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- PDB-4izb: Crystal structure of DmdD, a crotonase superfamily enzyme that ca... -

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Basic information

Entry
Database: PDB / ID: 4izb
TitleCrystal structure of DmdD, a crotonase superfamily enzyme that catalyzes the hydration and hydrolysis of methylthioacryloyl-CoA
ComponentsEnoyl-CoA hydratase/isomerase family protein
KeywordsHYDROLASE / ENOYL-COA HYDRATASE / Dimethyl-sulphoniopropionate (DMSP) METABOLISM / methylthioacryloyl-CoA (MTA-CoA) / CROTONASE FOLD
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 hydratase
Similarity search - Component
Biological speciesRuegeria pomeroyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.504 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 1.1Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)59,8782
Polymers59,8782
Non-polymers00
Water10,593588
1
A: Enoyl-CoA hydratase/isomerase family protein
B: Enoyl-CoA hydratase/isomerase family protein

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

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


Theoretical massNumber of molelcules
Total (without water)179,6336
Polymers179,6336
Non-polymers00
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 area29370 Å2
ΔGint-182 kcal/mol
Surface area43600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.660, 117.660, 117.660
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: 29938.906 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 588 / 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: 45.74 %
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: Jun 29, 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: 1.5→30 Å / Num. obs: 85345 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 31.7
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 7.8 / % possible all: 91.5

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Processing

Software
NameVersionClassification
CBASSdata collection
COMOphasing
PHENIX(phenix.refine: 1.7_650)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HIN

3hin


Resolution: 1.504→27.733 Å / SU ML: 0.16 / σ(F): 0 / Phase error: 13.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1604 4227 5.09 %
Rwork0.1334 --
obs0.1348 83052 96.64 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.028 Å2 / ksol: 0.41 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.504→27.733 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3735 0 0 588 4323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133801
X-RAY DIFFRACTIONf_angle_d1.5775144
X-RAY DIFFRACTIONf_dihedral_angle_d13.2511354
X-RAY DIFFRACTIONf_chiral_restr0.121580
X-RAY DIFFRACTIONf_plane_restr0.008677
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5043-1.52140.17231280.14012484X-RAY DIFFRACTION92
1.5214-1.53930.17391460.12872518X-RAY DIFFRACTION93
1.5393-1.5580.171480.12842528X-RAY DIFFRACTION94
1.558-1.57770.17591260.12692500X-RAY DIFFRACTION94
1.5777-1.59850.14911380.11652579X-RAY DIFFRACTION95
1.5985-1.62040.16411400.11632570X-RAY DIFFRACTION95
1.6204-1.64350.16031540.1142549X-RAY DIFFRACTION95
1.6435-1.66810.16591310.11012597X-RAY DIFFRACTION96
1.6681-1.69410.15321300.10972614X-RAY DIFFRACTION96
1.6941-1.72190.13131350.1062601X-RAY DIFFRACTION97
1.7219-1.75160.16881370.1112659X-RAY DIFFRACTION97
1.7516-1.78340.13351310.11052627X-RAY DIFFRACTION97
1.7834-1.81770.16011480.10592591X-RAY DIFFRACTION97
1.8177-1.85480.13971370.10762647X-RAY DIFFRACTION98
1.8548-1.89520.16021570.11312610X-RAY DIFFRACTION97
1.8952-1.93920.14541420.1182677X-RAY DIFFRACTION99
1.9392-1.98770.15251330.11662682X-RAY DIFFRACTION98
1.9877-2.04140.14521380.11992646X-RAY DIFFRACTION98
2.0414-2.10150.14821520.12662661X-RAY DIFFRACTION98
2.1015-2.16930.1441490.12262671X-RAY DIFFRACTION99
2.1693-2.24680.15891320.12392704X-RAY DIFFRACTION99
2.2468-2.33670.16311590.1282670X-RAY DIFFRACTION99
2.3367-2.4430.18061290.1262721X-RAY DIFFRACTION99
2.443-2.57170.18431290.13372692X-RAY DIFFRACTION99
2.5717-2.73270.15361350.13362744X-RAY DIFFRACTION99
2.7327-2.94350.16141510.142713X-RAY DIFFRACTION99
2.9435-3.23930.16391530.14922720X-RAY DIFFRACTION99
3.2393-3.70710.15971470.14222730X-RAY DIFFRACTION99
3.7071-4.66690.14081330.14182636X-RAY DIFFRACTION95
4.6669-27.73740.19791590.19252484X-RAY DIFFRACTION87

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