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

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Basic information

Entry
Database: PDB / ID: 6hdy
TitleCrystal structure of 2-Hydroxyisobutyryl-CoA Ligase (HCL) in the postadenylation state in complex with S3-HB-AMP
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
(3S)-3-HYDROXYBUTANOIC ACID / Chem-8LQ / 2-hydroxyisobutyryl-CoA synthetase
Similarity search - Component
Biological speciesAquincola tertiaricarbonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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)56,7696
Polymers55,9431
Non-polymers8265
Water2,702150
1
A: 2-hydroxyisobutyryl-CoA synthetase
hetero molecules

A: 2-hydroxyisobutyryl-CoA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,53712
Polymers111,8862
Non-polymers1,65110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4020 Å2
ΔGint-101 kcal/mol
Surface area35450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.190, 84.190, 219.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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-3HL / (3S)-3-HYDROXYBUTANOIC ACID


Mass: 104.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O3
#3: Chemical ChemComp-8LQ / [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (3~{S})-3-oxidanylbutanoate


Mass: 433.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N5O9P
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 3.48 Å3/Da / Density % sol: 64.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.05 M MES PH 6.0, 2.1 M LITHIUM SULFATE, 0.01 M MAGNESIUM CHLORIDE, 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: 2.2→24.65 Å / Num. obs: 41011 / % possible obs: 99.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 41.66 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 13.2
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.809 / Mean I/σ(I) obs: 2 / Num. unique obs: 5801 / % possible all: 99.7

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
BUSTER2.10.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Y4N

2y4n


Resolution: 2.2→24.11 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.925 / SU R Cruickshank DPI: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.185 / SU Rfree Blow DPI: 0.165 / SU Rfree Cruickshank DPI: 0.164
RfactorNum. reflection% reflectionSelection details
Rfree0.241 2056 5.02 %RANDOM
Rwork0.208 ---
obs0.209 40924 99.7 %-
Displacement parametersBiso mean: 50.17 Å2
Baniso -1Baniso -2Baniso -3
1--1.6149 Å20 Å20 Å2
2---1.6149 Å20 Å2
3---3.2297 Å2
Refine analyzeLuzzati coordinate error obs: 0.309 Å
Refinement stepCycle: LAST / Resolution: 2.2→24.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3737 0 51 150 3938
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013883HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.025270HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1322SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes91HARMONIC2
X-RAY DIFFRACTIONt_gen_planes573HARMONIC5
X-RAY DIFFRACTIONt_it3883HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.33
X-RAY DIFFRACTIONt_other_torsion18.68
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion481SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4533SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2925 137 4.85 %
Rwork0.2492 2690 -
all0.2513 2827 -
obs--95.37 %
Refinement TLS params.

S12: -0.5442 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (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)
11.945-1.57210.30933.4341-0.49061.8924-0.0014-0.2699-0.42020.4920.050.424-0.024-0.4906-0.1323-0.1342-0.10430.03880.0724-0.1624-23.7854-45.37338.6434
26.12111.20871.67064.00732.00563.0958-0.0291-0.2357-0.02660.1055-0.54420.10780.1964-0.0764-0.293-0.05020.07410.1657-0.152-0.04470.67-27.129715.8319
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|-1 - A|357}
2X-RAY DIFFRACTION2{A|358 - A|476}

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