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- PDB-7yls: Structure of a bacteria protein complex -

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Basic information

Entry
Database: PDB / ID: 7yls
TitleStructure of a bacteria protein complex
Components
  • Aromatic-ring-hydroxylating dioxygenase beta subunit
  • Rieske (2Fe-2S) domain protein
KeywordsMETAL BINDING PROTEIN / a bacteria protein complex / FLAVOPROTEIN
Function / homology
Function and homology information


3-phenylpropionate catabolic process / dioxygenase activity / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / iron ion binding
Similarity search - Function
Ring hydroxylating beta subunit / Ring-hydroxylating dioxygenase beta subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain ...Ring hydroxylating beta subunit / Ring-hydroxylating dioxygenase beta subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / NTF2-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / : / FE2/S2 (INORGANIC) CLUSTER / Rieske (2Fe-2S) domain protein / Aromatic-ring-hydroxylating dioxygenase beta subunit
Similarity search - Component
Biological speciesVariovorax paradoxus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZhang, H. / Ma, Y.J. / Yu, G.M. / Li, X.Z.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
CitationJournal: To Be Published
Title: Structure of a bacteria protein complex
Authors: Zhang, H. / Ma, Y.J. / Yu, G.M. / Li, X.Z.
History
DepositionJul 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aromatic-ring-hydroxylating dioxygenase beta subunit
B: Rieske (2Fe-2S) domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1108
Polymers68,6092
Non-polymers5016
Water8,503472
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-47 kcal/mol
Surface area25630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.613, 135.613, 135.613
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number195
Space group name H-MP23
Space group name HallP223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-348-

HOH

21A-440-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Aromatic-ring-hydroxylating dioxygenase beta subunit


Mass: 18952.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Variovorax paradoxus (bacteria) / Gene: Vapar_1494 / Production host: Escherichia coli (E. coli) / References: UniProt: C5CSP7
#2: Protein Rieske (2Fe-2S) domain protein


Mass: 49656.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Variovorax paradoxus (bacteria) / Gene: Vapar_1493 / Production host: Escherichia coli (E. coli) / References: UniProt: C5CSP6

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Non-polymers , 5 types, 478 molecules

#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.03 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 291.15 K / Method: liquid diffusion
Details: 2-Methyl-2,4-pentanediol, Sodium cacodylate trihydrate, Magnesium acetate tetrahydrate, 1,3-Propanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→135.61 Å / Num. obs: 77237 / % possible obs: 99.97 % / Redundancy: 26.8 % / Biso Wilson estimate: 25.23 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.93
Reflection shellResolution: 1.8→1.864 Å / Num. unique obs: 7635 / CC1/2: 0.888

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIX1.20_4459phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold2

Resolution: 1.8→37.61 Å / SU ML: 0.1186 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.4141
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1681 3815 4.94 %
Rwork0.1518 73400 -
obs0.1526 77215 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.88 Å2
Refinement stepCycle: LAST / Resolution: 1.8→37.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4784 0 23 472 5279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01294929
X-RAY DIFFRACTIONf_angle_d1.23346674
X-RAY DIFFRACTIONf_chiral_restr0.0668696
X-RAY DIFFRACTIONf_plane_restr0.0161882
X-RAY DIFFRACTIONf_dihedral_angle_d6.5066663
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.25871300.20132710X-RAY DIFFRACTION100
1.82-1.840.20321390.18722715X-RAY DIFFRACTION100
1.84-1.870.17611450.17972654X-RAY DIFFRACTION100
1.87-1.90.18891510.18152693X-RAY DIFFRACTION100
1.9-1.920.2238940.17892752X-RAY DIFFRACTION100
1.92-1.950.18391360.16462711X-RAY DIFFRACTION100
1.95-1.990.19241200.16332703X-RAY DIFFRACTION100
1.99-2.020.19951420.15652697X-RAY DIFFRACTION100
2.02-2.060.16681650.14292688X-RAY DIFFRACTION100
2.06-2.10.14611240.14582714X-RAY DIFFRACTION100
2.1-2.140.17281490.14932665X-RAY DIFFRACTION100
2.14-2.190.18791600.14872694X-RAY DIFFRACTION100
2.19-2.240.15851440.15222712X-RAY DIFFRACTION100
2.24-2.290.19741320.1492705X-RAY DIFFRACTION100
2.29-2.360.17471300.15072709X-RAY DIFFRACTION100
2.36-2.420.17351250.15792757X-RAY DIFFRACTION100
2.43-2.50.16571390.14942685X-RAY DIFFRACTION100
2.5-2.590.19791440.15252729X-RAY DIFFRACTION100
2.59-2.70.17451300.15222710X-RAY DIFFRACTION100
2.7-2.820.18071500.14842711X-RAY DIFFRACTION100
2.82-2.970.15331730.152708X-RAY DIFFRACTION100
2.97-3.150.14451510.14882727X-RAY DIFFRACTION100
3.15-3.40.15991620.13952687X-RAY DIFFRACTION100
3.4-3.740.17291530.13722730X-RAY DIFFRACTION100
3.74-4.280.13631560.13092757X-RAY DIFFRACTION100
4.28-5.390.16641310.1392788X-RAY DIFFRACTION99.97
5.39-37.610.17471400.19172889X-RAY DIFFRACTION99.77
Refinement TLS params.Method: refined / Origin x: 46.086138973 Å / Origin y: 15.9230939606 Å / Origin z: 44.9212675198 Å
111213212223313233
T0.258814801143 Å20.0743285130377 Å20.0697040021739 Å2-0.16422143571 Å20.0605533343903 Å2--0.22688011976 Å2
L0.673583199732 °2-0.29496997878 °20.0637760961938 °2-0.46615527527 °2-0.149982404152 °2--0.665330753527 °2
S-0.0355572563343 Å °-0.0552778191666 Å °-0.134034718807 Å °0.00687117822263 Å °0.011584318272 Å °0.00848774778571 Å °0.168568255121 Å °0.032273159051 Å °0.00844175972927 Å °
Refinement TLS groupSelection details: all

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