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- PDB-2y8n: Crystal structure of glycyl radical enzyme -

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Basic information

Entry
Database: PDB / ID: 2y8n
TitleCrystal structure of glycyl radical enzyme
Components
  • 4-HYDROXYPHENYLACETATE DECARBOXYLASE LARGE SUBUNIT
  • 4-HYDROXYPHENYLACETATE DECARBOXYLASE SMALL SUBUNIT
KeywordsLYASE / RADICAL CHEMISTRY / METALLOENZYME / IRON-SULFUR CENTER
Function / homology
Function and homology information


4-hydroxyphenylacetate decarboxylase / 4-hydroxyphenylacetate decarboxylase activity / 4 iron, 4 sulfur cluster binding / metal ion binding / cytosol
Similarity search - Function
Ubiquitin Ligase Nedd4; Chain: W; - #100 / 4-hydroxyphenylacetate decarboxylase small gamma subunit, C-terminal / 4-hydroxyphenylacetate decarboxylase small gamma subunit, N-terminal / : / High potential iron-sulfur protein like / 4-Hydroxyphenylacetate decarboxylase subunit gamma N-terminal / : / Pyruvate formate lyase domain / Pyruvate formate lyase-like / Pyruvate formate-lyase domain profile. ...Ubiquitin Ligase Nedd4; Chain: W; - #100 / 4-hydroxyphenylacetate decarboxylase small gamma subunit, C-terminal / 4-hydroxyphenylacetate decarboxylase small gamma subunit, N-terminal / : / High potential iron-sulfur protein like / 4-Hydroxyphenylacetate decarboxylase subunit gamma N-terminal / : / Pyruvate formate lyase domain / Pyruvate formate lyase-like / Pyruvate formate-lyase domain profile. / Glycine radical / Glycine radical domain / Glycine radical domain profile. / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain - #20 / Ubiquitin Ligase Nedd4; Chain: W; / Single Sheet / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / 4-hydroxyphenylacetate decarboxylase small subunit / 4-hydroxyphenylacetate decarboxylase glycyl radical subunit
Similarity search - Component
Biological speciesCLOSTRIDIUM SCATOLOGENES (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMartins, B.M. / Blaser, M. / Feliks, M. / Ullmann, G.M. / Selmer, T.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Structural Basis for a Kolbe-Type Decarboxylation Catalyzed by a Glycyl Radical Enzyme.
Authors: Martins, B.M. / Blaser, M. / Feliks, M. / Ullmann, G.M. / Buckel, W. / Selmer, T.
History
DepositionFeb 8, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Database references
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Oct 16, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status / reflns_shell
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf / _reflns_shell.Rmerge_I_obs
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 4-HYDROXYPHENYLACETATE DECARBOXYLASE LARGE SUBUNIT
B: 4-HYDROXYPHENYLACETATE DECARBOXYLASE SMALL SUBUNIT
C: 4-HYDROXYPHENYLACETATE DECARBOXYLASE LARGE SUBUNIT
D: 4-HYDROXYPHENYLACETATE DECARBOXYLASE SMALL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,6058
Polymers220,1984
Non-polymers1,4074
Water38,0842114
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12310 Å2
ΔGint-136.2 kcal/mol
Surface area56330 Å2
MethodPISA
2
A: 4-HYDROXYPHENYLACETATE DECARBOXYLASE LARGE SUBUNIT
B: 4-HYDROXYPHENYLACETATE DECARBOXYLASE SMALL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,8024
Polymers110,0992
Non-polymers7032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-60.2 kcal/mol
Surface area29930 Å2
MethodPISA
3
C: 4-HYDROXYPHENYLACETATE DECARBOXYLASE LARGE SUBUNIT
D: 4-HYDROXYPHENYLACETATE DECARBOXYLASE SMALL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,8024
Polymers110,0992
Non-polymers7032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-60.8 kcal/mol
Surface area30130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.280, 227.760, 148.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2338-

HOH

21C-2303-

HOH

31C-2698-

HOH

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Components

#1: Protein 4-HYDROXYPHENYLACETATE DECARBOXYLASE LARGE SUBUNIT / GLYCYL RADICAL ENZYME / 4-HYDROXYPHENYLACETATE DECARBOXYLASE GLYCYL RADICAL SUBUNIT / P- ...GLYCYL RADICAL ENZYME / 4-HYDROXYPHENYLACETATE DECARBOXYLASE GLYCYL RADICAL SUBUNIT / P-HYDROXYPHENYLACETATE DECARBOXYLASE LARGE SUBUNIT


Mass: 100745.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM SCATOLOGENES (bacteria) / Description: GERMAN COLLECTION OF MICROORGANISMS / Plasmid: PASK-IBA7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA
References: UniProt: Q38HX4, 4-hydroxyphenylacetate decarboxylase
#2: Protein 4-HYDROXYPHENYLACETATE DECARBOXYLASE SMALL SUBUNIT / GLYCYL RADICAL ENZYME / P-HYDROXYPHENYLACETATE DECARBOXYLASE SMALL SUBUNIT


Mass: 9353.634 Da / Num. of mol.: 2 / Fragment: NONE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM SCATOLOGENES (bacteria) / Description: GERMAN COLLECTION OF MICROORGANISMS / Plasmid: PASK-IBA7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA
References: UniProt: Q38HX3, 4-hydroxyphenylacetate decarboxylase
#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2114 / 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: 5

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: 22 % PEG MME 550, 30 MM MGCL2, 100 MM TRIS/HCL PH 7.5 - 8.4 .

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→29.18 Å / Num. obs: 217979 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 17.09 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.5
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 5.7 / % possible all: 95

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Processing

Software
NameClassification
XDSdata reduction
XDSdata scaling
AMoREphasing
SHARPphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R9D

1r9d


Resolution: 1.75→29.184 Å / SU ML: 0.23 / σ(F): 1.36 / Phase error: 22.98 / Stereochemistry target values: ML
Details: FIRST 29 RESIDUES IN CHAINS A, C DISORDERED. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY.
RfactorNum. reflection% reflection
Rfree0.2278 10962 5 %
Rwork0.1843 --
obs0.1865 217979 97.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.149 Å2 / ksol: 0.348 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.175 Å20 Å20 Å2
2---0.2602 Å20 Å2
3---0.4352 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.184 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14948 0 32 2114 17094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715354
X-RAY DIFFRACTIONf_angle_d1.08520790
X-RAY DIFFRACTIONf_dihedral_angle_d17.7915572
X-RAY DIFFRACTIONf_chiral_restr0.0732218
X-RAY DIFFRACTIONf_plane_restr0.0052682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.81250.367610520.341520050X-RAY DIFFRACTION95
1.8125-1.88510.350210630.309720182X-RAY DIFFRACTION96
1.8851-1.97090.297810670.262220264X-RAY DIFFRACTION96
1.9709-2.07480.26911290.222220383X-RAY DIFFRACTION97
2.0748-2.20470.243710710.19620592X-RAY DIFFRACTION97
2.2047-2.37490.229910750.175820674X-RAY DIFFRACTION98
2.3749-2.61370.22810700.167220938X-RAY DIFFRACTION99
2.6137-2.99160.221611270.161221022X-RAY DIFFRACTION99
2.9916-3.76780.188211020.148221230X-RAY DIFFRACTION100
3.7678-29.18840.172512060.136621682X-RAY DIFFRACTION100

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