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- PDB-6mh5: Crystal Structure of 1-deoxy-D-xylulose-5-phosphate reductoisomer... -

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Basic information

Entry
Database: PDB / ID: 6mh5
TitleCrystal Structure of 1-deoxy-D-xylulose-5-phosphate reductoisomerase from Staphylococcus schleiferi in complex with Fosmidomycin (FOM)
Components1-deoxy-D-xylulose 5-phosphate reductoisomerase
KeywordsOXIDOREDUCTASE / reductoisomerase / staphylococci / MEP pathway / fosmidomycin / GlpT
Function / homology
Function and homology information


1-deoxy-D-xylulose-5-phosphate reductoisomerase / 1-deoxy-D-xylulose-5-phosphate reductoisomerase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / NADPH binding / isomerase activity / metal 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
3-[FORMYL(HYDROXY)AMINO]PROPYLPHOSPHONIC ACID / 1-deoxy-D-xylulose 5-phosphate reductoisomerase
Similarity search - Component
Biological speciesStaphylococcus schleiferi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.887 Å
AuthorsLee, S.G. / Jez, J.M.
CitationJournal: Plos Pathog. / Year: 2020
Title: Potent, specific MEPicides for treatment of zoonotic staphylococci.
Authors: Edwards, R.L. / Heueck, I. / Lee, S.G. / Shah, I.T. / Miller, J.J. / Jezewski, A.J. / Mikati, M.O. / Wang, X. / Brothers, R.C. / Heidel, K.M. / Osbourn, D.M. / Burnham, C.D. / Alvarez, S. / ...Authors: Edwards, R.L. / Heueck, I. / Lee, S.G. / Shah, I.T. / Miller, J.J. / Jezewski, A.J. / Mikati, M.O. / Wang, X. / Brothers, R.C. / Heidel, K.M. / Osbourn, D.M. / Burnham, C.D. / Alvarez, S. / Fritz, S.A. / Dowd, C.S. / Jez, J.M. / Odom John, A.R.
History
DepositionSep 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)84,8634
Polymers84,4972
Non-polymers3662
Water00
1
A: 1-deoxy-D-xylulose 5-phosphate reductoisomerase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)84,8634
Polymers84,4972
Non-polymers3662
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545x+1/2,y-1/2,z1
Buried area4420 Å2
ΔGint-18 kcal/mol
Surface area30600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.713, 53.983, 115.799
Angle α, β, γ (deg.)90.000, 91.617, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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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: 42248.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus schleiferi (bacteria) / Gene: dxr, SSCHL_1510 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0K1A7V6, 1-deoxy-D-xylulose-5-phosphate reductoisomerase
#2: Chemical ChemComp-FOM / 3-[FORMYL(HYDROXY)AMINO]PROPYLPHOSPHONIC ACID / FOSMIDOMYCIN


Mass: 183.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10NO5P / Comment: antibiotic*YM

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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: 2.45 Å3/Da / Density % sol: 49.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES/MOPS (pH 7.5), 20 mM D-glucose, 20 mM D-mannose, 20 mM D-galactose, 20 mM L-fucose, 20 mM D-xylose, 20 mM N-acetyl-D-glucosamine, 20% (v/v) glycerol, 10% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 6, 2017
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.887→46.08 Å / Num. obs: 18289 / % possible obs: 97.4 % / Redundancy: 3.2 % / Net I/σ(I): 14.7
Reflection shellResolution: 2.887→2.99 Å / Num. unique obs: 1831

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-3000data collection
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.887→46.08 Å / SU ML: 0.4187 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.68
RfactorNum. reflection% reflection
Rfree0.277 1818 9.95 %
Rwork0.2122 --
obs0.2187 18276 97.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 64.3065754791 Å2
Refinement stepCycle: LAST / Resolution: 2.887→46.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5898 0 22 0 5920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009559855282016028
X-RAY DIFFRACTIONf_angle_d1.194144169658155
X-RAY DIFFRACTIONf_chiral_restr0.0587603405858939
X-RAY DIFFRACTIONf_plane_restr0.006586251825181046
X-RAY DIFFRACTIONf_dihedral_angle_d4.173319812733663
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.887-2.96520.35941310.29861130X-RAY DIFFRACTION88.8028169014
2.9652-3.05240.34371300.27981272X-RAY DIFFRACTION98.11056683
3.0524-3.15090.37171410.27791221X-RAY DIFFRACTION95.9830866808
3.1509-3.26350.34691460.26781285X-RAY DIFFRACTION99.0997229917
3.2635-3.39410.33391300.26041280X-RAY DIFFRACTION99.1561181435
3.3941-3.54850.28481450.23461265X-RAY DIFFRACTION98.8086895585
3.5485-3.73550.31531450.23981267X-RAY DIFFRACTION98.3286908078
3.7355-3.96940.30071410.231269X-RAY DIFFRACTION97.8487161693
3.9694-4.27570.28091370.19981267X-RAY DIFFRACTION97.3647711512
4.2757-4.70560.26341440.18471272X-RAY DIFFRACTION98.7447698745
4.7056-5.38560.2531370.19661308X-RAY DIFFRACTION98.7021857923
5.3856-6.78190.27631450.21781286X-RAY DIFFRACTION97.8796169631
6.7819-46.080.20061460.15721336X-RAY DIFFRACTION97.692814766

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