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- PDB-5kry: 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Vibrio vulnificus -

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Basic information

Entry
Database: PDB / ID: 5kry
Title1-deoxy-D-xylulose 5-phosphate reductoisomerase from Vibrio vulnificus
Components1-deoxy-D-xylulose 5-phosphate reductoisomerase
KeywordsOXIDOREDUCTASE / Dxr 1-deoxy-D-xylulose 5-phosphate reductoisomerase
Function / homology
Function and homology information


isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway involved in terpenoid biosynthetic process / 1-deoxy-D-xylulose-5-phosphate reductoisomerase / 1-deoxy-D-xylulose-5-phosphate reductoisomerase activity / NADPH binding / manganese ion binding
Similarity search - Function
1-deoxy-D-xylulose 5-phosphate reductoisomerase / 1-deoxy-D-xylulose 5-phosphate reductoisomerase, N-terminal / 1-deoxy-D-xylulose 5-phosphate reductoisomerase, C-terminal / DXP reductoisomerase C-terminal domain / DXP reductoisomerase, C-terminal domain superfamily / 1-deoxy-D-xylulose 5-phosphate reductoisomerase / 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal domain / DXP reductoisomerase C-terminal domain / RNA polymerase sigma factor, region 2, helix turn helix motif / Rna Polymerase Sigma Factor; Chain: A ...1-deoxy-D-xylulose 5-phosphate reductoisomerase / 1-deoxy-D-xylulose 5-phosphate reductoisomerase, N-terminal / 1-deoxy-D-xylulose 5-phosphate reductoisomerase, C-terminal / DXP reductoisomerase C-terminal domain / DXP reductoisomerase, C-terminal domain superfamily / 1-deoxy-D-xylulose 5-phosphate reductoisomerase / 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal domain / DXP reductoisomerase C-terminal domain / RNA polymerase sigma factor, region 2, helix turn helix motif / Rna Polymerase Sigma Factor; Chain: A / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1-deoxy-D-xylulose 5-phosphate reductoisomerase
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsUssin, N. / Abdulsalam, R.W. / Chruszcz, M.
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2018
Title: Structural characterization of 1-deoxy-D-xylulose 5-phosphate Reductoisomerase from Vibrio vulnificus.
Authors: Ussin, N.K. / Bagnell, A.M. / Offermann, L.R. / Abdulsalam, R. / Perdue, M.L. / Magee, P. / Chruszcz, M.
History
DepositionJul 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 reductoisomerase
B: 1-deoxy-D-xylulose 5-phosphate reductoisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4306
Polymers87,1822
Non-polymers2484
Water6,666370
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-10 kcal/mol
Surface area31470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.356, 149.853, 246.008
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-746-

HOH

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Components

#1: Protein 1-deoxy-D-xylulose 5-phosphate reductoisomerase / DXP reductoisomerase / 1-deoxyxylulose-5-phosphate reductoisomerase / 2-C-methyl-D-erythritol 4- ...DXP reductoisomerase / 1-deoxyxylulose-5-phosphate reductoisomerase / 2-C-methyl-D-erythritol 4-phosphate synthase


Mass: 43591.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (strain CMCP6) (bacteria)
Strain: CMCP6 / Gene: dxr, VV1_1866 / Plasmid: pJExpress411 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8DBF5, 1-deoxy-D-xylulose-5-phosphate reductoisomerase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 3.4 Å3/Da / Density % sol: 63.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.0 M Succinic acid pH 7.0, 0.1 M HEPES pH 7.0, 1% w/v PEG 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 53399 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 21
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.668 / Mean I/σ(I) obs: 2.1 / CC1/2: 0.859 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5KQO

5kqo


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.186 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22452 2571 4.8 %RANDOM
Rwork0.1847 ---
obs0.18663 50748 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 49.587 Å2
Baniso -1Baniso -2Baniso -3
1-2.42 Å20 Å2-0 Å2
2---2.21 Å2-0 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5938 0 16 370 6324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0196055
X-RAY DIFFRACTIONr_bond_other_d00.025983
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.9758208
X-RAY DIFFRACTIONr_angle_other_deg3.727313748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6895787
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.86225.569246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.176151055
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3191529
X-RAY DIFFRACTIONr_chiral_restr0.0940.2983
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216876
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021263
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.62.4833157
X-RAY DIFFRACTIONr_mcbond_other1.62.4823156
X-RAY DIFFRACTIONr_mcangle_it2.6553.713941
X-RAY DIFFRACTIONr_mcangle_other2.6553.7113942
X-RAY DIFFRACTIONr_scbond_it2.2782.8262898
X-RAY DIFFRACTIONr_scbond_other2.2762.8262898
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6914.1024268
X-RAY DIFFRACTIONr_long_range_B_refined7.44120.5456773
X-RAY DIFFRACTIONr_long_range_B_other7.44120.5516774
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 192 -
Rwork0.268 3681 -
obs--99.85 %
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)
11.36490.2389-0.941.6920.26333.2952-0.22590.0779-0.0944-0.02530.11440.0760.1906-0.21470.11140.20870.00730.01460.07830.0050.01281.31923.81121.855
21.64610.6576-0.99391.62060.90857.6954-0.1810.21410.0531-0.18980.04330.03530.0562-0.64610.13760.245-0.10830.0050.1704-0.02910.01757.47225.55598.393
31.11921.652-0.11453.8725-1.7071.91470.03610.0071-0.4281-0.0042-0.2817-0.73410.31770.14240.24560.4643-0.11380.08650.1877-0.0530.226720.46514.567102.564
40.99441.3183-0.01963.3351-0.15041.28230.0473-0.0227-0.29750.0955-0.1796-0.36990.3527-0.10780.13230.3344-0.07530.02690.0732-0.00240.103314.4718.766108.043
50.9780.2047-0.08871.6399-0.56533.4284-0.06780.29680.1114-0.13150.01130.0583-0.1783-0.3320.05660.3262-0.0315-0.02220.35310.04060.016517.90646.971.703
62.99190.0353-1.66640.8235-0.04112.42530.04470.2891-0.3072-0.138-0.08680.0583-0.1690.13760.04220.4673-0.0606-0.03680.2526-0.01660.06133.0342.28791.364
71.10740.8741-0.46011.04350.17541.7503-0.15280.1988-0.0953-0.09210.0442-0.0561-0.0494-0.02420.10850.37-0.05730.00330.1854-0.00020.014424.73137.39792.615
83.7429-1.7737-0.16442.7250.31382.34580.14710.1740.6135-0.2844-0.0617-0.2281-0.52490.4493-0.08550.4394-0.1650.01890.24830.04890.111739.42558.57487.326
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 144
2X-RAY DIFFRACTION2A145 - 180
3X-RAY DIFFRACTION3A181 - 271
4X-RAY DIFFRACTION4A272 - 401
5X-RAY DIFFRACTION5B0 - 160
6X-RAY DIFFRACTION6B161 - 225
7X-RAY DIFFRACTION7B226 - 311
8X-RAY DIFFRACTION8B312 - 401

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