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- PDB-6da6: Crystal structure of the TtnD decarboxylase from the tautomycetin... -

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Basic information

Entry
Database: PDB / ID: 6da6
TitleCrystal structure of the TtnD decarboxylase from the tautomycetin biosynthesis pathway of Streptomyces griseochromogenes, apo form at 2.6 A resolution (P212121)
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 / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity / ferulate metabolic process / cinnamic acid catabolic process / ubiquinone biosynthetic process / nucleotide binding / metal ion binding / cytosol
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: 2.59 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 ...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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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
A: UbiD-like decarboxylase
B: UbiD-like decarboxylase
C: UbiD-like decarboxylase
D: UbiD-like decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,68025
Polymers219,1344
Non-polymers1,54621
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, GEL FILTRATION SUPPORTS THE ASSIGNEMNT OF A TETRAMER AS THE BIOLOGICAL ASSEMBLY.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20690 Å2
ΔGint-100 kcal/mol
Surface area64350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.215, 137.117, 284.074
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 54783.375 Da / Num. of mol.: 4
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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#5: 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: 2.36 Å3/Da / Density % sol: 47.99 %
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
10.0 %(w/v)PEG 400051precipitant
0.062 MMES61precipitant
0.038 Mimidazole71precipitant
0.030 Mcalcium chloride81precipitant
0.030 Mmagnesium chloride91precipitant
20. percent_volume_by_volumeglycerol101precipitant
Experiment crystal grow sol
Crystal-IDSol-IDpHVolume (Å3)
1macromolecule7.50.3 µL
1precipitant6.50.3 µL
1reservoir6.50.3 mL
Experiment crystal cryo treatmentCooling details: Direct immersion in liquid nitrogen.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9785 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 21, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.59→48.87 Å / Num. obs: 65796 / % possible obs: 99.6 % / Redundancy: 7.8 % / Biso Wilson estimate: 65.14 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.058 / Rrim(I) all: 0.162 / Χ2: 0.967 / Net I/σ(I): 14 / Num. measured all: 512250
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
2.59-2.667.61.3140.63556447060.5790.5041.4091.3141.796.9
2.66-2.7381.1580.73688146320.6830.4361.2381.1582100
2.73-2.817.90.9470.83635445780.7540.3581.0130.9472.5100
2.81-2.980.75213492443900.8230.2840.8040.7523.2100
2.9-2.997.90.6141.23445343410.8890.2310.6560.6144100
2.99-3.17.90.4961.53293941450.9170.1870.5310.4965100
3.1-3.227.90.4071.83170140010.9450.1530.4360.4076.1100
3.22-3.357.90.3042.43090339170.9630.1150.3250.3048.2100
3.35-3.57.90.2263.22918136850.980.0850.2410.22611100
3.5-3.677.90.1724.12799335520.9870.0650.1840.17214100
3.67-3.867.80.135.52685134290.9930.0490.1390.1317.9100
3.86-4.17.80.0997.22532932530.9960.0380.1060.09922.4100
4.1-4.387.80.0789.12347930230.9970.030.0840.07827100
4.38-4.737.70.06510.92180428340.9980.0250.0690.06531.2100
4.73-5.187.70.06211.52022726210.9980.0240.0670.06230100
5.18-5.87.70.06411.31848524030.9980.0250.0690.06427.8100
5.8-6.697.60.05313.61636021610.9980.0210.0570.05330.7100
6.69-8.27.40.0417.81343718070.9990.0150.0420.0438.3100
8.2-11.597.10.02624.31032914620.9990.0110.0290.02651.7100
11.59-48.875.90.02721.550858560.9990.0110.0290.02742.198.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å48.87 Å
Translation3 Å48.87 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: 4WIS

4wis


Resolution: 2.59→26.13 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.906 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.696 / SU Rfree Blow DPI: 0.272
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 HIGHER ...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 HIGHER RESOLUTION APO TTND STRUCTURE (PDBID 6DA7) WERE INCLUDED ALONG WITH NCS RESTRAINTS. 4. AN UNKNOWN LIGAND (UNL) IS MODELED. THERE ARE 2 UNL'S BOUND IN THE TETRAMER. THE SHAPE IN THE HIGHER RESOLUTION I222 CRYSTAL FORM LOOKS LIKE BENZOATE OR NIACIN. IT WAS MOLDELED IN A SIMILAR CONFIGURATION. 5. MAGNESIUM SITES INCLUDED GEOMETRIC RESTRAINTS. 6. DENSITY IS POOR IN PARTS OF CHAINS C AND D. MODELING WAS BASED ON THE NCS AND HIGH RESOLUTION TARGET STRUTURE FOR THESE REGIOINS.
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1998 3.04 %RANDOM
Rwork0.195 ---
obs0.196 65644 99.8 %-
Displacement parametersBiso max: 263.34 Å2 / Biso mean: 71.61 Å2 / Biso min: 19.91 Å2
Baniso -1Baniso -2Baniso -3
1-5.252 Å20 Å20 Å2
2---3.8759 Å20 Å2
3----1.3761 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: final / Resolution: 2.59→26.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14205 0 117 233 14555
Biso mean--69.39 46.66 -
Num. residues----1852
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d6226SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes4495HARMONIC5
X-RAY DIFFRACTIONt_it28976HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1918SEMIHARMONIC5
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_contact30711SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d28976HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg52581HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion3.55
X-RAY DIFFRACTIONt_other_torsion14.46
LS refinement shellResolution: 2.59→2.66 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2383 142 3.02 %
Rwork0.2143 4556 -
all0.215 4698 -
obs--96.86 %
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)
10.0293-0.12370.40310.5435-1.01670.37090.04630.0584-0.07420.1072-0.01450.05230.16620.0842-0.0318-0.06760.0373-0.0171-0.04930.02510.0256-3.689-18.427579.2574
20.47020.1368-0.00550.0886-0.03720.4640.15570.02750.10090.0934-0.0732-0.06780.0391-0.0574-0.0825-0.07620.00170.0046-0.07330.01780.0659-4.6913-1.71780.0629
30.3245-0.11890.23350.38840.040.4892-0.0418-0.0303-0.0540.02720.0460.0252-0.0506-0.0258-0.0042-0.1328-0.03090.01020.00810.04910.0402-19.9985-6.19155.0056
41.6291.1613-0.08093.2324-2.86560-0.08230.0032-0.1632-0.035-0.12860.3144-0.08350.01820.2108-0.2910.00070.1245-0.12220.18210.3521-32.8748-33.510557.9777
51.3229-1.80670.00950.0737-0.2910.48940.35740.24160.033-0.2556-0.5418-0.0596-0.214-0.10120.1844-0.0704-0.0044-0.00860.07320.1065-0.1261-30.955438.827624.2112
60.46-0.6386-0.42430.63950.47090.2345-0.02230.07880.03250.0843-0.051-0.0448-0.0827-0.01140.0733-0.029-0.0431-0.023-0.03930.01-0.0313-30.397238.09740.9746
70-0.08430.15470.28770.0920.3294-0.0164-0.0392-0.0658-0.03310.01-0.0345-0.1108-0.00060.0064-0.0865-0.06910.01470.03240.0356-0.012-13.609514.750635.1675
82.26434.74311.78490-2.84983.7719-0.2898-0.384-0.0984-0.42340.27010.1398-0.03120.67610.0197-0.0929-0.3040.09770.22580.0993-0.2443-0.414219.48198.0615
90-0.04461.25770-1.75810.28410.0868-0.4404-0.4657-0.03970.01630.3788-0.08630.2607-0.1031-0.29750.00190.1452-0.26820.2010.5241-19.1227-46.191652.894
100.4019-0.5793-0.10030.38290.150500.22130.079-0.6076-0.0093-0.31170.1925-0.23630.18770.0904-0.21890.1057-0.0177-0.2257-0.20930.4391-21.3516-46.084136.3507
110.2073-0.1838-0.27790.3075-0.45360.1328-0.02840.0187-0.0563-0.0402-0.0098-0.00180.02220.01850.0382-0.1339-0.02980.03390.00180.00480.0711-9.4459-19.490239.1018
121.4622-1.06841.85010.5632-2.85485.9629-0.26170.33590.180.07270.298-0.04490.30.5644-0.0363-0.19730.2220.02090.09440.08350.02958.7262-20.237164.194
130.79252.072-2.76880-2.80170.0947-0.26170.33350.3417-0.03330.70620.3633-0.29640.3948-0.4445-0.1319-0.304-0.09570.41160.2247-0.3165-13.223515.1192-4.9872
1401.36191.641401.39330.9359-0.27231.0256-0.39490.32560.81620.1559-0.23370.4944-0.5439-0.2094-0.304-0.06410.5405-0.304-0.2102-11.2241-1.8721-5.767
150.08810.29430.25130.2819-0.06580.4004-0.06730.0404-0.0317-0.06770.0712-0.01370.0194-0.0599-0.0039-0.118-0.08360.02140.06860.0014-0.0194-23.4038-0.775320.9238
162.3698-0.6959-0.52444.1304-2.95580-0.08490.3058-0.4110.0586-0.44870.1429-0.2435-0.1180.5336-0.164-0.0001-0.11320.19-0.1989-0.1173-42.320323.23121.0101
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|461 }A310 - 461
4X-RAY DIFFRACTION4{ A|462 - A|485 }A462 - 485
5X-RAY DIFFRACTION5{ B|0 - B|44 }B0 - 44
6X-RAY DIFFRACTION6{ B|45 - B|309 }B45 - 309
7X-RAY DIFFRACTION7{ B|310 - B|461 }B310 - 461
8X-RAY DIFFRACTION8{ B|462 - B|485 }B462 - 485
9X-RAY DIFFRACTION9{ C|0 - C|44 }C0 - 44
10X-RAY DIFFRACTION10{ C|45 - C|309 }C45 - 309
11X-RAY DIFFRACTION11{ C|310 - C|461 }C310 - 461
12X-RAY DIFFRACTION12{ C|462 - C|485 }C462 - 485
13X-RAY DIFFRACTION13{ D|2 - D|44 }D2 - 44
14X-RAY DIFFRACTION14{ D|45 - D|309 }D45 - 309
15X-RAY DIFFRACTION15{ D|310 - D|461 }D310 - 461
16X-RAY DIFFRACTION16{ D|462 - D|485 }D462 - 485

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