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- PDB-5dul: 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Yersinia pes... -

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Basic information

Entry
Database: PDB / ID: 5dul
Title1-deoxy-D-xylulose 5-phosphate reductoisomerase from Yersinia pestis in complex with NADPH
Components1-deoxy-D-xylulose 5-phosphate reductoisomerase
KeywordsOXIDOREDUCTASE / structural genomics / IDP00499 / xylulose / reductoisomerase / Center for Structural Genomics of Infectious Diseases / CSGID
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
Chem-NDP / 1-deoxy-D-xylulose 5-phosphate reductoisomerase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsOsipiuk, J. / Mulligan, R. / Stam, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272200700058C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
CitationJournal: to be published
Title: 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Yersinia pestis in complex with NADPH .
Authors: Osipiuk, J. / Mulligan, R. / Stam, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)176,7048
Polymers173,7224
Non-polymers2,9824
Water30617
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)88,3524
Polymers86,8612
Non-polymers1,4912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-34 kcal/mol
Surface area30270 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)88,3524
Polymers86,8612
Non-polymers1,4912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-34 kcal/mol
Surface area30220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.306, 121.306, 86.827
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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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: 43430.547 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: dxr, YPO1048, y3131, YP_2802 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8ZH62, 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.: 17 / 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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M sodium chloride, 0.1 M HEPES buffer, 25% PEG 3350, 10 mM NADPH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 28, 2013
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.558
11K, H, -L20.442
ReflectionResolution: 2.6→35.1 Å / Num. all: 43562 / Num. obs: 43562 / % possible obs: 99.6 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.054 / Rrim(I) all: 0.123 / Χ2: 1.372 / Net I/av σ(I): 16.666 / Net I/σ(I): 10.2 / Num. measured all: 230854
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.644.60.738221850.8710.3790.8320.87498.8
2.64-2.694.90.68321690.8870.3420.7660.86699.9
2.69-2.745.20.64221650.9210.3140.7160.89499.8
2.74-2.85.30.55622050.9470.2670.6170.90599.7
2.8-2.865.40.48421760.9380.2310.5370.936100
2.86-2.935.40.43621480.9630.2080.4840.98899.6
2.93-35.40.35221820.9740.1680.3911.11199.5
3-3.085.50.28821900.9740.1360.3191.24799.8
3.08-3.175.50.26322210.9770.1240.2911.28899.9
3.17-3.285.60.22221450.9810.1030.2451.3299.4
3.28-3.395.70.1821540.9870.0830.1981.529100
3.39-3.535.70.14522200.9890.0670.161.677100
3.53-3.695.70.12221670.9940.0560.1341.708100
3.69-3.885.60.10521840.9940.0490.1161.74100
3.88-4.135.50.09222050.9960.0440.1021.715100
4.13-4.455.30.08321670.9940.0410.0931.77599.9
4.45-4.895.20.07521800.9950.0370.0841.714100
4.89-5.65.20.07921800.9950.0390.0881.704100
5.6-7.055.10.07522150.9950.0370.0841.6100
7.05-504.30.06521040.9920.0360.0751.74596.2

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IIE

3iie


Resolution: 2.6→35.02 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.934 / SU B: 24.602 / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2382 2208 5.1 %RANDOM
Rwork0.1936 ---
obs0.1959 41318 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 162.69 Å2 / Biso mean: 75.532 Å2 / Biso min: 37.22 Å2
Baniso -1Baniso -2Baniso -3
1-45.12 Å20 Å20 Å2
2--45.12 Å20 Å2
3----90.24 Å2
Refinement stepCycle: final / Resolution: 2.6→35.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11481 0 192 17 11690
Biso mean--70.87 51.75 -
Num. residues----1519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01911844
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211504
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.99416083
X-RAY DIFFRACTIONr_angle_other_deg0.82326434
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.63551508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.84424.283474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.744152038
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1281585
X-RAY DIFFRACTIONr_chiral_restr0.0740.21921
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02113271
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022534
X-RAY DIFFRACTIONr_mcbond_it4.2416.1836065
X-RAY DIFFRACTIONr_mcbond_other4.2426.1836064
X-RAY DIFFRACTIONr_mcangle_it6.2749.2667562
LS refinement shellResolution: 2.603→2.671 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 124 -
Rwork0.303 3003 -
all-3127 -
obs--95.83 %
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)
10.08120.045-0.21720.1061-0.20540.6906-0.02370.02890.0346-0.10250.06420.00550.1517-0.1417-0.04050.1096-0.0607-0.02690.06730.02740.220915.15421.9716-18.3992
20.36640.02010.1860.125-0.05220.254-0.03610.05710.0353-0.01680.0045-0.0560.0384-0.00470.03160.083-0.0009-0.01180.02390.02280.238335.912914.280918.7972
30.13270.09140.03330.194-0.09810.73880.013-0.0112-0.01060.12040.03010.017-0.1625-0.1273-0.04310.10360.0370.03470.05190.02560.279715.320347.889333.8854
40.4346-0.0322-0.09510.0866-0.1030.2134-0.0243-0.0279-0.02-0.01540.0064-0.0349-0.03960.0010.01790.1058-0.00220.01140.00250.01010.286935.94155.684-3.2807
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 701
2X-RAY DIFFRACTION2B1 - 701
3X-RAY DIFFRACTION3C-2 - 701
4X-RAY DIFFRACTION4D1 - 701

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