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- PDB-8rpi: JanthE from Janthinobacterium sp. HH01, lactyl-ThDP -

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Basic information

Entry
Database: PDB / ID: 8rpi
TitleJanthE from Janthinobacterium sp. HH01, lactyl-ThDP
ComponentsThiamine pyrophosphate-binding protein
KeywordsTRANSFERASE / THDP / FAD
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / Chem-TDL
Function and homology information
Biological speciesJanthinobacterium sp. HH01 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsLanza, L. / Leogrande, C. / Rabe von Pappenheim, F. / Tittmann, K. / Mueller, M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission956631European Union
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Identification and Characterization of Thiamine Diphosphate-Dependent Lyases with an Unusual CDG Motif.
Authors: Lanza, L. / Rabe von Pappenheim, F. / Bjarnesen, D. / Leogrande, C. / Paul, A. / Krug, L. / Tittmann, K. / Muller, M.
History
DepositionJan 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Aug 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Aug 21, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiamine pyrophosphate-binding protein
B: Thiamine pyrophosphate-binding protein
C: Thiamine pyrophosphate-binding protein
D: Thiamine pyrophosphate-binding protein
E: Thiamine pyrophosphate-binding protein
F: Thiamine pyrophosphate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)416,37725
Polymers408,0236
Non-polymers8,35419
Water3,783210
1
A: Thiamine pyrophosphate-binding protein
B: Thiamine pyrophosphate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,0699
Polymers136,0082
Non-polymers3,0617
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12450 Å2
ΔGint-105 kcal/mol
Surface area39050 Å2
MethodPISA
2
C: Thiamine pyrophosphate-binding protein
D: Thiamine pyrophosphate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,6548
Polymers136,0082
Non-polymers2,6466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12460 Å2
ΔGint-104 kcal/mol
Surface area39000 Å2
MethodPISA
3
E: Thiamine pyrophosphate-binding protein
F: Thiamine pyrophosphate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,6548
Polymers136,0082
Non-polymers2,6466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12950 Å2
ΔGint-102 kcal/mol
Surface area39150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.149, 118.539, 202.047
Angle α, β, γ (deg.)90.000, 96.720, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Thiamine pyrophosphate-binding protein


Mass: 68003.844 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Janthinobacterium sp. HH01 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: acetolactate synthase

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Non-polymers , 5 types, 229 molecules

#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-TDL / 3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-(1-CARBOXY-1-HYDROXYETHYL)-5-(2-{[HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM / 2-LACTYLTHIAMIN DIPHOSPHATE


Mass: 513.376 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H23N4O10P2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.61 Å3/Da / Density % sol: 52.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Bis-Tris, Tris, Ammonium acetate, PEG 10000, Magnesium chloride, Thiamine diphosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Mar 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.709→85.69 Å / Num. obs: 105972 / % possible obs: 95.5 % / Redundancy: 7 % / Biso Wilson estimate: 60.46 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.108 / Net I/σ(I): 12.9
Reflection shellResolution: 2.709→2.756 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5488 / CC1/2: 0.756 / Rrim(I) all: 0.944 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSJan 10, 2022data reduction
Aimless0.7.7data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.71→85.69 Å / SU ML: 0.3781 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.8255
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2343 5314 5.02 %
Rwork0.1946 100630 -
obs0.1966 105944 95.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.84 Å2
Refinement stepCycle: LAST / Resolution: 2.71→85.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27891 0 544 210 28645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004329207
X-RAY DIFFRACTIONf_angle_d0.621439737
X-RAY DIFFRACTIONf_chiral_restr0.04374381
X-RAY DIFFRACTIONf_plane_restr0.00455161
X-RAY DIFFRACTIONf_dihedral_angle_d12.081210609
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-2.740.33821720.31453412X-RAY DIFFRACTION98.73
2.74-2.770.33031700.29293513X-RAY DIFFRACTION98.82
2.77-2.810.34442040.28753407X-RAY DIFFRACTION98.66
2.81-2.840.31251800.27843465X-RAY DIFFRACTION98.89
2.84-2.880.29571850.2743443X-RAY DIFFRACTION98.91
2.88-2.920.32221730.27943491X-RAY DIFFRACTION99.03
2.92-2.960.33561900.26753455X-RAY DIFFRACTION98.97
2.96-30.28671970.26923445X-RAY DIFFRACTION98.65
3-3.050.29941920.27323416X-RAY DIFFRACTION98.69
3.05-3.10.3251760.27123483X-RAY DIFFRACTION98.97
3.1-3.150.29682050.26653425X-RAY DIFFRACTION98.91
3.16-3.210.31031640.26343488X-RAY DIFFRACTION98.92
3.21-3.270.27711640.25643461X-RAY DIFFRACTION98.77
3.27-3.340.3041890.23633437X-RAY DIFFRACTION98.61
3.34-3.410.27611940.23153455X-RAY DIFFRACTION97.99
3.41-3.490.29021890.22473378X-RAY DIFFRACTION97.22
3.49-3.580.26531860.21923442X-RAY DIFFRACTION98.29
3.58-3.650.27241310.21182424X-RAY DIFFRACTION96.09
3.69-3.790.2691530.21313180X-RAY DIFFRACTION98.41
3.79-3.850.2364950.21621714X-RAY DIFFRACTION95.87
3.92-4.050.20671810.1773192X-RAY DIFFRACTION99.32
4.05-4.210.21961870.16813488X-RAY DIFFRACTION99.38
4.21-4.40.22621710.15943499X-RAY DIFFRACTION99.38
4.4-4.630.18511700.14923465X-RAY DIFFRACTION99.37
4.63-4.920.17791940.14943502X-RAY DIFFRACTION99.25
4.92-5.30.21871880.16073480X-RAY DIFFRACTION99.27
5.3-5.840.20441640.16583538X-RAY DIFFRACTION98.85
5.84-6.680.19181580.16383487X-RAY DIFFRACTION98.01
6.68-8.420.18331810.14553523X-RAY DIFFRACTION98.75
8.42-85.690.15772110.14943522X-RAY DIFFRACTION97.42

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