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- PDB-3o3m: (R)-2-Hydroxyisocaproyl-CoA Dehydratase -

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Basic information

Entry
Database: PDB / ID: 3o3m
Title(R)-2-Hydroxyisocaproyl-CoA Dehydratase
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 / 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 / MAD / Resolution: 1.82 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 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
C: alpha subunit 2-hydroxyisocaproyl-CoA dehydratase
D: beta subunit 2-hydroxyacyl-CoA dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,67712
Polymers180,0104
Non-polymers1,6678
Water30,3191683
1
A: alpha subunit 2-hydroxyisocaproyl-CoA dehydratase
B: beta subunit 2-hydroxyacyl-CoA dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,8386
Polymers90,0052
Non-polymers8334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-91 kcal/mol
Surface area29110 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)90,8386
Polymers90,0052
Non-polymers8334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-91 kcal/mol
Surface area29250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.764, 129.192, 179.166
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) CodonPlus-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, 1691 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#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.: 1683 / 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: 2.27 Å3/Da / Density % sol: 45.93 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 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: 0.91841,1.73980,1.74203
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 24, 2008
Details: Double crystal monochromator with 2 sets of mirrors
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918411
21.73981
31.742031
ReflectionResolution: 1.82→30 Å / Num. all: 147537 / Num. obs: 146208 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rsym value: 0.063 / Net I/σ(I): 12.52
Reflection shellResolution: 1.82→1.9 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.71 / Rsym value: 0.477 / % possible all: 98.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.82→19.699 Å / SU ML: 0.24 / σ(F): 1.99 / Phase error: 22.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2204 7309 5 %
Rwork0.1732 --
obs0.1755 146131 99.15 %
all-147384 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.45 Å2 / ksol: 0.377 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.389 Å20 Å2-0 Å2
2--6.813 Å20 Å2
3----8.202 Å2
Refinement stepCycle: LAST / Resolution: 1.82→19.699 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12276 0 44 1683 14003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712758
X-RAY DIFFRACTIONf_angle_d1.89817378
X-RAY DIFFRACTIONf_dihedral_angle_d12.3114952
X-RAY DIFFRACTIONf_chiral_restr0.0731894
X-RAY DIFFRACTIONf_plane_restr0.0032230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.8850.29067150.233813580X-RAY DIFFRACTION98
1.885-1.96040.27597240.211113743X-RAY DIFFRACTION99
1.9604-2.04950.25287280.193613824X-RAY DIFFRACTION100
2.0495-2.15750.24577290.18313862X-RAY DIFFRACTION100
2.1575-2.29250.22997320.17213890X-RAY DIFFRACTION100
2.2925-2.46910.22197310.163813881X-RAY DIFFRACTION100
2.4691-2.71710.22727330.166813947X-RAY DIFFRACTION100
2.7171-3.10890.21227320.168113911X-RAY DIFFRACTION99
3.1089-3.91180.2067340.154713927X-RAY DIFFRACTION98
3.9118-19.70.18047510.157414257X-RAY DIFFRACTION98
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)
10.29090.23450.3670.42450.3551.0884-0.06560.0486-0.0332-0.26580.0664-0.0759-0.26870.0261-0.00310.2583-0.01080.02130.0529-0.00260.139242.118316.60935.5442
20.19680.170.48480.92350.52881.59130.0976-0.26340.00020.0803-0.21580.12740.1825-0.73640.10820.0866-0.09360.00220.3931-0.02690.10820.82396.62832.6327
30.2975-0.05640.00210.15420.11160.7815-0.0064-0.02840.01460.0625-0.01970.07680.0931-0.02820.02530.105-0.01720.01090.0591-0.00750.14828.943915.923186.9818
40.27670.0005-0.03970.63510.14110.8953-0.01540.0783-0.0411-0.0148-0.0151-0.06490.1610.23530.02080.10030.03610.00060.1721-0.0010.110750.32275.935459.7747
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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