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- PDB-5krv: 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Vibrio vulni... -

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Basic information

Entry
Database: PDB / ID: 5krv
Title1-deoxy-D-xylulose 5-phosphate reductoisomerase from Vibrio vulnificus in complex Arginine
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
ARGININE / S,R MESO-TARTARIC ACID / 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. / Magee, P. / 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)93,34316
Polymers92,3002
Non-polymers1,04314
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-3 kcal/mol
Surface area32180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.165, 149.129, 245.089
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AB

#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: 46149.750 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

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Non-polymers , 5 types, 189 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 3.23 Å3/Da / Density % sol: 61.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.8 M Sodium potassium tartrate 20% (w/v) PEG 3350 5 mM Arginine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 29, 2015
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: 53084 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 22.7
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.766 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.871 / % possible all: 98.2

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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: 0.967 / Cor.coef. Fo:Fc free: 0.955 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.176 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21469 2686 5.1 %RANDOM
Rwork0.18553 ---
obs0.18701 50360 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 66.277 Å2
Baniso -1Baniso -2Baniso -3
1-3.35 Å20 Å2-0 Å2
2---1.65 Å20 Å2
3----1.71 Å2
Refinement stepCycle: 1 / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5904 0 67 175 6146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196047
X-RAY DIFFRACTIONr_bond_other_d00.025983
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.9818179
X-RAY DIFFRACTIONr_angle_other_deg3.715313741
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4315783
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.22225.685241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.639151046
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4931527
X-RAY DIFFRACTIONr_chiral_restr0.0770.2983
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216834
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021245
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_it1.7354.2493150
X-RAY DIFFRACTIONr_mcbond_other1.7314.2473149
X-RAY DIFFRACTIONr_mcangle_it2.8456.3543927
X-RAY DIFFRACTIONr_mcangle_other2.8456.3563928
X-RAY DIFFRACTIONr_scbond_it2.3324.6562897
X-RAY DIFFRACTIONr_scbond_other2.3324.6562897
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8296.8064253
X-RAY DIFFRACTIONr_long_range_B_refined6.12433.4936460
X-RAY DIFFRACTIONr_long_range_B_other6.12433.5026461
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.303→2.362 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 181 -
Rwork0.304 3588 -
obs--97.11 %
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)
11.40040.1595-1.07051.52850.31924.2961-0.20420.1424-0.06490.00340.10060.07930.1632-0.33920.10350.18870.02870.02080.0796-0.00180.01230.82123.798121.342
20.73310.3149-1.3162.39241.20226.5551-0.12010.25960.0477-0.01750.03490.11140.0555-0.67770.08530.2256-0.0936-0.0120.2037-0.01740.04227.20825.69598.232
32.51610.99160.26944.2689-1.62682.33960.0951-0.0231-0.36170.1006-0.3491-0.67530.33710.04820.25410.4167-0.10570.04370.070.00720.188619.71210.797104.484
41.18381.3966-0.18073.0391-0.22691.28760.0549-0.0576-0.27790.1585-0.2318-0.34710.279-0.06870.17680.3433-0.08970.01010.08110.01620.081314.88210.998105.851
51.2486-0.2574-0.03031.677-0.81984.7523-0.00590.31460.1901-0.0448-0.0581-0.0148-0.375-0.28250.06410.2493-0.0465-0.02010.27540.07190.035517.89746.67471.517
65.04240.1201-3.01450.6216-0.07023.0590.14740.2578-0.2199-0.0367-0.08570.0529-0.38190.1676-0.06180.4098-0.1228-0.01760.2028-0.030.063833.71742.75791.451
71.05280.8783-0.19931.3271-0.6582.3278-0.08630.1204-0.0703-0.0181-0.0231-0.0653-0.21950.050.10950.3106-0.0886-0.01740.12460.00270.010623.78436.53292.002
83.2202-1.6373-0.04373.93190.19313.13470.18560.09240.5175-0.3406-0.0621-0.2125-0.5510.53-0.12350.5155-0.26070.03360.23190.01990.095639.63157.72687.475
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 144
2X-RAY DIFFRACTION2A145 - 179
3X-RAY DIFFRACTION3A180 - 249
4X-RAY DIFFRACTION4A250 - 401
5X-RAY DIFFRACTION5B0 - 161
6X-RAY DIFFRACTION6B162 - 228
7X-RAY DIFFRACTION7B229 - 308
8X-RAY DIFFRACTION8B309 - 401

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