.0059-0.0606-0.13450.18980.29880.1443-0.3310.00490.5152-0.0837-0.02740.0481-0.0669-0.02-0.0667-0.110731.401753.596419.8327
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|-1 - A|361}
2X-RAY DIFFRACTION2{A|362 - A|475}

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