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- PDB-3o3o: (R)-2-hydroxyisocaproyl-CoA dehydratase in complex with (R)-2-hyd... -

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Basic information

Entry
Database: PDB / ID: 3o3o
Title(R)-2-hydroxyisocaproyl-CoA dehydratase in complex with (R)-2-hydroxyisocaproate
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
(2R)-2-hydroxy-4-methylpentanoic acid / HYDROSULFURIC ACID / 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 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,8746
Polymers90,0052
Non-polymers8704
Water13,799766
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-72 kcal/mol
Surface area30450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.309, 85.584, 149.508
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, 2 molecules AB

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


Mass: 46383.852 Da / Num. of mol.: 1
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) CodoPlus-RIL / References: UniProt: Q5U924
#2: Protein beta-subunit 2-hydroxyacyl-CoA dehydratase


Mass: 43621.109 Da / Num. of mol.: 1
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, 770 molecules

#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-2RH / (2R)-2-hydroxy-4-methylpentanoic acid / (R)-2-hydroxyisocaproate


Mass: 132.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O3
#5: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE / Hydrogen sulfide


Mass: 34.081 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 766 / 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: 2.31 Å3/Da / Density % sol: 46.85 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: The dehydratase was cocrystallized by incubation with 5 mM (R)-2-hydroxyisocaproate 10 minutes prior to crystallization. Reservoir solution: 23 % PEG 3350, 0.1M Bis-Tris, pH 6.5, VAPOR ...Details: The dehydratase was cocrystallized by incubation with 5 mM (R)-2-hydroxyisocaproate 10 minutes prior to crystallization. Reservoir solution: 23 % PEG 3350, 0.1M Bis-Tris, 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: Jul 24, 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: 1.994→30 Å / Num. all: 57440 / Num. obs: 55143 / % possible obs: 96 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 0.09 / Net I/σ(I): 9.25
Reflection shellResolution: 1.994→2.1 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 3.04 / Rsym value: 0.277 / % possible all: 88.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3O3M

3o3m


Resolution: 2→29.072 Å / SU ML: 0.28 / σ(F): 1.99 / Phase error: 26.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2571 2758 5 %
Rwork0.2038 --
obs0.2064 55133 96.08 %
all-57712 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 82.242 Å2 / ksol: 0.325 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.8887 Å2-0 Å20 Å2
2---8.8265 Å2-0 Å2
3----2.0622 Å2
Refinement stepCycle: LAST / Resolution: 2→29.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6135 0 26 766 6927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016309
X-RAY DIFFRACTIONf_angle_d1.3478605
X-RAY DIFFRACTIONf_dihedral_angle_d13.4362426
X-RAY DIFFRACTIONf_chiral_restr0.076931
X-RAY DIFFRACTIONf_plane_restr0.0041097
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.07150.31732470.24284675X-RAY DIFFRACTION87
2.0715-2.15440.32042680.25495092X-RAY DIFFRACTION95
2.1544-2.25240.28922810.22465335X-RAY DIFFRACTION98
2.2524-2.37110.31312760.23165246X-RAY DIFFRACTION98
2.3711-2.51960.27452790.1985306X-RAY DIFFRACTION98
2.5196-2.7140.27552780.19115289X-RAY DIFFRACTION98
2.714-2.98690.26462790.20625296X-RAY DIFFRACTION97
2.9869-3.41850.25982800.20455319X-RAY DIFFRACTION97
3.4185-4.30470.20952790.17345306X-RAY DIFFRACTION96
4.3047-29.07490.21332910.18765511X-RAY DIFFRACTION96
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)
10.261-0.1738-0.05370.31120.09830.6516-0.0328-0.0237-0.03580.02940.0226-0.02070.21060.0388-00.11990.01630.01070.04880.00570.0595-17.2416-23.272323.4421
20.124-0.0226-0.07010.40480.09970.55930.01550.00430.0567-0.0681-0.00360.0212-0.1812-0.079400.08150.03030.00830.08320.01370.0877-28.55756.80236.0718
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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