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- PDB-6da7: Crystal structure of the TtnD decarboxylase from the tautomycetin... -

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Basic information

Entry
Database: PDB / ID: 6da7
TitleCrystal structure of the TtnD decarboxylase from the tautomycetin biosynthesis pathway of Streptomyces griseochromogenes with apo form at 1.83 A resolution (I222)
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
Unknown ligand / Pyrrole-2-carboxylic acid decarboxylase
Similarity search - Component
Biological speciesStreptomyces griseochromogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.83 Å
AuthorsHan, L. / Rudolf, J.D. / Chang, C.-Y. / Miller, M.D. / Soman, J. / 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)56,70222
Polymers54,7831
Non-polymers1,91921
Water4,197233
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)226,80988
Polymers219,1344
Non-polymers7,67684
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 area39180 Å2
ΔGint-133 kcal/mol
Surface area60510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.352, 114.387, 194.351
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-520-

GOL

21A-521-

UNL

31A-521-

UNL

41A-763-

HOH

51A-812-

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, 254 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 18 / 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.: 233 / 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: clear / Density Matthews: 2.66 Å3/Da / Density % sol: 53.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 40.0 v/v pentaerythritol propoxylate (5/4 PO/OH); 0.10 M HEPES, pH=7.0; 0.20 M sodium thiocyanate, VAPOR DIFFUSION, SITTING DROP
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: 20% glycerol in precipitant solution

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 28, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.83→26.77 Å / Num. obs: 52018 / % possible obs: 99.8 % / Redundancy: 3.858 % / Biso Wilson estimate: 27.23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.031 / Rrim(I) all: 0.085 / Χ2: 0.944 / Net I/σ(I): 18.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allRsym valueΧ2% possible all
1.83-1.887.21.7680.42698237470.5340.6991.9031.7681.397.6
1.88-1.937.41.3640.62743236890.6390.5351.4661.3641.7100
1.93-1.987.40.9930.82675036090.7690.391.0670.9932.3100
1.98-2.047.40.7451.12600734950.8410.2920.8010.7453100
2.04-2.117.40.5861.32532534060.9040.230.630.5863.8100
2.11-2.197.50.461.72478533240.9290.180.4940.464.8100
2.19-2.277.40.3422.32354931610.9630.1340.3680.3426.3100
2.27-2.367.50.2692.92296830800.9750.1050.2890.2698100
2.36-2.477.50.2133.72193329420.9860.0840.2290.2139.9100
2.47-2.597.50.1714.62105228200.9890.0670.1840.17112.1100
2.59-2.737.40.1365.82000226870.9930.0530.1460.13614.9100
2.73-2.897.40.1047.51900225520.9960.0410.1120.10418.8100
2.89-3.097.40.07410.51779623990.9980.0290.0790.07425.4100
3.09-3.347.40.05414.21647222250.9990.0210.0580.05434100
3.34-3.667.40.03719.61537220840.9990.0150.040.03746.1100
3.66-4.097.30.02824.613782189310.0110.030.02860.1100
4.09-4.727.30.02131.112177167610.0080.0230.02172.7100
4.72-5.787.20.02132.210364144410.0080.0220.02170.5100
5.78-8.1870.0233.17875112710.0080.0210.0272.4100
8.18-47.66.30.01636.4415665810.0070.0170.01683.898.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.25 Å47.6 Å
Translation7.25 Å47.6 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XDSdata scaling
PHASER2.5.6phasing
BUSTER2.10.3refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DA6

6da6


Resolution: 1.83→26.77 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.944 / SU R Cruickshank DPI: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.118 / SU Rfree Blow DPI: 0.109 / SU Rfree Cruickshank DPI: 0.108
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. HEPES FROM THE CRYSTALLIZATION BUFFER IS ...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. HEPES FROM THE CRYSTALLIZATION BUFFER IS BOUND IN THE pr-FMN BINDING SITE. 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
Rfree0.213 1999 3.84 %RANDOM
Rwork0.189 ---
obs0.19 52003 99.9 %-
Displacement parametersBiso max: 166.49 Å2 / Biso mean: 44.26 Å2 / Biso min: 14.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.7263 Å20 Å20 Å2
2---4.0143 Å20 Å2
3---4.7407 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: final / Resolution: 1.83→26.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3553 0 133 237 3923
Biso mean--60.64 53.33 -
Num. residues----463
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1693SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1171HARMONIC5
X-RAY DIFFRACTIONt_it7646HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion489SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies12HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8303SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7646HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg13849HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion3.61
X-RAY DIFFRACTIONt_other_torsion14.63
LS refinement shellResolution: 1.83→1.88 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 144 3.84 %
Rwork0.3397 3602 -
all0.341 3746 -
obs--98.44 %
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)
11.52780.26050.42930.31580.4861.68450.0035-0.404-0.05220.29780.065-0.04720.05650.0523-0.0686-0.02860.0181-0.0070.1227-0.1021-0.13247.979218.413441.5785
20.76480.20170.43740.60930.36530.8399-0.0585-0.07230.10830.03620.05090.0212-0.27340.03370.00760.0143-0.0113-0.00560.0392-0.1229-0.06628.356730.622229.7647
30.317-0.02630.05880.31560.09370.9787-0.0485-0.09730.0354-0.01720.04150.0236-0.1138-0.04830.007-0.0620.0222-0.00330.0788-0.0178-0.0289-4.880610.460813.5367
42.3222-1.61191.56591.4414-2.72181.376-0.09070.16430.25270.33660.14620.33920.03060.022-0.0554-0.11380.08510.11320.14360.0891-0.0332-20.9084-6.04133.9157
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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