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- PDB-1r0l: 1-deoxy-D-xylulose 5-phosphate reductoisomerase from zymomonas mo... -

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Basic information

Entry
Database: PDB / ID: 1r0l
Title1-deoxy-D-xylulose 5-phosphate reductoisomerase from zymomonas mobilis in complex with NADPH
Components1-deoxy-D-xylulose 5-phosphate reductoisomerase
KeywordsOXIDOREDUCTASE / reductoisomerase / NADPH complex / Fosmidomycin / non-mevalonate pathway / zymomonas mobilis
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 / NADPH binding / 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
Chem-NDP / 1-deoxy-D-xylulose 5-phosphate reductoisomerase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / fourier difference / Resolution: 2.7 Å
AuthorsRicagno, S. / Grolle, S. / Bringer-Meyer, S. / Sahm, H. / Lindqvist, Y. / Schneider, G.
CitationJournal: Biochim.Biophys.Acta / Year: 2004
Title: Crystal structure of 1-deoxy-d-xylulose-5-phosphate reductoisomerase from Zymomonas mobilis at 1.9-A resolution.
Authors: Ricagno, S. / Grolle, S. / Bringer-Meyer, S. / Sahm, H. / Lindqvist, Y. / Schneider, G.
History
DepositionSep 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Aug 23, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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


Theoretical massNumber of molelcules
Total (without water)170,5428
Polymers167,5604
Non-polymers2,9824
Water1,946108
1
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)85,2714
Polymers83,7802
Non-polymers1,4912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-17 kcal/mol
Surface area30620 Å2
MethodPISA
2
C: 1-deoxy-D-xylulose 5-phosphate reductoisomerase
D: 1-deoxy-D-xylulose 5-phosphate reductoisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2714
Polymers83,7802
Non-polymers1,4912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-18 kcal/mol
Surface area30670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.700, 93.200, 98.600
Angle α, β, γ (deg.)90.00, 90.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
1-deoxy-D-xylulose 5-phosphate reductoisomerase / DXP reductoisomerase / 1-deoxyxylulose-5-phosphate reductoisomerase


Mass: 41890.016 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis (bacteria) / Gene: DXR / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 [pREP4]
References: UniProt: Q9X5F2, 1-deoxy-D-xylulose-5-phosphate reductoisomerase
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG4000, Na citrate, Ammonium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.076 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 10, 2002 / Details: Vertically focusing cylindrical mirror
RadiationMonochromator: Single asymmetrically cut Si(111) crystal with horizontal diffraction plane
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.076 Å / Relative weight: 1
ReflectionResolution: 2.69→29.63 Å / Num. all: 43474 / Num. obs: 43474 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 57.5 Å2 / Limit h max: 32 / Limit h min: -32 / Limit k max: 34 / Limit k min: -32 / Limit l max: 36 / Limit l min: 0 / Observed criterion F max: 1806562.97 / Observed criterion F min: 17.9 / Rsym value: 0.095 / Net I/σ(I): 10.1
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 3.1 / Num. unique all: 6370 / Rsym value: 0.376 / % possible all: 99.6

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: fourier difference
Starting model: PDB entry 1R0K, 1-deoxy-D-xylulose 5-phosphate reductoisomerase

1r0k


Resolution: 2.7→29.63 Å / Rfactor Rfree error: 0.017 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.269 493 1.1 %RANDOM
Rwork0.249 ---
obs0.249 43304 98.9 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 16.3294 Å2 / ksol: 0.302473 e/Å3
Displacement parametersBiso max: 109.46 Å2 / Biso mean: 45.12 Å2 / Biso min: 6.52 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å2-4 Å2
2--3.95 Å20 Å2
3----5.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.66 Å0.61 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.61 Å
Luzzati d res high-2.7
Refinement stepCycle: LAST / Resolution: 2.7→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11436 0 108 108 11652
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_torsion_deg21.7
X-RAY DIFFRACTIONc_torsion_impr_deg1.06
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.7-2.820.486581.10.4251530.0645499521194.7
2.82-2.970.523691.30.42153260.0635409539599.7
2.97-3.160.382581.10.41854010.055467545999.9
3.16-3.40.3775210.40454030.0525461545599.9
3.4-3.740.397691.30.39453650.0485448543499.7
3.74-4.280.285661.20.36453800.0355473544699.5
4.28-5.390.4055710.33853910.0545485544899.3
5.39-29.630.294641.20.28253920.0375585545697.7
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3nadph.parnadph.top

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