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- PDB-6h6v: Structure of the UbiD-class enzyme HmfF from Pelotomaculum thermo... -

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Basic information

Entry
Database: PDB / ID: 6h6v
TitleStructure of the UbiD-class enzyme HmfF from Pelotomaculum thermopropionicum in complex with FMN
Components3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases
KeywordsFLAVOPROTEIN / prFMN / decarboxylation / thermophilic / UbiD / HmfF
Function / homologyUbiD decarboxylyase family / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase Rift-related domain / carboxy-lyase activity / FLAVIN MONONUCLEOTIDE / : / : / 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases
Function and homology information
Biological speciesPelotomaculum thermopropionicum SI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.66 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 ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
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 / _pdbx_seq_map_depositor_info.one_letter_code_mod

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)297,79330
Polymers294,2506
Non-polymers3,54324
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35440 Å2
ΔGint-321 kcal/mol
Surface area94400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.910, 139.250, 136.880
Angle α, β, γ (deg.)90.00, 93.74, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A4 - 449
2010B4 - 449
1020A4 - 449
2020C4 - 449
1030A4 - 449
2030D4 - 449
1040A4 - 449
2040E4 - 449
1050A4 - 449
2050F4 - 449
1060B4 - 449
2060C4 - 449
1070B4 - 449
2070D4 - 449
1080B4 - 449
2080E4 - 449
1090B4 - 449
2090F4 - 449
10100C4 - 449
20100D4 - 449
10110C4 - 449
20110E4 - 449
10120C4 - 449
20120F4 - 449
10130D4 - 449
20130E4 - 449
10140D4 - 449
20140F4 - 449
10150E4 - 449
20150F4 - 449

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

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Protein , 1 types, 6 molecules ABCDEF

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


Mass: 49041.711 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pelotomaculum thermopropionicum SI (bacteria)
Gene: UbiD, PTH_0496 / Production host: Escherichia coli (E. coli) / References: UniProt: A5D4Z9

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Non-polymers , 5 types, 267 molecules

#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#5: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.76 Å3/Da / Density % sol: 55.44 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris/BICINE buffer pH 8.5, 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-F / Detector: PIXEL / Date: Feb 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.66→74.2 Å / Num. obs: 343818 / % possible obs: 99.8 % / Redundancy: 3.8 % / CC1/2: 1 / Rrim(I) all: 0.144 / Net I/σ(I): 9.8
Reflection shellResolution: 2.66→2.73 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 6736 / CC1/2: 0.5 / Rrim(I) all: 1.103 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 2.66→74.2 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.917 / SU B: 15.111 / SU ML: 0.287 / Cross valid method: THROUGHOUT / ESU R: 1.423 / ESU R Free: 0.314 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23599 4311 4.7 %RANDOM
Rwork0.1992 ---
obs0.20097 86650 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 55.86 Å2
Baniso -1Baniso -2Baniso -3
1-3.24 Å20 Å2-0.68 Å2
2---3.19 Å20 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 2.66→74.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20433 0 204 243 20880
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01921102
X-RAY DIFFRACTIONr_bond_other_d0.0020.0220538
X-RAY DIFFRACTIONr_angle_refined_deg1.581.99828734
X-RAY DIFFRACTIONr_angle_other_deg0.968347478
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2352670
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67923.05846
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.685153408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.19115180
X-RAY DIFFRACTIONr_chiral_restr0.0880.23318
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02123238
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024050
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_it3.745.37710698
X-RAY DIFFRACTIONr_mcbond_other3.7385.37710697
X-RAY DIFFRACTIONr_mcangle_it5.8918.06313362
X-RAY DIFFRACTIONr_mcangle_other5.8918.06413363
X-RAY DIFFRACTIONr_scbond_it4.435.83810404
X-RAY DIFFRACTIONr_scbond_other4.4315.83810403
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9568.54815373
X-RAY DIFFRACTIONr_long_range_B_refined9.97462.50922570
X-RAY DIFFRACTIONr_long_range_B_other9.97462.50722570
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A272160.03
12B272160.03
21A272880.03
22C272880.03
31A273580.03
32D273580.03
41A272900.03
42E272900.03
51A273360.03
52F273360.03
61B273060.03
62C273060.03
71B272360.03
72D272360.03
81B272900.03
82E272900.03
91B272980.03
92F272980.03
101C273220.02
102D273220.02
111C273280.03
112E273280.03
121C273500.03
122F273500.03
131D273260.03
132E273260.03
141D273680.03
142F273680.03
151E274100.02
152F274100.02
LS refinement shellResolution: 2.66→2.729 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 321 -
Rwork0.345 6405 -
obs--99.85 %

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