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- PDB-8rph: JanthE from Janthinobacterium sp. HH01,ketobutyryl-ThDP -

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Basic information

Entry
Database: PDB / ID: 8rph
TitleJanthE from Janthinobacterium sp. HH01,ketobutyryl-ThDP
ComponentsThiamine pyrophosphate-binding protein
KeywordsTRANSFERASE / THDP / FAD
Function / homology: / FLAVIN-ADENINE DINUCLEOTIDE / TRIETHYLENE GLYCOL
Function and homology information
Biological speciesJanthinobacterium sp. HH01 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 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)416,19725
Polymers408,0236
Non-polymers8,17419
Water362
1
A: Thiamine pyrophosphate-binding protein
B: Thiamine pyrophosphate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,6828
Polymers136,0082
Non-polymers2,6756
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12520 Å2
ΔGint-85 kcal/mol
Surface area38750 Å2
MethodPISA
2
C: Thiamine pyrophosphate-binding protein
D: Thiamine pyrophosphate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,8329
Polymers136,0082
Non-polymers2,8257
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12890 Å2
ΔGint-76 kcal/mol
Surface area39060 Å2
MethodPISA
3
E: Thiamine pyrophosphate-binding protein
F: Thiamine pyrophosphate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,6828
Polymers136,0082
Non-polymers2,6756
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12590 Å2
ΔGint-84 kcal/mol
Surface area38500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.326, 118.189, 201.166
Angle α, β, γ (deg.)90.000, 97.060, 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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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, 21 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-A1H2A / (2~{S})-2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-2-yl]-2-oxidanyl-butanoic acid / Ketobutyryl-thiamine diphosphate


Mass: 527.403 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C16H25N4O10P2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.55 Å3/Da / Density % sol: 51.78 %
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: 0.68879 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: 0.68879 Å / Relative weight: 1
ReflectionResolution: 2.96→99.82 Å / Num. obs: 79335 / % possible obs: 94.5 % / Redundancy: 7 % / Biso Wilson estimate: 65.62 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.144 / Net I/σ(I): 11.3
Reflection shellResolution: 2.96→3.014 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4130 / CC1/2: 0.701 / Rrim(I) all: 1.03

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.96→99.82 Å / SU ML: 0.3789 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.628
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2403 3859 4.87 %
Rwork0.2064 75429 -
obs0.2081 79288 94.48 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.61 Å2
Refinement stepCycle: LAST / Resolution: 2.96→99.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27226 0 532 2 27760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00328495
X-RAY DIFFRACTIONf_angle_d0.539338757
X-RAY DIFFRACTIONf_chiral_restr0.04344273
X-RAY DIFFRACTIONf_plane_restr0.00385031
X-RAY DIFFRACTIONf_dihedral_angle_d11.645510335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.96-30.34061500.31532823X-RAY DIFFRACTION98.74
3-3.040.37391620.30132738X-RAY DIFFRACTION98.71
3.04-3.080.30161380.28272824X-RAY DIFFRACTION98.77
3.08-3.120.30711370.27782803X-RAY DIFFRACTION98.59
3.12-3.160.28421380.26852770X-RAY DIFFRACTION98.64
3.16-3.210.34661290.28462821X-RAY DIFFRACTION98.46
3.21-3.260.3091310.29742780X-RAY DIFFRACTION97.91
3.26-3.310.28831320.27082782X-RAY DIFFRACTION98.45
3.31-3.370.2591150.25362876X-RAY DIFFRACTION98.65
3.37-3.430.27091320.24722774X-RAY DIFFRACTION98.38
3.43-3.50.31681530.24842824X-RAY DIFFRACTION98.22
3.5-3.570.25081320.22872766X-RAY DIFFRACTION98.37
3.57-3.650.28061470.22692769X-RAY DIFFRACTION97.36
3.65-3.730.22611030.22571919X-RAY DIFFRACTION67.83
3.73-3.830.25771320.22522774X-RAY DIFFRACTION98.01
3.83-3.930.2249590.2361114X-RAY DIFFRACTION39.06
3.93-4.040.27061610.20712773X-RAY DIFFRACTION97.83
4.04-4.180.23511540.19762788X-RAY DIFFRACTION97.61
4.18-4.320.21751540.18052733X-RAY DIFFRACTION97.5
4.32-4.50.21141320.17052773X-RAY DIFFRACTION96.93
4.5-4.70.21221420.1612743X-RAY DIFFRACTION96.04
4.7-4.950.21181440.17592723X-RAY DIFFRACTION95.22
4.95-5.260.20171390.1752726X-RAY DIFFRACTION94.99
5.26-5.670.2081560.18442780X-RAY DIFFRACTION98.52
5.67-6.240.23371560.19742843X-RAY DIFFRACTION98.62
6.24-7.140.23131350.17922813X-RAY DIFFRACTION98.4
7.14-8.990.1921380.16182851X-RAY DIFFRACTION97.84
8.99-99.820.20181580.17462726X-RAY DIFFRACTION92.55
Refinement TLS params.Method: refined / Origin x: 40.4727206368 Å / Origin y: -14.2401914575 Å / Origin z: 49.8534235079 Å
111213212223313233
T0.427683319821 Å20.083512955971 Å2-0.000177457010164 Å2-0.553209250054 Å20.0314022233911 Å2--0.492394673582 Å2
L0.23872534433 °20.0128173375402 °20.0277897373338 °2-0.246971492931 °20.0822293347062 °2--0.406883831613 °2
S-0.0434209379517 Å °0.0197524812032 Å °-0.0144263887444 Å °0.0768737902438 Å °0.0475198093923 Å °0.0850479993259 Å °-0.0088628656713 Å °0.0659765981409 Å °-0.00214055131034 Å °
Refinement TLS groupSelection details: all

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