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- PDB-4fzw: Crystal Structure of the PaaF-PaaG Hydratase-Isomerase Complex fr... -

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Basic information

Entry
Database: PDB / ID: 4fzw
TitleCrystal Structure of the PaaF-PaaG Hydratase-Isomerase Complex from E.coli
Components
  • 1,2-epoxyphenylacetyl-CoA isomerase
  • 2,3-dehydroadipyl-CoA hydratase
KeywordsISOMERASE/LYASE / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / crotonase fold / enzymes of the phenylacetate degradation pathway / ISOMERASE-LYASE complex
Function / homology
Function and homology information


2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase / enoyl-CoA hydratase / phenylacetate catabolic process / enoyl-CoA hydratase activity / fatty acid beta-oxidation / isomerase activity / identical protein binding
Similarity search - Function
Phenylacetate degradation probable enoyl-CoA hydratase PaaB / 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 ...Phenylacetate degradation probable enoyl-CoA hydratase PaaB / 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
2,3-dehydroadipyl-CoA hydratase / 1,2-epoxyphenylacetyl-CoA isomerase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsGrishin, A.M. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Protein-Protein Interactions in the beta-Oxidation Part of the Phenylacetate Utilization Pathway. Crystal Structure of the PaaF-PaaG Hydratase-Isomerase Complex
Authors: Grishin, A.M. / Ajamian, E. / Zhang, L. / Rouiller, I. / Bostina, M. / Cygler, M.
History
DepositionJul 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 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

Downloads & links

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Assembly

Deposited unit
A: 2,3-dehydroadipyl-CoA hydratase
B: 2,3-dehydroadipyl-CoA hydratase
C: 1,2-epoxyphenylacetyl-CoA isomerase
D: 1,2-epoxyphenylacetyl-CoA isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,0987
Polymers114,8224
Non-polymers2763
Water2,180121
1
A: 2,3-dehydroadipyl-CoA hydratase
B: 2,3-dehydroadipyl-CoA hydratase
C: 1,2-epoxyphenylacetyl-CoA isomerase
D: 1,2-epoxyphenylacetyl-CoA isomerase
hetero molecules

A: 2,3-dehydroadipyl-CoA hydratase
B: 2,3-dehydroadipyl-CoA hydratase
C: 1,2-epoxyphenylacetyl-CoA isomerase
D: 1,2-epoxyphenylacetyl-CoA isomerase
hetero molecules

A: 2,3-dehydroadipyl-CoA hydratase
B: 2,3-dehydroadipyl-CoA hydratase
C: 1,2-epoxyphenylacetyl-CoA isomerase
D: 1,2-epoxyphenylacetyl-CoA isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)345,29421
Polymers344,46512
Non-polymers8299
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area30440 Å2
ΔGint-220 kcal/mol
Surface area49450 Å2
Unit cell
Length a, b, c (Å)131.976, 131.976, 153.865
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11B-429-

HOH

DetailsThe two enzymes form a heterododecamer

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Components

#1: Protein 2,3-dehydroadipyl-CoA hydratase / Enoyl-CoA hydratase


Mass: 27638.791 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1393, JW1388, paaF, ydbR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P76082, enoyl-CoA hydratase
#2: Protein 1,2-epoxyphenylacetyl-CoA isomerase


Mass: 29772.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: paaG, ydbT, b1394, JW1389 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P77467, 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 3.37 Å3/Da / Density % sol: 63.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Sodium Citrate pH 5.5, 0.2 M Sodium acetate, 5% (w/w) PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Sep 14, 2010
RadiationMonochromator: ACCEL/BRUKER double crystal monochromator (DCM), featuring indirectly cryo-cooled first crystal and sagittally focusing second crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 51031 / % possible obs: 99.8 % / Redundancy: 8 % / Rmerge(I) obs: 0.107 / Χ2: 1.892 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.55-2.597.30.48525311.1571100
2.59-2.647.40.42825101.1951100
2.64-2.697.40.43125321.2291100
2.69-2.757.60.38525211.1811100
2.75-2.817.70.34825231.217199.9
2.81-2.877.70.30325221.2781100
2.87-2.947.80.27125491.2931100
2.94-3.027.90.22225201.342199.9
3.02-3.1180.20125231.4181100
3.11-3.218.10.16425661.5381100
3.21-3.338.30.13325491.621100
3.33-3.468.40.1225221.7111100
3.46-3.628.50.10125391.885199.9
3.62-3.818.50.09825602.157199.9
3.81-4.058.40.09625622.615199.9
4.05-4.368.30.08625483.033199.4
4.36-4.88.30.07525652.934199.6
4.8-5.498.40.07126092.575199.7
5.49-6.928.30.06726052.433199.7
6.92-507.70.05626753.425197.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 54.23 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.03 Å49.87 Å
Translation3.03 Å49.87 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.11data extraction
MxDCdata collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→46.793 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7337 / SU ML: 0.36 / σ(F): 0 / Phase error: 32.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3211 2589 3.89 %
Rwork0.2802 --
obs0.2818 49484 96.44 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.033 Å2 / ksol: 0.314 e/Å3
Displacement parametersBiso max: 161.73 Å2 / Biso mean: 49.2893 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-9.3795 Å2-0 Å2-0 Å2
2--9.3795 Å20 Å2
3----18.759 Å2
Refinement stepCycle: LAST / Resolution: 2.55→46.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7473 0 18 121 7612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017588
X-RAY DIFFRACTIONf_angle_d1.21410286
X-RAY DIFFRACTIONf_chiral_restr0.0741221
X-RAY DIFFRACTIONf_plane_restr0.0051352
X-RAY DIFFRACTIONf_dihedral_angle_d14.6922749
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5446-2.63550.33251730.28884319449289
2.6355-2.7410.37761790.27774504468392
2.741-2.86570.31741870.26834578476594
2.8657-3.01680.28751880.27994651483995
3.0168-3.20580.31241990.26454760495997
3.2058-3.45320.31862000.25314849504999
3.4532-3.80060.30431970.25344860505799
3.8006-4.35020.30731980.253349455143100
4.3502-5.47950.31212000.264250075207100
5.4795-46.80090.35032040.35175086529099

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