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- PDB-6ouv: 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Deinococcus r... -

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Basic information

Entry
Database: PDB / ID: 6ouv
Title1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Deinococcus radiodurans with methylacetylphosphonate (MAP) bound
Components1-deoxy-D-xylulose-5-phosphate synthase
KeywordsTRANSFERASE / 1-deoxy-D-xylulose 5-phosphate synthase / DXPS / thiamine diphosphate / thiamine pyrophosphate / ThDP / TPP / changes / the MEP pathway
Function / homology
Function and homology information


1-deoxy-D-xylulose-5-phosphate synthase / 1-deoxy-D-xylulose 5-phosphate biosynthetic process / 1-deoxy-D-xylulose-5-phosphate synthase activity / thiamine biosynthetic process / terpenoid biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / 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 binding site / Transketolase signature 2. / Transketolase, C-terminal domain / Rossmann fold - #920 / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain ...Deoxyxylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase / Transketolase, C-terminal domain / Transketolase binding site / Transketolase signature 2. / Transketolase, C-terminal domain / Rossmann fold - #920 / 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
Chem-TDK / 1-deoxy-D-xylulose-5-phosphate synthase
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.937 Å
AuthorsChen, P.Y.-T. / Drennan, C.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM126982 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: J.Biol.Chem. / Year: 2019
Title: X-ray crystallography-based structural elucidation of enzyme-bound intermediates along the 1-deoxy-d-xylulose 5-phosphate synthase reaction coordinate.
Authors: Chen, P.Y. / DeColli, A.A. / Freel Meyers, C.L. / Drennan, C.L.
History
DepositionMay 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)141,2808
Polymers140,0592
Non-polymers1,2216
Water10,935607
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10580 Å2
ΔGint-121 kcal/mol
Surface area36850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.503, 125.279, 151.699
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 70029.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: dxs, DR_1475 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9RUB5, 1-deoxy-D-xylulose-5-phosphate synthase
#2: Chemical ChemComp-TDK / 3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-{(1S)-1-HYDROXY-1-[(R)-HYDROXY(METHOXY)PHOSPHORYL]ETHYL}-5-(2-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM / 2-PHOSPHONOLACTYLTHIAMIN DIPHOSPHATE


Mass: 563.373 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H26N4O11P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 607 / Source method: isolated from a natural source / Formula: H2O

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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: 2.75 Å3/Da / Density % sol: 55.33 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BES, triethanolamine pH 7.5, 15% (w/v) PEG 3000, 20% (v/v) 1,2,4-butanetriol, 1% (w/v) non-detergents sulfobetaines (NDSB)-256 (Hampton), 25 mM L-arginine, 25 mM L-threonine, 25 mM L- ...Details: 0.1 M BES, triethanolamine pH 7.5, 15% (w/v) PEG 3000, 20% (v/v) 1,2,4-butanetriol, 1% (w/v) non-detergents sulfobetaines (NDSB)-256 (Hampton), 25 mM L-arginine, 25 mM L-threonine, 25 mM L-histidine, and 25 mM trans-4-hydroxy-L-proline

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.937→96.6 Å / Num. obs: 110177 / % possible obs: 98.6 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 22.4
Reflection shellResolution: 1.937→2.01 Å / Rmerge(I) obs: 0.719 / Num. unique obs: 10201

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O1X

2o1x


Resolution: 1.937→96.597 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.42
RfactorNum. reflection% reflection
Rfree0.1738 5515 5.01 %
Rwork0.1558 --
obs0.1567 110075 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.937→96.597 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8845 0 72 607 9524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039255
X-RAY DIFFRACTIONf_angle_d0.61512606
X-RAY DIFFRACTIONf_dihedral_angle_d18.3985540
X-RAY DIFFRACTIONf_chiral_restr0.0451418
X-RAY DIFFRACTIONf_plane_restr0.0041680
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9368-1.95880.3021590.26612942X-RAY DIFFRACTION84
1.9588-1.98190.2611740.23453264X-RAY DIFFRACTION94
1.9819-2.00610.2591760.22273391X-RAY DIFFRACTION96
2.0061-2.03150.23381810.2113385X-RAY DIFFRACTION97
2.0315-2.05820.23261830.20193401X-RAY DIFFRACTION97
2.0582-2.08640.22311800.19813403X-RAY DIFFRACTION97
2.0864-2.11620.23291860.18893469X-RAY DIFFRACTION98
2.1162-2.14780.19961790.17673431X-RAY DIFFRACTION99
2.1478-2.18140.18981880.16513517X-RAY DIFFRACTION99
2.1814-2.21710.1861790.16983458X-RAY DIFFRACTION100
2.2171-2.25540.19741830.1633500X-RAY DIFFRACTION100
2.2554-2.29640.19141840.16273493X-RAY DIFFRACTION99
2.2964-2.34050.1951850.16213495X-RAY DIFFRACTION99
2.3405-2.38830.18471860.15843506X-RAY DIFFRACTION100
2.3883-2.44030.19031840.15843515X-RAY DIFFRACTION100
2.4403-2.4970.18371810.15893502X-RAY DIFFRACTION100
2.497-2.55950.18541840.15923511X-RAY DIFFRACTION100
2.5595-2.62870.17641870.15363525X-RAY DIFFRACTION100
2.6287-2.7060.16731860.15563541X-RAY DIFFRACTION100
2.706-2.79340.17991840.15683502X-RAY DIFFRACTION100
2.7934-2.89320.17731830.16033509X-RAY DIFFRACTION99
2.8932-3.00910.18061860.1623518X-RAY DIFFRACTION100
3.0091-3.1460.18161850.16443565X-RAY DIFFRACTION100
3.146-3.31190.19371870.1673532X-RAY DIFFRACTION100
3.3119-3.51940.19191890.16853564X-RAY DIFFRACTION100
3.5194-3.79120.17531880.15333567X-RAY DIFFRACTION99
3.7912-4.17270.14621880.13323566X-RAY DIFFRACTION100
4.1727-4.77650.13641900.12243604X-RAY DIFFRACTION100
4.7765-6.01770.16411900.14153615X-RAY DIFFRACTION99
6.0177-96.71740.14082000.15153769X-RAY DIFFRACTION99
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)
10.7634-0.0496-0.10071.8730.33410.90160.07050.0227-0.0032-0.0047-0.08750.2878-0.0319-0.18390.01710.19650.026-0.04440.25160.00360.2525-15.4505-11.320536.3644
20.91020.1923-0.04591.7614-0.00960.88550.0702-0.1576-0.07460.2927-0.04-0.50980.06780.23710.00710.25990.0292-0.1160.2921-0.00540.383412.5615-10.922146.1617
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'

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