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- PDB-8a9c: Structure of truncated 1-deoxy-D-xylulose 5-phosphate synthase (D... -

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Basic information

Entry
Database: PDB / ID: 8a9c
TitleStructure of truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Klebsiella pneumoniae in complex with cofactor TPP
Components1-deoxy-D-xylulose-5-phosphate synthase
KeywordsTRANSFERASE / Primary metabolism / synthase / complex
Function / homology
Function and homology information


1-deoxy-D-xylulose-5-phosphate synthase / : / 1-deoxy-D-xylulose-5-phosphate synthase activity / thiamine biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / thiamine pyrophosphate binding / 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 (ThDP)-binding fold, Pyr/PP domains / Thiamin diphosphate-binding fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THIAMINE DIPHOSPHATE / 1-deoxy-D-xylulose-5-phosphate synthase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAdam, S. / Hirsch, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
Helmholtz Association Germany
CitationJournal: To Be Published
Title: Structure of truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Klebsiella pneumoniae in complex with cofactor TPP
Authors: Adam, S. / Hirsch, A.
History
DepositionJun 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,9584
Polymers126,5082
Non-polymers4502
Water14,160786
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8970 Å2
ΔGint-75 kcal/mol
Surface area33350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.673, 72.559, 91.438
Angle α, β, γ (deg.)90.00, 108.46, 90.00
Int Tables number4
Space group name H-MP1211
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: 63254.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: dxs_3, dxs, dxs_1, BN49_1346, FXN67_12755, GJJ18_13560, GJJ26_020415, NCTC11679_04435, NCTC13465_06397, NCTC3279_00555, NCTC5047_01280, NCTC5052_00313, NCTC9140_02292, NCTC9645_03343, NCTC9661_ ...Gene: dxs_3, dxs, dxs_1, BN49_1346, FXN67_12755, GJJ18_13560, GJJ26_020415, NCTC11679_04435, NCTC13465_06397, NCTC3279_00555, NCTC5047_01280, NCTC5052_00313, NCTC9140_02292, NCTC9645_03343, NCTC9661_05006, SAMEA3649733_02709, SAMEA4364603_02966, dxs_3, dxs, dxs_1, dxs_2, BN49_1346, DRB11_07540, FXN67_12755, NCTC11679_04435, NCTC13465_06397, NCTC3279_00555, NCTC5047_01280, NCTC5052_00313, NCTC9140_02292, NCTC9645_03343, NCTC9661_05006, SAMEA3512100_02923, SAMEA3649733_02709, SAMEA4364603_02966
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0S3F934, 1-deoxy-D-xylulose-5-phosphate synthase
#2: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 786 / Source method: isolated from a natural source / Formula: H2O
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: 2.23 Å3/Da / Density % sol: 44.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 3000, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.8→43.37 Å / Num. obs: 100675 / % possible obs: 97.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 25.3600941464 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.4
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.561 / Num. unique obs: 14606

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2o1s

2o1s


Resolution: 1.8→43.37 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1906 4854 4.82 %
Rwork0.1544 --
obs0.1561 100622 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→43.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8012 0 27 786 8825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016
X-RAY DIFFRACTIONf_angle_d1.253
X-RAY DIFFRACTIONf_dihedral_angle_d6.9281130
X-RAY DIFFRACTIONf_chiral_restr0.0941255
X-RAY DIFFRACTIONf_plane_restr0.0111442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.33131590.26633205X-RAY DIFFRACTION98
1.82-1.840.2781600.24473185X-RAY DIFFRACTION98
1.84-1.860.27311740.22553146X-RAY DIFFRACTION96
1.86-1.890.25091530.21273128X-RAY DIFFRACTION96
1.89-1.910.25131850.19583210X-RAY DIFFRACTION99
1.91-1.940.25291610.19163189X-RAY DIFFRACTION99
1.94-1.970.21741850.193223X-RAY DIFFRACTION99
1.97-20.26441760.19353253X-RAY DIFFRACTION99
2-2.030.21071930.17543190X-RAY DIFFRACTION99
2.03-2.060.21971830.16423185X-RAY DIFFRACTION99
2.06-2.10.19991720.16413237X-RAY DIFFRACTION99
2.1-2.130.2251560.1543238X-RAY DIFFRACTION99
2.13-2.180.1811510.15063224X-RAY DIFFRACTION99
2.18-2.220.18851380.14473251X-RAY DIFFRACTION99
2.22-2.270.18581580.14433219X-RAY DIFFRACTION99
2.27-2.320.1951520.15163223X-RAY DIFFRACTION99
2.32-2.380.18841660.15923239X-RAY DIFFRACTION99
2.38-2.440.21381330.15563211X-RAY DIFFRACTION98
2.44-2.510.18221750.15533184X-RAY DIFFRACTION97
2.51-2.60.2091570.16183124X-RAY DIFFRACTION95
2.6-2.690.23111650.16023113X-RAY DIFFRACTION95
2.69-2.80.18841690.15183222X-RAY DIFFRACTION99
2.8-2.920.20311480.15473220X-RAY DIFFRACTION98
2.92-3.080.20651700.1513211X-RAY DIFFRACTION98
3.08-3.270.18971870.14923193X-RAY DIFFRACTION98
3.27-3.520.16561320.14523217X-RAY DIFFRACTION97
3.52-3.880.14981390.14013184X-RAY DIFFRACTION96
3.88-4.440.15791810.12943109X-RAY DIFFRACTION95
4.44-5.590.15581400.1363038X-RAY DIFFRACTION91
5.59-43.370.17251360.15673197X-RAY DIFFRACTION94
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)
15.1152-1.1831-1.17713.9475-2.54883.8628-0.1329-0.3213-0.24940.4137-0.07860.24480.3464-0.12380.2090.3788-0.07880.05150.3344-0.01290.182841.260227.7781107.6851
21.01420.75380.32381.6790.45621.8051-0.0083-0.11020.00920.1098-0.06260.0908-0.0453-0.00940.06550.1837-0.00050.01470.1693-0.01440.146843.824533.767590.6552
30.85970.19570.071.0130.24090.60920.02770.0052-0.0977-0.1178-0.08880.21780.057-0.08530.05540.20310.0088-0.03570.1575-0.02410.201534.21158.16868.1803
41.14580.1782-1.00542.3743-1.85313.90920.16850.42560.0837-0.6491-0.00830.1184-0.7943-0.0184-0.11560.9773-0.12550.2230.44930.02130.275165.608138.018542.2287
51.53170.3008-0.11030.9807-0.45582.0433-0.01070.21320.0449-0.48550.0323-0.0446-0.14090.10010.01620.3914-0.0330.0290.21790.00810.152856.520627.445254.7105
63.17350.8518-1.03462.2036-1.47182.75030.1166-0.13570.2166-0.16790.0826-0.2973-0.5380.5256-0.15150.3395-0.13880.09760.4068-0.03140.258268.071234.79663.9166
70.72040.20720.05641.06490.31840.5636-0.07850.13020.1812-0.4067-0.0890.4651-0.2767-0.12850.15140.39320.0628-0.16940.2307-0.03010.3526.11934.889360.9455
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 66 )
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 286 )
3X-RAY DIFFRACTION3chain 'A' and (resid 287 through 585 )
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 66 )
5X-RAY DIFFRACTION5chain 'B' and (resid 67 through 170 )
6X-RAY DIFFRACTION6chain 'B' and (resid 171 through 237 )
7X-RAY DIFFRACTION7chain 'B' and (resid 238 through 585 )

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