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- PDB-2o1x: 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Deinococcus ra... -

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Basic information

Entry
Database: PDB / ID: 2o1x
Title1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Deinococcus radiodurans
Components1-deoxy-D-xylulose-5-phosphate synthase
KeywordsTRANSFERASE / thiamin / isoprenoid / dxs / 1-deoxy-D-xylulose-5-phosphate
Function / homology
Function and homology information


1-deoxy-D-xylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase activity / 1-deoxy-D-xylulose 5-phosphate biosynthetic process / 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 binding site / Transketolase signature 2. / Transketolase, C-terminal domain / 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 binding site / Transketolase signature 2. / Transketolase, C-terminal domain / 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
THIAMINE DIPHOSPHATE / 1-deoxy-D-xylulose-5-phosphate synthase
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsXiang, S. / Usunow, G. / Lange, G. / Busch, M. / Tong, L.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystal Structure of 1-Deoxy-D-xylulose 5-Phosphate Synthase, a Crucial Enzyme for Isoprenoids Biosynthesis.
Authors: Xiang, S. / Usunow, G. / Lange, G. / Busch, M. / Tong, L.
History
DepositionNov 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Aug 4, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
C: 1-deoxy-D-xylulose-5-phosphate synthase
D: 1-deoxy-D-xylulose-5-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,82612
Polymers271,0284
Non-polymers1,7988
Water0
1
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)136,4136
Polymers135,5142
Non-polymers8994
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9870 Å2
ΔGint-77 kcal/mol
Surface area36890 Å2
MethodPISA
2
C: 1-deoxy-D-xylulose-5-phosphate synthase
D: 1-deoxy-D-xylulose-5-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,4136
Polymers135,5142
Non-polymers8994
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9530 Å2
ΔGint-76 kcal/mol
Surface area34980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.261, 154.062, 124.881
Angle α, β, γ (deg.)90.00, 98.91, 90.00
Int Tables number4
Space group name H-MP1211
DetailsDimers of chains A/B and C/D

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Components

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


Mass: 67756.961 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: dxs / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: Q9RUB5, 1-deoxy-D-xylulose-5-phosphate synthase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N4O7P2S

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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: 2.74 Å3/Da / Density % sol: 55.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM Tris, pH7.5, 200 mM ammonium acetate, 150 mM NaCl, and 20% (w/v) PEG 6000 or PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9795
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Apr 25, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 65814 / Num. obs: 64098 / % possible obs: 97.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Net I/σ(I): 13.4
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.3 / Num. unique all: 6571 / Rsym value: 0.42 / % possible all: 96.6

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0003refinement
PDB_EXTRACT2data extraction
MAR345345DTBdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.855 / SU B: 37.282 / SU ML: 0.323 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.431 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.272 3206 5.1 %RANDOM
Rwork0.209 ---
obs0.212 62969 97.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.511 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å21.25 Å2
2--4.18 Å20 Å2
3----3.12 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16802 0 108 0 16910
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02117240
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.95123430
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.58952215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.58823.452733
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.056152752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.79615133
X-RAY DIFFRACTIONr_chiral_restr0.0930.22671
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213077
X-RAY DIFFRACTIONr_nbd_refined0.2270.28853
X-RAY DIFFRACTIONr_nbtor_refined0.310.211555
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2564
X-RAY DIFFRACTIONr_metal_ion_refined0.1420.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0390.21
X-RAY DIFFRACTIONr_mcbond_it0.3741.511243
X-RAY DIFFRACTIONr_mcangle_it0.66217574
X-RAY DIFFRACTIONr_scbond_it1.01236708
X-RAY DIFFRACTIONr_scangle_it1.7214.55856
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 232 -
Rwork0.29 4314 -
obs-4546 96.46 %
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)
12.6313-0.2881-0.48260.7113-0.03441.126-0.03160.0301-0.19490.0049-0.00920.21260.0996-0.16740.0408-0.2831-0.0318-0.0286-0.2418-0.0049-0.13848.6785-7.72928.2102
21.166-0.2346-0.06291.3919-0.00691.22690.1050.23060.0032-0.1802-0.00860.0855-0.0982-0.1281-0.0964-0.220.0208-0.0438-0.1781-0.0252-0.131526.24936.06054.8213
31.99250.39380.50852.7929-0.41180.83870.13170.14260.4245-0.0083-0.086-0.0984-0.27670.1521-0.0457-0.185-0.00050.0469-0.4032-0.0169-0.145129.73928.668713.9118
41.6943-0.3776-0.64021.77160.48491.3811-0.0606-0.142-0.1957-0.01990.1244-0.10140.21830.1364-0.0638-0.25610.0082-0.034-0.3478-0.0431-0.149847.1294-20.23810.3
51.4631-0.5518-0.74540.68350.14451.3088-0.0482-0.3025-0.02350.11380.1049-0.06160.03840.2116-0.0567-0.23510.0394-0.0472-0.0816-0.0432-0.107941.4474-0.398435.0847
63.3703-0.9213-1.3482.71150.83162.88210.0466-0.42130.41580.08170.1233-0.4122-0.37980.3238-0.1699-0.2626-0.0872-0.0406-0.2362-0.1201-0.07353.136320.181527.8322
70.90120.3526-1.00032.17370.39183.70440.878-0.81250.54660.3025-0.0301-0.1285-1.89741.192-0.84791.1255-0.74280.39170.4238-0.37790.117843.4997-51.670457.332
83.82821.0017-4.4960.8589-1.058610.61070.5261-0.61880.29010.1029-0.17260.0254-0.70931.2464-0.3535-0.0109-0.1213-0.00820.0019-0.0614-0.158346.405-70.948629.526
95.43440.8604-2.83762.387-0.06545.6486-0.417-1.2541-0.928-0.0492-0.397-0.5432.14882.64130.8140.48730.74340.24260.7930.4331-0.050954.8784-91.830639.6807
101.713-0.4089-0.93871.5733-0.75135.72990.48770.9550.60740.00620.14570.3128-1.4307-2.5946-0.63350.38150.71060.15471.17710.35560.174216.0662-61.820325.1389
113.70.4135-4.85581.2308-0.268112.06360.16730.41170.11560.16490.12390.2058-0.2389-1.144-0.2912-0.1012-0.0881-0.03730.06670.0307-0.154623.0214-77.153553.9519
123.43820.7461-3.93831.2512-0.37676.0409-1.22180.2906-0.968-0.13920.1479-0.00772.7584-0.51711.07391.2115-0.31650.3173-0.139-0.04570.057728.2321-99.933745.6285
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA5 - 3185 - 318
22AA319 - 493319 - 493
33AA494 - 627494 - 627
44BB8 - 3188 - 318
55BB319 - 493319 - 493
66BB494 - 629494 - 629
77CC7 - 2907 - 290
88CC321 - 493321 - 493
99CC494 - 628494 - 628
1010DD17 - 29017 - 290
1111DD321 - 493321 - 493
1212DD494 - 629494 - 629

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