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- PDB-2jd0: X-ray structure of mutant 1-deoxy-D-xylulose 5-phosphate reductoi... -

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Basic information

Entry
Database: PDB / ID: 2jd0
TitleX-ray structure of mutant 1-deoxy-D-xylulose 5-phosphate reductoisomerase, DXR, Rv2870c, from Mycobacterium tuberculosis, in complex with NADPH
Components1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE
KeywordsOXIDOREDUCTASE / DOXP/MEP PATHWAY / ISOPRENE BIOSYNTHESIS / 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE / NADP / RV2870C / METAL-BINDING
Function / homology
Function and homology information


terpenoid biosynthetic process, mevalonate-independent / 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 / cobalt ion binding / NADPH binding / manganese ion binding / magnesium 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 / 1-deoxy-D-xylulose 5-phosphate reductoisomerase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHenriksson, L.M. / Unge, T. / Jones, T.A. / Mowbray, S.L.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structures of Mycobacterium Tuberculosis 1-Deoxy-D- Xylulose-5-Phosphate Reductoisomerase Provide New Insights Into Catalysis.
Authors: Henriksson, L.M. / Unge, T. / Carlsson, J. / Aqvist, J. / Mowbray, S.L. / Jones, T.A.
History
DepositionJan 4, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4326
Polymers83,3982
Non-polymers1,0344
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)67.629, 65.611, 86.016
Angle α, β, γ (deg.)90.00, 102.02, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.4991, 0.8531, 0.1523), (0.8434, 0.4379, 0.3111), (0.1987, 0.2837, -0.9381)
Vector: 22.4859, -20.3382, 35.4415)

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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: 41699.000 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-389 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PET101D-TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P64012, UniProt: P9WNS1*PLUS, 1-deoxy-D-xylulose-5-phosphate reductoisomerase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 151 TO ASN ENGINEERED RESIDUE IN CHAIN A, GLU 222 TO GLN ...ENGINEERED RESIDUE IN CHAIN A, ASP 151 TO ASN ENGINEERED RESIDUE IN CHAIN A, GLU 222 TO GLN ENGINEERED RESIDUE IN CHAIN B, ASP 151 TO ASN ENGINEERED RESIDUE IN CHAIN B, GLU 222 TO GLN

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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: 2.2 Å3/Da / Density % sol: 44.5 %

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 5, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.3→35 Å / Num. obs: 32964 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.4
Reflection shellResolution: 2.3→2.36 Å / Rmerge(I) obs: 0.43 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C82

2c82


Resolution: 2.3→35 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.891 / SU B: 7.694 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.406 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS ENTRY CONTAINS ATOMS WITH REFINED B- FACTORS AND ZERO OCCUPANCY.
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1672 5.1 %RANDOM
Rwork0.199 ---
obs0.202 31255 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.75 Å2
2--2.56 Å20 Å2
3----2.86 Å2
Refinement stepCycle: LAST / Resolution: 2.3→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5562 0 63 263 5888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0215732
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1141.9587839
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2585760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.88623.593231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43515846
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6981545
X-RAY DIFFRACTIONr_chiral_restr0.0680.2918
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024373
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1910.22718
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2920.23942
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2309
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.275
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4791.53857
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.85426016
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.16932091
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9734.51823
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.328 117
Rwork0.234 2285

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