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- PDB-6da9: Crystal structure of the TtnD decarboxylase from the tautomycetin... -

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Basic information

Entry
Database: PDB / ID: 6da9
TitleCrystal structure of the TtnD decarboxylase from the tautomycetin biosynthesis pathway of Streptomyces griseochromogenes with FMN bound at 2.05 A resolution
ComponentsUbiD-like decarboxylase
KeywordsLYASE / TtnD / decarboxylase / tautomycetin biosynthesis / prFMN binding / Structural Genomics / PSI-Biology / Enzyme Discovery for Natural Product Biosynthesis / NatPro
Function / homology
Function and homology information


pyrrole-2-carboxylate decarboxylase / ferulate metabolic process / cinnamic acid catabolic process / carboxy-lyase activity / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
UbiD-like decarboxylase/ferulic acid decarboxylase 1 / : / : / : / 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
FLAVIN MONONUCLEOTIDE / : / Unknown ligand / Pyrrole-2-carboxylic acid decarboxylase
Similarity search - Component
Biological speciesStreptomyces griseochromogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.05 Å
AuthorsHan, L. / Rudolf, J.D. / Chang, C.-Y. / Miller, M.D. / Soman, J. / Xu, W. / Phillips Jr., G.N. / Shen, B. / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U01GM098248 United States
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Biochemical and Structural Characterization of TtnD, a Prenylated FMN-Dependent Decarboxylase from the Tautomycetin Biosynthetic Pathway.
Authors: Annaval, T. / Han, L. / Rudolf, J.D. / Xie, G. / Yang, D. / Chang, C.Y. / Ma, M. / Crnovcic, I. / Miller, M.D. / Soman, J. / Xu, W. / Phillips Jr., G.N. / Shen, B.
History
DepositionMay 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UbiD-like decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,30815
Polymers54,7831
Non-polymers1,52414
Water3,369187
1
A: UbiD-like decarboxylase
hetero molecules

A: UbiD-like decarboxylase
hetero molecules

A: UbiD-like decarboxylase
hetero molecules

A: UbiD-like decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,23160
Polymers219,1344
Non-polymers6,09756
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area31840 Å2
ΔGint-140 kcal/mol
Surface area62750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.070, 116.109, 193.969
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-514-

UNL

21A-728-

HOH

31A-767-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein UbiD-like decarboxylase / TtnD decarboxylase from the tautomycetin biosynthesis pathway of Streptomyces griseochromogenes


Mass: 54783.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseochromogenes (bacteria)
Gene: ttnD
Plasmid details: ttnD gene cloned in pCDFDuet-1 between EcoRI and HindIII sites
Plasmid: pBS13033 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: C6ZCR8, Lyases; Carbon-carbon lyases; Carboxy-lyases

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Non-polymers , 5 types, 201 molecules

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


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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

CrystalColour: yellow / Density Matthews: 2.68 Å3/Da / Density % sol: 54.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 3 mM TtnD1, 3 mM MnCl2, 0.5 mM FMN, 20% (v/v) glycerol in precipitant solution
Experiment crystal grow comp
ConcComp nameComp-IDCrystal-IDSol-ID
18.6 mg/mlprotein11macromolecule
10. mMTetraethylammonium hydroxide, TEAOH21macromolecule
20. mMNaCl31macromolecule
10. mMKCl41macromolecule
40.0 percent_volume_by_volumepentaerythritol propoxylate (5/4 PO/OH)51precipitant
0.1 MHEPES61precipitant
0.2 Msodium thiocyanate71precipitant
Experiment crystal grow sol
Crystal-IDSol-IDpHVolume (Å3)
1macromolecule7.50.3 µL
1precipitant70.3 µL
1reservoir70.3 mL
Experiment crystal cryo treatmentCooling details: Direct immersion in liquid nitrogen.
Final solution details: 3mM TtnD1, 3mM MnCl2, 0.5 mM FMN, 20% glycerol in precipitant solution

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 12, 2015
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.05→48.5 Å / Num. obs: 37316 / % possible obs: 97.8 % / Redundancy: 7.24 % / Biso Wilson estimate: 40.59 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.053 / Rrim(I) all: 0.144 / Net I/σ(I): 10.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.05-2.161.3920.61574826240.5770.6041.5221.3921.396.4
2.1-2.167.11.2110.61901126700.6720.4841.3061.2111.6100
2.16-2.227.30.9950.81893225800.7410.3931.0710.9952.1100
2.22-2.297.40.7911857225030.8380.3110.8490.792.6100
2.29-2.377.50.6711.21853024860.8690.2630.7220.6713100
2.37-2.457.50.5381.51735223220.9210.2110.5790.5383.7100
2.45-2.547.40.4831.61710223010.9280.190.5190.4834.3100
2.54-2.657.40.38321658022260.9520.150.4120.3835.1100
2.65-2.767.50.3112.51567421000.9680.1220.3350.3116.2100
2.76-2.97.40.2383.31519520420.9810.0940.2560.2387.9100
2.9-3.067.40.1814.31442419370.9880.0710.1950.18110.2100
3.06-3.247.40.1335.71355318210.9930.0520.1430.13313.3100
3.24-3.477.40.0987.51272617180.9960.0390.1060.09817.2100
3.47-3.747.40.0769.21195216260.9970.030.0810.07621.8100
3.74-4.17.30.06210.81084614820.9980.0250.0670.06226.799.9
4.1-4.587.20.05312.5977413500.9980.0210.0570.05331.499.8
4.58-5.297.20.05411.6873512160.9980.0210.0580.05430.9100
5.29-6.487.10.05511.6729510310.9980.0220.060.05529.9100
6.48-9.176.90.0431555958150.9980.0180.0460.04332.9100
9.17-48.495.60.04314.325904660.9980.0190.0470.04331.197.3

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XDSdata scaling
PHENIX1.10_2155phasing
BUSTER2.10.3refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6DA7

6da7


Resolution: 2.05→19.98 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.299 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.17 / SU Rfree Blow DPI: 0.143 / SU Rfree Cruickshank DPI: 0.143
Details: 1. TLS GROUPS WERE ASSIGNED WITH THE AID OF TLSMD. 2. ZERO OCCUPANCY HYDROGENS IN THEIR RIDING POSITION WERE USED AS ANTI-BUMPING RESTRAINTS. 3. LSSR TARGET RESTRAINTS TO THE APO TTND ...Details: 1. TLS GROUPS WERE ASSIGNED WITH THE AID OF TLSMD. 2. ZERO OCCUPANCY HYDROGENS IN THEIR RIDING POSITION WERE USED AS ANTI-BUMPING RESTRAINTS. 3. LSSR TARGET RESTRAINTS TO THE APO TTND STRUCTURE (PDBID 6DA7) WERE INCLUDED. 4. CRYSTAL WAS SOAKED WITH FMN AS A MIMIC OF THE REQUIRED CO-FACTOR, PRENYLATED-FMN (prFMN). 4. AN UNKNOWN LIGAND (UNL) IS MODELED. THERE ARE 2 UNL's BOUND IN THE TETRAMER. THE SHAPE LOOKS LIKE BENZOATE OR NIACIN. THE SITE IS ON A CRYSTALLOGRPAHIC TWO-FOLD AXIS.
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1437 3.86 %RANDOM
Rwork0.193 ---
obs0.194 37267 99.7 %-
Displacement parametersBiso max: 252.28 Å2 / Biso mean: 54.85 Å2 / Biso min: 19.41 Å2
Baniso -1Baniso -2Baniso -3
1-2.4327 Å20 Å20 Å2
2---7.7616 Å20 Å2
3---5.3289 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: final / Resolution: 2.05→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3553 0 107 187 3847
Biso mean--65.44 52.98 -
Num. residues----463
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1642SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1189HARMONIC5
X-RAY DIFFRACTIONt_it7513HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion489SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8028SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7513HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg13612HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion3.71
X-RAY DIFFRACTIONt_other_torsion14.13
LS refinement shellResolution: 2.05→2.11 Å / Rfactor Rfree error: 0 / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2875 113 4.1 %
Rwork0.2776 2641 -
all0.278 2754 -
obs--96.35 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.46390.40950.59400.34631.60740.0333-0.4102-0.04560.1804-0.0272-0.02250.12190.0216-0.0061-0.0339-0.0013-0.01170.0775-0.1147-0.13557.756118.495741.0712
20.43760.09270.19210.33490.49430.4732-0.0245-0.06570.07930.02870.08480.0072-0.164-0.001-0.0603-0.013-0.008-0.00070.0424-0.12-0.05538.429430.706529.5001
30.3080.01640.06530.2644-0.05550.5663-0.0256-0.08760.01610.00020.01610.0249-0.0629-0.02660.0094-0.06020.01180.0050.0664-0.0172-0.0236-4.932610.431413.6824
41.6707-2.3347-0.90571.9056-1.10780.3361-0.06690.12750.12110.18820.07970.163-0.0570.0627-0.0128-0.09850.0820.09140.13440.0505-0.0606-20.9109-6.429434.033
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|0 - A|44 }A0 - 44
2X-RAY DIFFRACTION2{ A|45 - A|309 }A45 - 309
3X-RAY DIFFRACTION3{ A|310 - A|460 }A310 - 460
4X-RAY DIFFRACTION4{ A|461 - A|485 }A461 - 485

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