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- PDB-6he2: Crystal structure of an open conformation of 2-Hydroxyisobutyryl-... -

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Basic information

Entry
Database: PDB / ID: 6he2
TitleCrystal structure of an open conformation of 2-Hydroxyisobutyryl-CoA Ligase (HCL) in complex with 2-HIB-AMP and CoA
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, N-terminal domain / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme
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: 2.3 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: 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_atoms
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: 2-hydroxyisobutyryl-CoA synthetase
B: 2-hydroxyisobutyryl-CoA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,9828
Polymers111,8862
Non-polymers3,0966
Water5,242291
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-39 kcal/mol
Surface area35770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.852, 101.847, 109.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 2-hydroxyisobutyryl-CoA synthetase


Mass: 55943.062 Da / Num. of mol.: 2
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-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: 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.: 2 / Source method: obtained synthetically / Formula: C14H20N5O9P
#4: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
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: 2.3→40 Å / Num. obs: 47279 / % possible obs: 99.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 45.74 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 11.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 6830 / % possible all: 100

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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: 2.3→39.72 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.91 / SU R Cruickshank DPI: 0.279 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.287 / SU Rfree Blow DPI: 0.203 / SU Rfree Cruickshank DPI: 0.203
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1467 3.11 %RANDOM
Rwork0.184 ---
obs0.186 47200 99.8 %-
Displacement parametersBiso mean: 43.31 Å2
Baniso -1Baniso -2Baniso -3
1--13.0457 Å20 Å20 Å2
2--6.72 Å20 Å2
3---6.3257 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.3→39.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7010 0 200 291 7501
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0097414HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0210091HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2531SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes163HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1141HARMONIC5
X-RAY DIFFRACTIONt_it7414HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.28
X-RAY DIFFRACTIONt_other_torsion17.37
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion914SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies36HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8275SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 112 3.24 %
Rwork0.1982 3346 -
all0.2003 3458 -
obs--99.97 %
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)
11.39810.0345-0.17310.7113-0.29951.08580.0731-0.0023-0.0843-0.0536-0.054-0.06830.19650.0961-0.0191-0.01790.0551-0.0046-0.1140.0115-0.09649.5441-8.4909-11.9939
22.32820.5972-0.83993.3314-1.15795.23530.01160.08590.01690.0792-0.1201-0.09420.08840.12140.1086-0.12530.0457-0.063-0.0633-0.0062-0.068924.7961-17.928317.4373
31.39010.21550.09211.26550.00490.6007-0.03310.00860.1979-0.06070.02380.21-0.017-0.11670.0093-0.0830.01380.0022-0.09790.0025-0.0621-21.52388.8372-15.1667
40-0.4144-1.31030.89131.19292.6690.00430.05790.0180.104-0.00590.0005-0.0035-0.05060.00160.01460.152-0.14420.0552-0.1482-0.0964-39.930418.625610.9395
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|-4 - A|359}
2X-RAY DIFFRACTION2{A|360 - A|462}
3X-RAY DIFFRACTION3{B|-2 - B|359}
4X-RAY DIFFRACTION4{B|360 - B|459}

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