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- PDB-1r0k: Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomer... -

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Basic information

Entry
Database: PDB / ID: 1r0k
TitleCrystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Zymomonas mobilis
Components1-deoxy-D-xylulose 5-phosphate reductoisomerase
KeywordsOXIDOREDUCTASE / reductoisomerase / NADPH dependent / Fosmidomycin / non-mevalonate pathway / zymomonas mobilis
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
ACETATE ION / 1-deoxy-D-xylulose 5-phosphate reductoisomerase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 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 1.3Oct 3, 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)167,7968
Polymers167,5604
Non-polymers2364
Water22,0501224
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)83,8984
Polymers83,7802
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-19 kcal/mol
Surface area30420 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)83,8984
Polymers83,7802
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-18 kcal/mol
Surface area30230 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1224 / 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: Na citrate, PEG 4000, 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: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8452 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 23, 2001
RadiationMonochromator: Premirror, Triangular monochromator, Bent mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8452 Å / Relative weight: 1
ReflectionResolution: 1.91→29.63 Å / Num. all: 118460 / Num. obs: 118460 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 12.4 Å2 / Limit h max: 45 / Limit h min: -45 / Limit k max: 48 / Limit k min: -45 / Limit l max: 51 / Limit l min: 0 / Observed criterion F max: 2499288.66 / Observed criterion F min: 22.3 / Rsym value: 0.083 / Net I/σ(I): 9.5
Reflection shellResolution: 1.9→1.99 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.5 / Num. unique all: 19549 / Rsym value: 0.42 / % possible all: 95.1

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
DENZOdata reduction
CCP4(SCALA)data scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JVS, 1-deoxy-D-xylulose 5-phosphate reductoisomerase (E.coli)

1jvs


Resolution: 1.91→29.63 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2812 2.4 %RANDOM
Rwork0.2 ---
all0.2 123526 --
obs0.2 118460 95.9 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 50.4225 Å2 / ksol: 0.347591 e/Å3
Displacement parametersBiso max: 66.74 Å2 / Biso mean: 20.63 Å2 / Biso min: 6.1 Å2
Baniso -1Baniso -2Baniso -3
1--4.72 Å20 Å20.97 Å2
2--6.39 Å20 Å2
3----1.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.33 Å
Luzzati d res high-1.91
Refinement stepCycle: LAST / Resolution: 1.91→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11481 0 16 1224 12721
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_torsion_deg21.3
X-RAY DIFFRACTIONc_torsion_impr_deg0.75
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 (%)
1.91-1.990.3963102.40.359125710.022153851288183.7
1.99-2.10.3933352.40.354139150.021154001425092.5
2.1-2.230.3453692.50.335143350.018153801470495.6
2.23-2.40.3153582.40.323147260.017154291508497.8
2.4-2.640.3483502.30.317148890.019154381523998.7
2.64-3.030.3244072.70.313149010.016154641530899
3.03-3.810.3123352.20.282150640.017154931539999.4
3.81-29.630.243482.20.236152470.013156711559599.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3act.paramact.top

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