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- PDB-9hn8: Apo Structure of Truncated 1-deoxy-D-xylulose 5-phosphate synthas... -

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Basic information

Entry
Database: PDB / ID: 9hn8
TitleApo Structure of Truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Mycobacterium tuberculosis
Components1-deoxy-D-xylulose-5-phosphate synthase
KeywordsTRANSFERASE / apo / thiamine-dependent enzyme / synthase
Function / homology
Function and homology information


1-deoxy-D-xylulose-5-phosphate synthase / : / 1-deoxy-D-xylulose-5-phosphate synthase activity / thiamine binding / thiamine biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / thiamine pyrophosphate binding / manganese ion binding / positive regulation of gene expression ...1-deoxy-D-xylulose-5-phosphate synthase / : / 1-deoxy-D-xylulose-5-phosphate synthase activity / thiamine binding / thiamine biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / thiamine pyrophosphate binding / manganese ion binding / positive regulation of gene expression / magnesium ion binding / cytosol
Similarity search - Function
Deoxyxylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase / Transketolase, C-terminal domain / : / Transketolase signature 1. / Transketolase binding site / Transketolase signature 2. / Transketolase, C-terminal domain / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain ...Deoxyxylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase / Transketolase, C-terminal domain / : / Transketolase signature 1. / Transketolase binding site / Transketolase signature 2. / Transketolase, C-terminal domain / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate-binding fold
Similarity search - Domain/homology
1-deoxy-D-xylulose-5-phosphate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsGawriljuk, V.O. / Groves, M.R.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission860816European Union
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2025
Title: Apo structure of Mycobacterium tuberculosis 1-deoxy-d-xylulose 5-phosphate synthase DXPS: Dynamics and implications for inhibitor design.
Authors: Gawriljuk, V.O. / Alhayek, A. / Hirsch, A.K.H. / Groves, M.R.
History
DepositionDec 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1-deoxy-D-xylulose-5-phosphate synthase
B: 1-deoxy-D-xylulose-5-phosphate synthase


Theoretical massNumber of molelcules
Total (without water)127,2462
Polymers127,2462
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7520 Å2
ΔGint-38 kcal/mol
Surface area35090 Å2
Unit cell
Length a, b, c (Å)67.180, 126.772, 80.553
Angle α, β, γ (deg.)90.000, 107.700, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein 1-deoxy-D-xylulose-5-phosphate synthase / 1-deoxyxylulose-5-phosphate synthase / DXP synthase / DXPS


Mass: 63623.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: dxs, Rv2682c, MTCY05A6.03c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WNS3, 1-deoxy-D-xylulose-5-phosphate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
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: 2.55 Å3/Da / Density % sol: 51.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 0.1 M MES-Imidazole pH 6.3, 10% PEG 8000 , 20% Ethylene-glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.65→48.87 Å / Num. obs: 36816 / % possible obs: 98.6 % / Redundancy: 4.6 % / Biso Wilson estimate: 61.91 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.056 / Rrim(I) all: 0.125 / Net I/σ(I): 9.6
Reflection shellResolution: 2.65→2.77 Å / Num. unique obs: 4444 / CC1/2: 0.509

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→48.87 Å / SU ML: 0.3973 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.9912
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2733 1765 4.85 %
Rwork0.2474 34629 -
obs0.2486 36394 97.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.26 Å2
Refinement stepCycle: LAST / Resolution: 2.65→48.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7163 0 0 20 7183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00957311
X-RAY DIFFRACTIONf_angle_d1.30189929
X-RAY DIFFRACTIONf_chiral_restr0.07191160
X-RAY DIFFRACTIONf_plane_restr0.01061302
X-RAY DIFFRACTIONf_dihedral_angle_d15.55052623
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.720.38341380.37192605X-RAY DIFFRACTION96.18
2.72-2.80.34811460.35082719X-RAY DIFFRACTION99.34
2.8-2.890.33561380.30552690X-RAY DIFFRACTION99.58
2.89-30.31021350.30432715X-RAY DIFFRACTION99.55
3-3.120.35761350.28932729X-RAY DIFFRACTION99.83
3.12-3.260.33991210.3032737X-RAY DIFFRACTION99.76
3.26-3.430.31481530.28382696X-RAY DIFFRACTION99.82
3.43-3.640.28731300.2652591X-RAY DIFFRACTION94.64
3.64-3.920.29841330.29282352X-RAY DIFFRACTION86.59
3.93-4.320.24081430.23042661X-RAY DIFFRACTION98.14
4.32-4.940.24361370.19272697X-RAY DIFFRACTION97.93
4.94-6.230.29671270.23342665X-RAY DIFFRACTION95.98
6.23-48.870.19451290.19182772X-RAY DIFFRACTION99.45
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)
11.184551278362.40592738804-0.2297280880345.860655220150.8182745323252.95553757705-0.0444493190722-0.1139705939010.0717620091472-0.3642467296390.08115692479520.209730924171-0.524262538333-0.2154907130.03548957877240.4996495837570.0435403973880.01061302613570.4350175350150.002996725526020.38332474865843.42679643965.0781361243223.8074551189
26.973906150120.2950275299790.5362336079517.290464287561.607958824356.657665159290.4098117937560.1447795831370.02891802615550.05403842799860.0809475748552-0.255228086654-0.171849863754-0.318780990072-0.3607356880520.3458571318220.0499755333817-0.04531140223940.3069956759590.004572094521570.3669081622634.7241029371-12.061628239820.7990604245
32.035056760080.6765073836032.366511744440.5784058597121.309232518924.599772016150.358282662167-0.5493661422170.0222367694490.271849491601-0.117174567897-0.04840427202620.224716664287-0.788305213381-0.2196423958520.502505183707-0.05444488751790.04498382659720.718328081099-0.03648669754840.45244520327530.5938025935-7.4534467186432.5493399986
40.6781521052320.455414285354-1.400943687942.13415110147-1.716579023914.984140299540.310057140874-0.1282532968520.07561104393680.214999545605-0.1925857779930.129557973743-0.9986785425630.238223816891-0.1036559989810.519982402842-0.02117018927520.008121109324270.4959123674410.01772627921490.45587765715310.7174509534-0.544960376166-6.3618718196
53.086020366271.79094437553-1.207076253285.23930175224-1.310420149793.99100933095-0.107125182520.215452912303-0.667559578041-0.5891491429860.3256739711860.1260323624131.03296215488-0.248091508738-0.2032323936750.672890416086-0.00967721726081-0.1157572322240.580603162740.024905489420.62177066111-8.55919007001-30.021914837525.5404461958
61.620211188090.817208690607-1.749029685880.71794280347-0.1301823860384.753409901050.52536556615-0.3817555138820.1798243819990.191132357585-0.2638254903540.0581376756856-0.4670481944870.654529061628-0.2735439087460.429970754572-0.01139822315710.03204474730660.574469299024-0.008075632934880.3984447514661.88143752476-15.48886339329.5863504828
70.8656202634370.6861738411021.377246449462.416613926611.636046519113.885141415940.300679955965-0.219043237912-0.115036886050.335891986822-0.140657850224-0.1177283233080.606897422314-0.281274261649-0.1581043266530.355328957577-0.0575425404183-0.018558615510.4168812745640.07047239467720.46737995579523.261879961-27.814507819-4.57539951725
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 80 )AA0 - 801 - 76
22chain 'A' and (resid 81 through 149 )AA81 - 14977 - 120
33chain 'A' and (resid 150 through 315 )AA150 - 315121 - 188
44chain 'A' and (resid 316 through 627 )AA316 - 627189 - 484
55chain 'B' and (resid 0 through 116 )BB0 - 1161 - 75
66chain 'B' and (resid 117 through 315 )BB117 - 31576 - 178
77chain 'B' and (resid 316 through 627 )BB316 - 627179 - 470

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