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- PDB-2y1f: X-ray structure of 1-deoxy-D-xylulose 5-phosphate reductoisomeras... -

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Basic information

Entry
Database: PDB / ID: 2y1f
TitleX-ray structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase, DXR, Rv2870c, from Mycobacterium tuberculosis, in complex with a 3,4- dichlorophenyl-substituted fosmidomycin analogue, manganese and NADPH.
Components1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE
KeywordsOXIDOREDUCTASE / DOXP/MEP PATHWAY
Function / homology
Function and homology information


RNA polymerase sigma factor, region 2, helix turn helix motif / Rna Polymerase Sigma Factor; Chain: A / NAD(P)-binding Rossmann-like Domain / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-34F / : / Chem-NDP / :
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsHenriksson, L.M. / Larsson, A.M.S. / Bergfors, T. / Bjorkelid, C. / Unge, T. / Mowbray, S.L. / Jones, T.A.
Citation
Journal: J.Med.Chem / Year: 2011
Title: Design, Synthesis and X-Ray Crystallographic Studies of Alpha-Aryl Substituted Fosmidomycin Analogues as Inhibitors of Mycobacterium Tuberculosis 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase
Authors: Andaloussi, M. / Henriksson, L.M. / Wieckowska, A. / Lindh, M. / Bjorkelid, C. / Larsson, A.M.S. / Iyer, H. / Srinivasa, B.R. / Bergfors, T. / Unge, T. / Mowbray, S.L. / Larhed, M. / Jones, T.A. / Karlen, A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2006
Title: The 1.9 A Resolution Structure of Mycobacterium Tuberculosis 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase, a Potential Drug Target.
Authors: Henriksson, L.M. / Bjorkelid, C. / Mowbray, S.L. / Unge, T.
#2: Journal: 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
DepositionDec 8, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2011Group: Database references / Version format compliance
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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)85,5239
Polymers83,4022
Non-polymers2,1217
Water8,917495
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7390 Å2
ΔGint-71.4 kcal/mol
Surface area28260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.439, 65.019, 86.169
Angle α, β, γ (deg.)90.00, 102.05, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.4918, 0.857, 0.1542), (0.847, 0.4298, 0.3128), (0.2018, 0.2844, -0.9372)
Vector: 22.0019, -20.4291, 35.38)

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Components

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Protein , 1 types, 2 molecules AB

#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: 41700.973 Da / Num. of mol.: 2 / Fragment: RESIDUES 24-412
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) / Variant (production host): STAR
References: UniProt: A2VLK3, 1-deoxy-D-xylulose-5-phosphate reductoisomerase

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Non-polymers , 5 types, 502 molecules

#2: Chemical ChemComp-34F / (1S)-1-(3,4-DICHLOROPHENYL)-3-[FORMYL(HYDROXY)AMINO]PROPYL}PHOSPHONIC ACID


Mass: 328.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12Cl2NO5P
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 495 / 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: 2.2 Å3/Da / Density % sol: 44.5 % / Description: NONE

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-5 / Wavelength: 0.908
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: Jun 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 1.96→45 Å / Num. obs: 51333 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.6
Reflection shellResolution: 1.96→2.07 Å / Rmerge(I) obs: 0.41 / % possible all: 88.9

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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 2JCZ

2jcz
PDB Unreleased entry


Resolution: 1.96→45 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.447 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES A199-A204 WERE NOT OBSERVED. LIGAND 34F IS EQUIVALENT TO COMPOUND 9A IN THE PRIMARY REFERENCE.
RfactorNum. reflection% reflectionSelection details
Rfree0.20986 2600 5.1 %RANDOM
Rwork0.17198 ---
obs0.17393 48724 97.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.557 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å2-0.25 Å2
2--0.81 Å20 Å2
3----1.24 Å2
Refinement stepCycle: LAST / Resolution: 1.96→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5513 0 127 495 6135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0215766
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1621.9797880
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1155751
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.14123.684228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38915837
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0281544
X-RAY DIFFRACTIONr_chiral_restr0.0720.2924
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024357
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1890.22706
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2920.23961
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2442
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.276
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5531.53841
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.94125952
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.532174
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4594.51928
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: 1.961→2.012 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 165 -
Rwork0.234 2965 -
obs--82.48 %

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