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- PDB-7s04: 1-deoxy-D-xylulose 5-phosphate reductoisomerase (IspC) from Acine... -

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Basic information

Entry
Database: PDB / ID: 7s04
Title1-deoxy-D-xylulose 5-phosphate reductoisomerase (IspC) from Acinetobacter baumannii in complex with FR900098, NADPH, and a magnesium ion
Components1-deoxy-D-xylulose 5-phosphate reductoisomerase
KeywordsOXIDOREDUCTASE/INHIBITOR / isoprenoid biosynthesis / inhibitor / complex / OXIDOREDUCTASE-INHIBITOR complex
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 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
3-[ethanoyl(hydroxy)amino]propylphosphonic acid / Chem-NDP / 1-deoxy-D-xylulose 5-phosphate reductoisomerase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsNoble, S.M. / Ball, H.S. / Couch, R.D.
Funding support2items
OrganizationGrant numberCountry
Other governmentW81XWH-17-C-0066
Other governmentW0083_13_WR
CitationJournal: Acs Infect Dis. / Year: 2021
Title: Characterization and Inhibition of 1-Deoxy-d-Xylulose 5-Phosphate Reductoisomerase: A Promising Drug Target in Acinetobacter baumannii and Klebsiella pneumoniae .
Authors: Ball, H.S. / Girma, M.B. / Zainab, M. / Soojhawon, I. / Couch, R.D. / Noble, S.M.
History
DepositionAug 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0634
Polymers44,0961
Non-polymers9673
Water2,648147
1
A: 1-deoxy-D-xylulose 5-phosphate reductoisomerase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)90,1258
Polymers88,1912
Non-polymers1,9346
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6000 Å2
ΔGint-40 kcal/mol
Surface area30230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.572, 118.251, 53.911
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-728-

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: 44095.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: dxr, ABA1_02159, Aba9102_18380, ABUW_1739, AN415_01721, C6N18_11275, DLI69_14610, F2P40_10340, FDO31_03370, GNY86_03270, HYI42_18125, NCTC13421_01630
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0D5YGN4, 1-deoxy-D-xylulose-5-phosphate reductoisomerase
#2: Chemical ChemComp-F98 / 3-[ethanoyl(hydroxy)amino]propylphosphonic acid


Mass: 197.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12NO5P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 100 mM sodium citrate:HCl, pH 5.60, 250 mM ammonium sulfate, 24% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Mar 15, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.52→33.92 Å / Num. obs: 27390 / % possible obs: 98.61 % / Redundancy: 5.49 % / Biso Wilson estimate: 23.31 Å2 / Rmerge(I) obs: 0.2494 / Net I/σ(I): 23.09
Reflection shellResolution: 2.52→2.56 Å / Redundancy: 11.06 % / Rmerge(I) obs: 0.36 / Num. unique obs: 14804 / Rsym value: 0.12 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4ZN6

4zn6


Resolution: 2.52→33.92 Å / SU ML: 0.301 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.7134 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2447 2754 10.05 %
Rwork0.2295 24636 -
obs0.2311 27390 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.65 Å2
Refinement stepCycle: LAST / Resolution: 2.52→33.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3004 0 61 147 3212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00763130
X-RAY DIFFRACTIONf_angle_d0.98034268
X-RAY DIFFRACTIONf_chiral_restr0.0698508
X-RAY DIFFRACTIONf_plane_restr0.0053545
X-RAY DIFFRACTIONf_dihedral_angle_d24.00561847
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.560.31631430.27071237X-RAY DIFFRACTION98.01
2.56-2.610.34291370.29511223X-RAY DIFFRACTION98.48
2.61-2.660.32161400.28021245X-RAY DIFFRACTION99
2.66-2.710.30681360.29361215X-RAY DIFFRACTION99.41
2.71-2.770.30421440.28491267X-RAY DIFFRACTION99.72
2.77-2.840.28051380.27091218X-RAY DIFFRACTION99.12
2.84-2.910.31511410.29131225X-RAY DIFFRACTION98.77
2.91-2.990.30071370.29151252X-RAY DIFFRACTION98.51
2.99-3.080.24931310.29661196X-RAY DIFFRACTION97.57
3.08-3.170.28181390.25951264X-RAY DIFFRACTION97.43
3.17-3.290.26971340.26621180X-RAY DIFFRACTION97.62
3.29-3.420.28371320.24661240X-RAY DIFFRACTION97.3
3.42-3.580.26931320.24031241X-RAY DIFFRACTION98.92
3.58-3.760.22011360.20941211X-RAY DIFFRACTION98.75
3.76-40.26151350.2031213X-RAY DIFFRACTION97.61
4-4.310.17711420.18891232X-RAY DIFFRACTION98.14
4.31-4.740.19691440.17671242X-RAY DIFFRACTION99.07
4.74-5.420.14371340.18351241X-RAY DIFFRACTION99.35
5.42-6.820.21961450.19891240X-RAY DIFFRACTION100
6.82-33.920.16961340.14821254X-RAY DIFFRACTION99.78

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