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- PDB-4izd: Crystal structure of DmdD E121A in complex with MMPA-CoA -

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Basic information

Entry
Database: PDB / ID: 4izd
TitleCrystal structure of DmdD E121A in complex with MMPA-CoA
ComponentsEnoyl-CoA hydratase/isomerase family protein
Keywordshydrolase/substrate / ENOYL-COA HYDRATASE / HYDROLASE / Dimethyl-sulphoniopropionate (DMSP) METABOLISM / methylthioacryloyl-CoA (MTA-CoA) / CROTONASE FOLD / 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
3-methylmercaptopropionate-CoA (MMPA-CoA) / Methylthioacryloyl-CoA hydratase
Similarity search - Component
Biological speciesRuegeria pomeroyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / 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)61,5014
Polymers59,7622
Non-polymers1,7392
Water7,945441
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)184,50312
Polymers179,2856
Non-polymers5,2186
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
Unit cell
Length a, b, c (Å)117.130, 117.130, 117.130
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-1HE / 3-methylmercaptopropionate-CoA (MMPA-CoA)


Mass: 869.689 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H42N7O17P3S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 2.24 Å3/Da / Density % sol: 45 %
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: X29A / Wavelength: 1.075 / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 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: 49628 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 32.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 4.5 / % possible all: 96

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Processing

Software
NameVersionClassification
CBASSdata collection
COMOphasing
CNS1.3refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→35.32 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 209110.59 / 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
Rfree0.187 2388 5 %RANDOM
Rwork0.16 ---
obs0.16 47884 96.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.813 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 27.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.8→35.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3863 0 99 441 4403
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.47
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it1.782
X-RAY DIFFRACTIONc_scbond_it2.322
X-RAY DIFFRACTIONc_scangle_it3.192.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.246 226 5.3 %
Rwork0.235 4078 -
obs--87.5 %
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 DIFFRACTION6MMPA.paramMMPA.top

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