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- PDB-5ks1: 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Vibrio vulnificus -

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Basic information

Entry
Database: PDB / ID: 5ks1
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
: / PHOSPHATE ION / 1-deoxy-D-xylulose 5-phosphate reductoisomerase
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsUssin, N. / Abdulsalam, R.W. / Offermann, L.R. / 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 ...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

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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)87,85412
Polymers87,1822
Non-polymers67210
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-27 kcal/mol
Surface area30920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.063, 149.247, 243.768
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 3.34 Å3/Da / Density % sol: 63.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M Sodium citrate pH 5.0, 0.8 M Ammonium phosphate, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97912 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 46042 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 31
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 2.7 / CC1/2: 0.934 / % possible all: 92.4

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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: 2.4→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / Cross valid method: THROUGHOUT / ESU R: 0.26 / ESU R Free: 0.209 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22883 2274 5 %RANDOM
Rwork0.18875 ---
obs0.19077 43578 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 88.721 Å2
Baniso -1Baniso -2Baniso -3
1-6.43 Å20 Å2-0 Å2
2---2.97 Å20 Å2
3----3.46 Å2
Refinement stepCycle: 1 / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5890 0 36 158 6084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0196010
X-RAY DIFFRACTIONr_bond_other_d00.025919
X-RAY DIFFRACTIONr_angle_refined_deg1.9091.9798152
X-RAY DIFFRACTIONr_angle_other_deg3.629313589
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.525787
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.88625.714238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.119151028
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9781526
X-RAY DIFFRACTIONr_chiral_restr0.1130.2982
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216824
X-RAY DIFFRACTIONr_gen_planes_other0.0140.021242
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_it4.5395.7953151
X-RAY DIFFRACTIONr_mcbond_other4.545.7943150
X-RAY DIFFRACTIONr_mcangle_it6.5398.6643931
X-RAY DIFFRACTIONr_mcangle_other6.5398.6663932
X-RAY DIFFRACTIONr_scbond_it6.0086.3932859
X-RAY DIFFRACTIONr_scbond_other5.4666.3772851
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.3119.3214208
X-RAY DIFFRACTIONr_long_range_B_refined10.79946.2636767
X-RAY DIFFRACTIONr_long_range_B_other10.79946.2686768
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 137 -
Rwork0.319 3024 -
obs--92.92 %
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)
11.392-0.53821.86111.7268-0.04895.5399-0.3814-0.33880.1396-0.03060.23410.1048-0.1857-0.84920.14730.2337-0.0127-0.0460.1962-0.01060.06180.444-24.0443.13
22.6618-0.44320.76384.2909-0.94074.1596-0.433-0.22830.6668-0.0262-0.0889-0.4105-0.9713-0.39220.5220.53660.1828-0.16870.0794-0.08760.251914.839-13.94820.413
32.2899-0.41411.45771.4369-1.20095.0888-0.30920.02210.43340.1202-0.1207-0.0991-0.1089-0.13030.430.25510.0795-0.02340.0764-0.00240.137819.036-26.41819.944
43.2399-1.10190.03626.3823-1.75191.9671-0.24090.0170.8126-0.1669-0.0297-0.4589-1.0041-0.30690.27070.85670.2294-0.26720.1073-0.04540.48459.0910.70214.842
50.95080.32070.76082.327-1.27264.74730.0642-0.449-0.09420.0778-0.1498-0.11590.4884-0.78950.08550.2754-0.06030.01810.36080.02940.016616.689-46.62150.158
65.8103-0.31922.50470.7578-0.42744.13310.044-0.2640.2446-0.0571-0.1206-0.01330.47120.62020.07650.38910.18720.05180.2631-0.00050.0235.73-42.31631.603
71.6948-0.27551.2630.3726-0.49913.317-0.0133-0.11150.0552-0.041-0.14330.01180.56460.29360.15660.40080.15680.05520.16560.02090.019229.632-43.33131.233
87.03352.5559-1.22451.5909-0.27570.48550.2815-0.4214-0.66050.2272-0.2157-0.15330.22140.0991-0.06580.44140.1158-0.11930.15880.06750.338836.146-64.93338.954
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 160
2X-RAY DIFFRACTION2A161 - 245
3X-RAY DIFFRACTION3A246 - 313
4X-RAY DIFFRACTION4A314 - 400
5X-RAY DIFFRACTION5B0 - 169
6X-RAY DIFFRACTION6B170 - 227
7X-RAY DIFFRACTION7B228 - 364
8X-RAY DIFFRACTION8B365 - 401

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