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- PDB-3o3n: (R)-2-hydroxyisocaproyl-CoA dehydratase in complex with its subst... -

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Basic information

Entry
Database: PDB / ID: 3o3n
Title(R)-2-hydroxyisocaproyl-CoA dehydratase in complex with its substrate (R)-2-hydroxyisocaproyl-CoA
Components
  • alpha-subunit 2-hydroxyisocaproyl-CoA dehydratase
  • beta-subunit 2-hydroxyacyl-CoA dehydratase
KeywordsLYASE / atypical dehydratase
Function / homology
Function and homology information


(R)-2-hydroxyisocaproyl-CoA dehydratase / L-leucine metabolic process / hydro-lyase activity / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #370 / Rossmann fold - #11890 / Rossmann fold - #11900 / FldB/FldC dehydratase alpha/beta subunit / 2-hydroxyglutaryl-CoA dehydratase, D-component / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
HYDROSULFURIC ACID / Chem-IRC / IRON/SULFUR CLUSTER / (R)-2-hydroxyisocaproyl-CoA dehydratase beta subunit / (R)-2-hydroxyisocaproyl-CoA dehydratase alpha subunit
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKnauer, S.H. / Buckel, W. / Dobbek, H.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Structural Basis for Reductive Radical Formation and Electron Recycling in (R)-2-Hydroxyisocaproyl-CoA Dehydratase.
Authors: Knauer, S.H. / Buckel, W. / Dobbek, H.
History
DepositionJul 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_label_seq_id / _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.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.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_label_seq_id / _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_ref_seq_dif.details / _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: alpha-subunit 2-hydroxyisocaproyl-CoA dehydratase
B: beta-subunit 2-hydroxyacyl-CoA dehydratase
C: alpha-subunit 2-hydroxyisocaproyl-CoA dehydratase
D: beta-subunit 2-hydroxyacyl-CoA dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,24812
Polymers180,0104
Non-polymers3,2388
Water21,7261206
1
A: alpha-subunit 2-hydroxyisocaproyl-CoA dehydratase
B: beta-subunit 2-hydroxyacyl-CoA dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6246
Polymers90,0052
Non-polymers1,6194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-72 kcal/mol
Surface area28460 Å2
MethodPISA
2
C: alpha-subunit 2-hydroxyisocaproyl-CoA dehydratase
D: beta-subunit 2-hydroxyacyl-CoA dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6246
Polymers90,0052
Non-polymers1,6194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-72 kcal/mol
Surface area28480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.648, 126.683, 177.699
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein alpha-subunit 2-hydroxyisocaproyl-CoA dehydratase


Mass: 46383.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Gene: hadB / Plasmid: pASK-IBA 3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon Plus-RIL / References: UniProt: Q5U924
#2: Protein beta-subunit 2-hydroxyacyl-CoA dehydratase


Mass: 43621.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Gene: hadC / Plasmid: pASK-IBA 3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) CodonPlus-RIL / References: UniProt: Q5U923

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Non-polymers , 4 types, 1214 molecules

#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-IRC / S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-phosphonooxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl ]oxy-hydroxy-phosphoryl]oxy-2-hydroxy-3,3-dimethyl-butanoyl]amino]propanoylamino]ethyl] (2R)-2-hydroxy-4-methyl-pentanethioate / (R)-2-hydroxy-4-methylpentanoyl-CoA


Mass: 881.677 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46N7O18P3S
#5: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1206 / 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: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: reservoir solution: 23 % PEG 3350, 0.1MBis-Tris Prior to freezing in liquid nitrogen the crystal was soaked in 0.1M Bis-Tris, 20 % PEG 3350, 25 % PEG 400 and 3.8 mM (R)-2-hydroxyisocaproyl- ...Details: reservoir solution: 23 % PEG 3350, 0.1MBis-Tris Prior to freezing in liquid nitrogen the crystal was soaked in 0.1M Bis-Tris, 20 % PEG 3350, 25 % PEG 400 and 3.8 mM (R)-2-hydroxyisocaproyl-CoA for 30 minutes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 14, 2008
Details: Double crystal monochromator with 2 sets of mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 71669 / Num. obs: 71258 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Rsym value: 0.099 / Net I/σ(I): 14.4
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 3.76 / Rsym value: 0.473 / % possible all: 98.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
CNS1.2refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3O3M

3o3m


Resolution: 2.3→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 3519 5 %RANDOM
Rwork0.2278 ---
all0.2345 71669 --
obs0.2345 71258 99.4 %-
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12279 0 146 1206 13631
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d1.382
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dtt.par
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4fs4s.par
X-RAY DIFFRACTION52hi_CoA_fs4.par

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