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- PDB-6h6x: Structure of an evolved dimeric form of the UbiD-class enzyme Hmf... -

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Basic information

Entry
Database: PDB / ID: 6h6x
TitleStructure of an evolved dimeric form of the UbiD-class enzyme HmfF from Pelotomaculum thermopropionicum in complex with prFMN
Components3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases
KeywordsFLAVOPROTEIN / prFMN / decarboxylation / thermophilic / UbiD / HmfF
Function / homology
Function and homology information


carboxy-lyase activity / nucleotide binding / metal ion binding
Similarity search - Function
: / : / : / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase N-terminal domain / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase C-terminal domain / UbiD decarboxylyase family / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase Rift-related domain
Similarity search - Domain/homology
Chem-4LU / : / : / 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases
Similarity search - Component
Biological speciesPelotomaculum thermopropionicum
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsPayne, K.A.P. / Leys, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research Councilpre-FAB 695013 United Kingdom
CitationJournal: Acs Catalysis / Year: 2019
Title: Enzymatic Carboxylation of 2-Furoic Acid Yields 2,5-Furandicarboxylic Acid (FDCA).
Authors: Payne, K.A.P. / Marshall, S.A. / Fisher, K. / Cliff, M.J. / Cannas, D.M. / Yan, C. / Heyes, D.J. / Parker, D.A. / Larrosa, I. / Leys, D.
History
DepositionJul 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases
A: 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,08210
Polymers97,7632
Non-polymers1,3198
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-78 kcal/mol
Surface area33180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.720, 63.930, 98.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010B3 - 448
2010A3 - 448

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases


Mass: 48881.383 Da / Num. of mol.: 2
Mutation: A315N, N348R, F351D, T355N, A388P, F393T, V395F, M399R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pelotomaculum thermopropionicum (strain DSM 13744 / JCM 10971 / SI) (bacteria)
Strain: DSM 13744 / JCM 10971 / SI / Gene: UbiD, PTH_0496 / Production host: Escherichia coli (E. coli) / References: UniProt: A5D4Z9

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Non-polymers , 5 types, 191 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-4LU / 1-deoxy-5-O-phosphono-1-(3,3,4,5-tetramethyl-9,11-dioxo-2,3,8,9,10,11-hexahydro-7H-quinolino[1,8-fg]pteridin-12-ium-7-y l)-D-ribitol / prenylated-FMN iminium form


Mass: 525.469 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H30N4O9P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.7 Å3/Da / Density % sol: 54.37 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.12 M alcohols, 0.1 M NaHEPES/MOPS buffer pH 7.5, 20% v/v ethylene glycol and 10% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.08→83.86 Å / Num. obs: 279066 / % possible obs: 97.3 % / Redundancy: 4.5 % / CC1/2: 1 / Rrim(I) all: 0.07 / Net I/σ(I): 12.1
Reflection shellResolution: 2.08→2.13 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 1.7 / CC1/2: 0.6 / Rrim(I) all: 0.92 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H6V

6h6v


Resolution: 2.25→83.86 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.615 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24772 2470 5 %RANDOM
Rwork0.19395 ---
obs0.19667 46764 96.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.524 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.25→83.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6494 0 78 183 6755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0196746
X-RAY DIFFRACTIONr_bond_other_d0.0020.026573
X-RAY DIFFRACTIONr_angle_refined_deg1.911.9939204
X-RAY DIFFRACTIONr_angle_other_deg1.114315182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5475853
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08423.106264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.604151091
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2981554
X-RAY DIFFRACTIONr_chiral_restr0.2210.21077
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217403
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021277
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_it4.8745.0593430
X-RAY DIFFRACTIONr_mcbond_other4.8715.0583429
X-RAY DIFFRACTIONr_mcangle_it7.0887.5684277
X-RAY DIFFRACTIONr_mcangle_other7.0877.5694278
X-RAY DIFFRACTIONr_scbond_it5.3975.6933316
X-RAY DIFFRACTIONr_scbond_other5.3965.6933317
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.2468.2714928
X-RAY DIFFRACTIONr_long_range_B_refined10.82159.9017036
X-RAY DIFFRACTIONr_long_range_B_other10.8259.9027037
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 25912 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.03 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 176 -
Rwork0.295 3512 -
obs--98.95 %

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