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- PDB-9u8r: Crystal structure of thiamine pyrophosphate (TPP)-dependent alpha... -

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Basic information

Entry
Database: PDB / ID: 9u8r
TitleCrystal structure of thiamine pyrophosphate (TPP)-dependent alpha-imino acid decarboxylase (AzcB and AzcC) from Streptomyces mobaraensis in complex with TTPP and 6-amino-4-oxo-4,5-dihydro-1,3,5-triazine-2-carboxylic acid.
Components(Thiamine pyrophosphate enzyme ...) x 2
KeywordsLYASE / thiamine pyrophosphate (TPP)-dependent decarboxylase / AzcB / AzcC / 5-azacytidine biosynthesis / 6-amino-4-oxo-4 / 5-dihydro-1 / 3 / 5-triazine-2-carboxylic acid
Function / homology: / Chem-TZD / : / :
Function and homology information
Biological speciesStreptomyces mobaraensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsNakashima, Y. / Tsunoda, T. / Ogasawara, Y. / Dairi, T. / Morita, H.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22H04976 Japan
Japan Society for the Promotion of Science (JSPS)18H03937 Japan
Japan Society for the Promotion of Science (JSPS)22H05130 Japan
CitationJournal: To Be Published
Title: Crystal structure of thiamine pyrophosphate (TPP)-dependent decarboxylase (AzcB and AzcC complexes) from Streptomyces mobaraensis in complex with TTPP and 6-amino-4-oxo-4,5-dihydro-1,3,5- ...Title: Crystal structure of thiamine pyrophosphate (TPP)-dependent decarboxylase (AzcB and AzcC complexes) from Streptomyces mobaraensis in complex with TTPP and 6-amino-4-oxo-4,5-dihydro-1,3,5-triazine-2-carboxylic acid.
Authors: Nakashima, Y. / Morita, H.
History
DepositionMar 26, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thiamine pyrophosphate enzyme N-terminal TPP-binding domain-containing protein
B: Thiamine pyrophosphate enzyme N-terminal TPP-binding domain-containing protein
C: Thiamine pyrophosphate enzyme N-terminal TPP-binding domain-containing protein
D: Thiamine pyrophosphate enzyme N-terminal TPP-binding domain-containing protein
E: Thiamine pyrophosphate enzyme N-terminal TPP-binding domain-containing protein
F: Thiamine pyrophosphate enzyme N-terminal TPP-binding domain-containing protein
G: Thiamine pyrophosphate enzyme TPP-binding domain-containing protein
H: Thiamine pyrophosphate enzyme TPP-binding domain-containing protein
I: Thiamine pyrophosphate enzyme TPP-binding domain-containing protein
J: Thiamine pyrophosphate enzyme TPP-binding domain-containing protein
K: Thiamine pyrophosphate enzyme TPP-binding domain-containing protein
L: Thiamine pyrophosphate enzyme TPP-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,17662
Polymers231,47012
Non-polymers6,70650
Water10,791599
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60300 Å2
ΔGint-913 kcal/mol
Surface area56500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)274.162, 158.845, 73.869
Angle α, β, γ (deg.)90.000, 99.200, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Thiamine pyrophosphate enzyme ... , 2 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Thiamine pyrophosphate enzyme N-terminal TPP-binding domain-containing protein


Mass: 18049.711 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces mobaraensis (bacteria) / Gene: H7K43_04135 / Production host: Streptomyces lividans (bacteria) / References: UniProt: A0A7X1IDQ3
#2: Protein
Thiamine pyrophosphate enzyme TPP-binding domain-containing protein


Mass: 20528.576 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces mobaraensis (bacteria) / Gene: H7K43_04130 / Production host: Streptomyces lividans (bacteria) / References: UniProt: A0A7X1IDK5

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Non-polymers , 6 types, 649 molecules

#3: Chemical
ChemComp-A1L8W / 2-azanyl-6-oxidanylidene-1~{H}-1,3,5-triazine-4-carboxylic acid


Mass: 156.100 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H4N4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-TZD / 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE / THIAMIN THIAZOLONE DIPHOSPHATE


Mass: 440.306 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H18N4O8P2S / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 599 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.43 Å3/Da / Density % sol: 64.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 3.7 mg/mL AzcB:AzcC, 2 mM TTPP, 200 mM NaCl, 100 mM CAPS/NaOH (pH 10.5), 20% (w/v) PEG 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.018 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.018 Å / Relative weight: 1
ReflectionResolution: 2.55→48.02 Å / Num. obs: 194768 / % possible obs: 99.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 33.69 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.121 / Net I/σ(I): 8.8
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 4 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4991 / CC1/2: 0.826 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→48.02 Å / SU ML: 0.2964 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3758
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2278 3848 1.98 %
Rwork0.1912 190920 -
obs0.192 194768 97.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.07 Å2
Refinement stepCycle: LAST / Resolution: 2.55→48.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16291 0 227 599 17117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002416780
X-RAY DIFFRACTIONf_angle_d0.57322912
X-RAY DIFFRACTIONf_chiral_restr0.04192677
X-RAY DIFFRACTIONf_plane_restr0.0042935
X-RAY DIFFRACTIONf_dihedral_angle_d16.75412409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.580.3511410.29347143X-RAY DIFFRACTION98.37
2.58-2.620.37131450.30047181X-RAY DIFFRACTION98.32
2.62-2.650.33091460.29347175X-RAY DIFFRACTION98.68
2.65-2.690.34221440.29347032X-RAY DIFFRACTION97.03
2.69-2.730.33941450.28217199X-RAY DIFFRACTION98.21
2.73-2.770.32121460.2727080X-RAY DIFFRACTION98.27
2.77-2.820.26741400.25727224X-RAY DIFFRACTION98.38
2.82-2.870.28711450.24387158X-RAY DIFFRACTION98.11
2.87-2.920.29041440.23127111X-RAY DIFFRACTION98.17
2.92-2.980.27071460.24547137X-RAY DIFFRACTION98.09
2.98-3.040.30061410.23717087X-RAY DIFFRACTION97.93
3.04-3.10.28171430.23547122X-RAY DIFFRACTION97.23
3.1-3.170.29551430.21547080X-RAY DIFFRACTION96.94
3.17-3.250.22521370.20276968X-RAY DIFFRACTION95.97
3.25-3.340.25241360.20576858X-RAY DIFFRACTION93.95
3.34-3.440.20361400.19836806X-RAY DIFFRACTION93.49
3.44-3.550.23971430.18816851X-RAY DIFFRACTION94.9
3.55-3.680.21341410.17477082X-RAY DIFFRACTION95.74
3.68-3.820.17611410.15736900X-RAY DIFFRACTION96.5
3.82-40.18821420.15237028X-RAY DIFFRACTION96.53
4-4.210.17391450.14057107X-RAY DIFFRACTION97.56
4.21-4.470.16751450.13427131X-RAY DIFFRACTION97.25
4.47-4.820.17431390.14347082X-RAY DIFFRACTION97.45
4.82-5.30.18561470.15737157X-RAY DIFFRACTION97.7
5.3-6.070.20751360.17367102X-RAY DIFFRACTION97.65
6.07-7.640.21691450.17777086X-RAY DIFFRACTION97.66
7.64-48.020.16271420.15167033X-RAY DIFFRACTION96.45

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