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- PDB-8rpj: JanthE from Janthinobacterium sp. HH01 -

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Basic information

Entry
Database: PDB / ID: 8rpj
TitleJanthE from Janthinobacterium sp. HH01
ComponentsThiamine pyrophosphate-binding protein
KeywordsTRANSFERASE / THDP / FAD
Function / homologyACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / TRIETHYLENE GLYCOL / THIAMINE DIPHOSPHATE
Function and homology information
Biological speciesJanthinobacterium sp. HH01 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)416,80433
Polymers408,0236
Non-polymers8,78127
Water38,1922120
1
A: Thiamine pyrophosphate-binding protein
B: Thiamine pyrophosphate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,92612
Polymers136,0082
Non-polymers2,91910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12810 Å2
ΔGint-102 kcal/mol
Surface area39440 Å2
MethodPISA
2
C: Thiamine pyrophosphate-binding protein
E: Thiamine pyrophosphate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,34012
Polymers136,0082
Non-polymers3,33210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13410 Å2
ΔGint-97 kcal/mol
Surface area39520 Å2
MethodPISA
3
D: Thiamine pyrophosphate-binding protein
F: Thiamine pyrophosphate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,5379
Polymers136,0082
Non-polymers2,5297
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12940 Å2
ΔGint-106 kcal/mol
Surface area38730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.196, 105.169, 193.605
Angle α, β, γ (deg.)90.000, 96.510, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Components on special symmetry positions
IDModelComponents
11F-1064-

HOH

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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 , 9 types, 2147 molecules

#2: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C18H38O10 / Comment: precipitant*YM
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2120 / 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: 2.3 Å3/Da / Density % sol: 46.43 %
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: 0.97625 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Apr 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.9→84.34 Å / Num. obs: 286766 / % possible obs: 99.3 % / Redundancy: 6.8 % / Biso Wilson estimate: 26.88 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.125 / Net I/σ(I): 10
Reflection shellResolution: 1.9→1.935 Å / Redundancy: 7 % / Mean I/σ(I) obs: 2 / Num. unique obs: 14248 / CC1/2: 0.71 / Rrim(I) all: 1.04 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIX1.20.1-4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→68.16 Å / SU ML: 0.1817 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.7475
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1858 14290 4.98 %
Rwork0.1534 272438 -
obs0.155 286728 99.24 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.59 Å2
Refinement stepCycle: LAST / Resolution: 1.9→68.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27791 0 572 2120 30483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004529105
X-RAY DIFFRACTIONf_angle_d0.790639558
X-RAY DIFFRACTIONf_chiral_restr0.0464344
X-RAY DIFFRACTIONf_plane_restr0.00725113
X-RAY DIFFRACTIONf_dihedral_angle_d14.026510559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.26134820.2298996X-RAY DIFFRACTION99
1.92-1.950.26785000.22139032X-RAY DIFFRACTION99.06
1.95-1.970.24924920.20139034X-RAY DIFFRACTION98.95
1.97-20.22744780.19028914X-RAY DIFFRACTION98.96
2-2.020.24034720.18649074X-RAY DIFFRACTION99.21
2.02-2.050.21224610.18059077X-RAY DIFFRACTION99.24
2.05-2.080.21775000.17999045X-RAY DIFFRACTION99.27
2.08-2.110.21864710.17569019X-RAY DIFFRACTION99.32
2.11-2.140.19944470.16649060X-RAY DIFFRACTION99.18
2.14-2.180.21314700.16829108X-RAY DIFFRACTION99.12
2.18-2.210.20914520.16439006X-RAY DIFFRACTION99.02
2.21-2.260.21184130.16839067X-RAY DIFFRACTION98.85
2.26-2.30.20695010.15569036X-RAY DIFFRACTION99.14
2.3-2.350.20554500.15049079X-RAY DIFFRACTION99.22
2.35-2.40.18555000.15449013X-RAY DIFFRACTION98.97
2.4-2.450.20625460.14558994X-RAY DIFFRACTION99.35
2.45-2.510.17345220.13839040X-RAY DIFFRACTION99.51
2.51-2.580.19154900.149102X-RAY DIFFRACTION99.46
2.58-2.660.17365120.13449063X-RAY DIFFRACTION99.5
2.66-2.740.17184690.1379098X-RAY DIFFRACTION99.45
2.74-2.840.18914700.14469061X-RAY DIFFRACTION99.35
2.84-2.960.18944930.15019103X-RAY DIFFRACTION99.32
2.96-3.090.17984970.14699060X-RAY DIFFRACTION99.44
3.09-3.250.18124590.14229144X-RAY DIFFRACTION99.39
3.25-3.460.17154770.14139102X-RAY DIFFRACTION99.07
3.46-3.720.16334400.13829162X-RAY DIFFRACTION99.53
3.72-4.10.15234630.13099188X-RAY DIFFRACTION99.4
4.1-4.690.15655250.13149078X-RAY DIFFRACTION99.17
4.69-5.910.17974270.1579304X-RAY DIFFRACTION99.79
5.91-68.160.20084110.18799379X-RAY DIFFRACTION99.06

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