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- PDB-4izc: Crystal structure of DmdD E121A in complex with MTA-CoA -

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Basic information

Entry
Database: PDB / ID: 4izc
TitleCrystal structure of DmdD E121A in complex with MTA-CoA
ComponentsEnoyl-CoA hydratase/isomerase family protein
Keywordshydrolase/substrate / ENOYL-COA HYDRATASE / HYDROLASE / methylthioacryloyl-CoA (MTA-CoA) / Dimethyl-sulphoniopropionate (DMSP) METABOLISM / CROTONASE FOLD / ENYOL-COA HYDRATASE / hydrolase-hydrolase inhibitor complex / hydrolase-substrate complex
Function / homology
Function and homology information


(methylthio)acryloyl-CoA hydratase / enoyl-CoA hydratase activity / hydro-lyase activity / protein hexamerization / fatty acid beta-oxidation
Similarity search - Function
Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
methylthioacryloyl-CoA / Methylthioacryloyl-CoA hydratase
Similarity search - Component
Biological speciesRuegeria pomeroyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTan, D. / Tong, L.
CitationJournal: Plos One / Year: 2013
Title: Crystal Structure of DmdD, a Crotonase Superfamily Enzyme That Catalyzes the Hydration and Hydrolysis of Methylthioacryloyl-CoA.
Authors: Tan, D. / Crabb, W.M. / Whitman, W.B. / Tong, L.
History
DepositionJan 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Enoyl-CoA hydratase/isomerase family protein
B: Enoyl-CoA hydratase/isomerase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4974
Polymers59,7622
Non-polymers1,7352
Water9,314517
1
A: Enoyl-CoA hydratase/isomerase family protein
B: Enoyl-CoA hydratase/isomerase family protein
hetero molecules

A: Enoyl-CoA hydratase/isomerase family protein
B: Enoyl-CoA hydratase/isomerase family protein
hetero molecules

A: Enoyl-CoA hydratase/isomerase family protein
B: Enoyl-CoA hydratase/isomerase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,49112
Polymers179,2856
Non-polymers5,2066
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_645-z+1,x-1/2,-y+1/21
crystal symmetry operation11_556y+1/2,-z+1/2,-x+11
Buried area42140 Å2
ΔGint-217 kcal/mol
Surface area44430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.630, 117.630, 117.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Enoyl-CoA hydratase/isomerase family protein


Mass: 29880.871 Da / Num. of mol.: 2 / Mutation: E121A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruegeria pomeroyi (bacteria) / Strain: DSS-3 / Gene: dmdD / Plasmid: PET 26B / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 STAR / References: UniProt: Q5LLW6
#2: Chemical ChemComp-1GZ / methylthioacryloyl-CoA


Mass: 867.673 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H40N7O17P3S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 517 / 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: 45.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris, 25% (w/v) PEG 3350, 200 mM NaCl , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.075 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 12, 2011 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 50418 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 21.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 5.4 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
COMOphasing
CNS1.3refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→48.02 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 119324.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.181 2481 5 %RANDOM
Rwork0.159 ---
obs0.159 49625 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.8396 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 22.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.8→48.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3906 0 108 517 4531
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.48
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.131.5
X-RAY DIFFRACTIONc_mcangle_it1.612
X-RAY DIFFRACTIONc_scbond_it2.062
X-RAY DIFFRACTIONc_scangle_it2.872.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.301 243 5.1 %
Rwork0.268 4510 -
obs--94.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6MTA.paramMTA.top

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