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- PDB-4eht: Activator of the 2-Hydroxyisocaproyl-CoA dehydratase from Clostri... -

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Basic information

Entry
Database: PDB / ID: 4eht
TitleActivator of the 2-Hydroxyisocaproyl-CoA dehydratase from Clostridium difficile with bound ADP
ComponentsActivator of 2-hydroxyisocaproyl-CoA dehydratase
KeywordsELECTRON TRANSPORT / actin fold / ATPase / electron transfer / ATP/ADP binding / 2-hydroxyisocaproyl-CoA dehydratase binding
Function / homology
Function and homology information


L-leucine metabolic process / Hydrolases / 4 iron, 4 sulfur cluster binding / hydrolase activity / ATP binding / metal ion binding
Similarity search - Function
CoA enzyme activase / ATPase, BadF/BadG/BcrA/BcrD type / BadF/BadG/BcrA/BcrD ATPase family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / AMMONIUM ION / IRON/SULFUR CLUSTER / 2-hydroxyisocaproyl-CoA dehydratase activator
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKnauer, S.H. / Dobbek, H.
CitationJournal: Biochemistry / Year: 2012
Title: On the ATP-Dependent Activation of the Radical Enzyme (R)-2-Hydroxyisocaproyl-CoA Dehydratase.
Authors: Knauer, S.H. / Buckel, W. / Dobbek, H.
History
DepositionApr 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Database references
Revision 1.2Sep 13, 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_comp_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.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_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.ptnr3_label_comp_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_conn.ptnr2_label_seq_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: Activator of 2-hydroxyisocaproyl-CoA dehydratase
B: Activator of 2-hydroxyisocaproyl-CoA dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,83213
Polymers59,3122
Non-polymers1,52111
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-90 kcal/mol
Surface area23040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.154, 161.005, 63.576
Angle α, β, γ (deg.)90.00, 110.75, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-409-

HOH

21A-417-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Activator of 2-hydroxyisocaproyl-CoA dehydratase


Mass: 29655.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Gene: hadI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus-RIL / References: UniProt: Q5U925

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Non-polymers , 7 types, 282 molecules

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


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.67 Å3/Da / Density % sol: 53.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25 mg/mL protein in 50 mM MOPS, pH 7.2, 0.3 M sodium chloride, 1 mM ADP, 10 mM magnesium chloride, 2.5 mM D-desthiobiotin, 2 mM DTT, 10 mM sodium dithionite, reservoir: 4 M ammonium acetate, ...Details: 25 mg/mL protein in 50 mM MOPS, pH 7.2, 0.3 M sodium chloride, 1 mM ADP, 10 mM magnesium chloride, 2.5 mM D-desthiobiotin, 2 mM DTT, 10 mM sodium dithionite, reservoir: 4 M ammonium acetate, 0.1 M Tris/HCl, pH 8.5 (drop: 2 uL + 2 uL), VAPOR DIFFUSION, HANGING DROP, temperature 289K

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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: Aug 26, 2008
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. all: 44923 / Num. obs: 44923 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rsym value: 0.048
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.8 % / Num. unique all: 3282 / Rsym value: 0.501 / % possible all: 99.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HUX

1hux


Resolution: 1.95→19.7 Å / SU ML: 0.23 / σ(F): 1.99 / Phase error: 22.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2051 2145 4.78 %RANDOM
Rwork0.1756 ---
obs0.1771 44923 99.61 %-
all-44923 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.272 Å2 / ksol: 0.411 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.3213 Å2-0 Å211.0121 Å2
2---4.7705 Å2-0 Å2
3---0.4493 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3933 0 79 271 4283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094094
X-RAY DIFFRACTIONf_angle_d1.3625541
X-RAY DIFFRACTIONf_dihedral_angle_d14.5921528
X-RAY DIFFRACTIONf_chiral_restr0.072662
X-RAY DIFFRACTIONf_plane_restr0.004707
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.01960.28792220.23474258X-RAY DIFFRACTION100
2.0196-2.10040.25562210.22464233X-RAY DIFFRACTION99
2.1004-2.19590.20632170.18454262X-RAY DIFFRACTION100
2.1959-2.31150.24062030.18444236X-RAY DIFFRACTION99
2.3115-2.45610.20912140.1674324X-RAY DIFFRACTION100
2.4561-2.64530.23352100.16754285X-RAY DIFFRACTION100
2.6453-2.91070.22112100.18654259X-RAY DIFFRACTION100
2.9107-3.33020.22972150.18734304X-RAY DIFFRACTION100
3.3302-4.1890.16882150.164288X-RAY DIFFRACTION100
4.189-19.70070.16952180.15054312X-RAY DIFFRACTION99
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)
10.7425-0.1635-0.33331.5942-0.69471.40260.0040.0881-0.167-0.1511-0.01410.15210.1957-0.16940.01260.1356-0.03130.00120.1193-0.04160.147918.245761.019613.5993
22.86010.22720.57170.48030.55291.426-0.18110.24750.666-0.0798-0.04120.3235-0.3892-0.07340.2080.26410.0547-0.05130.15960.05860.3557.1022101.347821.1058
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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