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- PDB-4mi2: Crystal structure of putative Enoyl-CoA hydratase/isomerase from ... -

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Basic information

Entry
Database: PDB / ID: 4mi2
TitleCrystal structure of putative Enoyl-CoA hydratase/isomerase from Mycobacterium abscessus
ComponentsPutative enoyl-CoA hydratase/isomerase
KeywordsISOMERASE / SSGCID / NIH / NIAID / SBRI / EMERALD BIO / PHENYLACETATE DEGRADATION / PHENYLETHYLAMINE DEGRADATION / Structural Genomics / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


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 / 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 ...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 / 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
Enoyl-CoA hydratase/isomerase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of putative Enoyl-CoA hydratase/isomerase from Mycobacterium abscessus
Authors: Davies, D.R. / Lukacs, C. / Lorimer, D. / Edwards, T.E.
History
DepositionAug 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative enoyl-CoA hydratase/isomerase
B: Putative enoyl-CoA hydratase/isomerase
C: Putative enoyl-CoA hydratase/isomerase


Theoretical massNumber of molelcules
Total (without water)82,1013
Polymers82,1013
Non-polymers00
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10550 Å2
ΔGint-75 kcal/mol
Surface area28460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.920, 94.920, 195.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsTHE ASYMMETRIC UNIT IS THE SAME AS THE BIOLOGICAL ASSEMBLY

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Components

#1: Protein Putative enoyl-CoA hydratase/isomerase


Mass: 27367.086 Da / Num. of mol.: 3 / Fragment: PUTATIVE ENOYL-COA HYDRATASE/ISOMERASE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Strain: ATCC 19977 / Gene: MAB_0905 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B1MJ43, 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.68 Å3/Da / Density % sol: 54.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: EBS INTERNAL TRACKING NUMBER 500 MM NACL, 2 MM DTT, 0.025% SODIUM AZIDE, 5% GLYCEROL, 0.4 UL X 0.4 UL DROP WITH MORPHEUS SCREEN CONDITION E12: 0.12 M DI -ETHYLENEGLYCOL; TRI-ETHYLENEGLYCOL, ...Details: EBS INTERNAL TRACKING NUMBER 500 MM NACL, 2 MM DTT, 0.025% SODIUM AZIDE, 5% GLYCEROL, 0.4 UL X 0.4 UL DROP WITH MORPHEUS SCREEN CONDITION E12: 0.12 M DI -ETHYLENEGLYCOL; TRI-ETHYLENEGLYCOL, TETRA-ETHYLENEGLYCOL AND PENTA-ETHYLENEGLYCOL, 0.1 M BUFFER SYSTEM 3 (TRIS BASE, BICINE, PH 8.5), 37.5% MPD/PEG 1000/ PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97625, 0.9774
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 1, 2012
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.976251
20.97741
ReflectionHighest resolution: 2.3 Å / Num. obs: 40335 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 29.93 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 15.31
Reflection shellResolution: 2.3→2.36 Å / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 4.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.7.0032refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→47.51 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.924 / SU B: 10.107 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.262 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2019 5 %RANDOM
Rwork0.179 ---
obs0.181 40335 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2--0.26 Å2-0 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5515 0 0 301 5816
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195623
X-RAY DIFFRACTIONr_bond_other_d0.0010.025450
X-RAY DIFFRACTIONr_angle_refined_deg1.0981.9647682
X-RAY DIFFRACTIONr_angle_other_deg0.77312420
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8535787
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46423.412211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81515793
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8141545
X-RAY DIFFRACTIONr_chiral_restr0.060.2930
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216631
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021220
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5011.2543136
X-RAY DIFFRACTIONr_mcbond_other0.5011.2543135
X-RAY DIFFRACTIONr_mcangle_it0.9061.8773918
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 141 -
Rwork0.216 2803 -
obs--99.83 %
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)
10.55680.14410.56050.2575-0.10111.50850.0202-0.10260.08780.0618-0.05470.0354-0.2514-0.19870.03450.14640.00740.04680.0595-0.02810.13210.417729.502753.4307
20.63440.04080.76870.2405-0.21543.6160.0873-0.07090.04730.0743-0.04780.1142-0.0469-0.3048-0.03950.1333-0.03080.06250.0736-0.0090.11670.900419.448456.5496
30.3224-0.02820.20330.187-0.21221.34770.1191-0.05260.0480.0199-0.04840.0721-0.03550.0834-0.07070.1303-0.04120.02770.0928-0.00420.124314.511220.326150.5323
40.22390.17540.2110.33890.28750.84480.01340.0024-0.0029-0.0623-0.00980.009-0.0602-0.0091-0.00360.08490.01430.01730.09090.02810.13081.819917.297332.8027
51.0408-0.6067-0.79541.03650.12150.7919-0.07340.1389-0.0476-0.05920.04370.00890.0757-0.14630.02960.1632-0.02260.01170.1451-0.03170.065410.6094-3.990112.2721
60.6241-0.4076-0.08320.35340.16560.47570.00530.02620.0128-0.06540.0277-0.0160.0375-0.0069-0.0330.1173-0.00890.01890.10730.00630.10817.35112.627622.7031
70.2097-0.26570.27960.6471-0.25361.0688-0.0265-0.03570.026-0.02150.1139-0.04090.04430.1258-0.08740.07040.02540.04280.1168-0.01540.11420.9853-0.957631.0343
85.265-1.63852.09820.5189-0.72051.34710.2608-0.2583-0.072-0.14150.00310.05150.51740.2796-0.26380.36050.3014-0.13330.3064-0.13440.127633.2517-18.636533.6484
90.0481-0.05930.03081.4340.64151.4494-0.0241-0.05-0.02170.1465-0.0266-0.06520.17670.43270.05070.04940.0957-0.01220.31980.03880.096736.6586-7.48755.0303
100.151-0.0294-0.37880.56760.30191.23180.0133-0.0348-0.01430.0159-0.0895-0.0591-0.01850.15860.07620.04960.0511-0.00880.16560.00240.124829.1257-0.914346.8805
110.8566-0.1395-0.22631.19910.94982.5460.0245-0.00360.1412-0.08590.0939-0.1287-0.1090.3327-0.11830.0488-0.0176-0.03060.15460.01350.077932.392810.44848.7542
121.31410.23280.55421.11830.47740.8621-0.0096-0.1112-0.00640.1236-0.00450.07310.12710.04830.01410.1057-0.03970.00630.1077-0.01180.072514.247214.510163.9345
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 79
2X-RAY DIFFRACTION2A80 - 110
3X-RAY DIFFRACTION3A111 - 171
4X-RAY DIFFRACTION4A172 - 267
5X-RAY DIFFRACTION5B8 - 37
6X-RAY DIFFRACTION6B38 - 171
7X-RAY DIFFRACTION7B172 - 238
8X-RAY DIFFRACTION8B239 - 267
9X-RAY DIFFRACTION9C8 - 90
10X-RAY DIFFRACTION10C91 - 169
11X-RAY DIFFRACTION11C170 - 215
12X-RAY DIFFRACTION12C216 - 267

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