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- PDB-4eia: Activator of the 2-Hydroxyisocaproyl-CoA Dehydratase from Clostri... -

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Basic information

Entry
Database: PDB / ID: 4eia
TitleActivator of the 2-Hydroxyisocaproyl-CoA Dehydratase from Clostridium difficile without nucleotide
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
IRON/SULFUR CLUSTER / 2-hydroxyisocaproyl-CoA dehydratase activator
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 5, 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: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / 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 / _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

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Assembly

Deposited unit
A: Activator of 2-hydroxyisocaproyl-CoA dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0072
Polymers29,6561
Non-polymers3521
Water00
1
A: Activator of 2-hydroxyisocaproyl-CoA dehydratase
hetero molecules

A: Activator of 2-hydroxyisocaproyl-CoA dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0154
Polymers59,3122
Non-polymers7032
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565-x,-y+1,z1
Buried area1690 Å2
ΔGint-44 kcal/mol
Surface area23910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.136, 113.136, 56.032
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

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


Mass: 29655.859 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4

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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: 3.02 Å3/Da / Density % sol: 59.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 23 mg/mL protein in 50 mM MOPS, pH 7.2, 120 mM sodium chloride, 1.4 mM ADP, 9 mM magnesium chloride, 1 mM D-desthiobiotin, 6 mM DTT, 1.4 mM sodium dithionite, 100 mM sodium fluoride, 10 mM ...Details: 23 mg/mL protein in 50 mM MOPS, pH 7.2, 120 mM sodium chloride, 1.4 mM ADP, 9 mM magnesium chloride, 1 mM D-desthiobiotin, 6 mM DTT, 1.4 mM sodium dithionite, 100 mM sodium fluoride, 10 mM aluminum trifluoride, reservoir: 8% w/v PEG8000, 25% v/v MPD, 0.35 M sodium chloride, pH 8.5 (drop: 1 uL + 1 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: Jul 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: 3→30 Å / Num. all: 7197 / Num. obs: 7197 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rsym value: 0.059 / Net I/σ(I): 21.32
Reflection shellResolution: 3→3.1 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 4.35 / Rsym value: 0.486 / % 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 4EHT

4eht


Resolution: 3→19.672 Å / SU ML: 0.35 / σ(F): 1.99 / Phase error: 28.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2356 360 5 %
Rwork0.1717 --
obs0.1751 7195 99.76 %
all-7197 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.682 Å2 / ksol: 0.265 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.1371 Å2-0 Å20 Å2
2---8.1371 Å2-0 Å2
3---16.2743 Å2
Refinement stepCycle: LAST / Resolution: 3→19.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1936 0 4 0 1940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091956
X-RAY DIFFRACTIONf_angle_d1.1382635
X-RAY DIFFRACTIONf_dihedral_angle_d15.116728
X-RAY DIFFRACTIONf_chiral_restr0.065319
X-RAY DIFFRACTIONf_plane_restr0.003339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.43240.32761190.24142258X-RAY DIFFRACTION100
3.4324-4.31690.25921190.16862266X-RAY DIFFRACTION100
4.3169-19.6720.20021220.15212311X-RAY DIFFRACTION100
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)
12.58010.72940.88224.8772.42382.83240.1383-0.18940.1752-0.0941-0.2115-0.6146-0.0652-0.36590.04370.16550.0237-0.14360.18870.05890.2103-11.20119.100625.8285
20.916-0.1811-0.27256.0056-1.31852.14780.178-0.0718-0.0014-0.9351-0.3171-1.76450.18010.50560.15550.33370.04060.11930.4199-0.07740.74748.84943.15520.4612
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:91 or resseq 242:258)
2X-RAY DIFFRACTION2chain 'A' and (resseq 92:241)

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