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- PDB-3zhy: Structure of Mycobacterium tuberculosis DXR in complex with a di-... -

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Basic information

Entry
Database: PDB / ID: 3zhy
TitleStructure of Mycobacterium tuberculosis DXR in complex with a di- substituted fosmidomycin analogue
Components1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE
KeywordsOXIDOREDUCTASE / RV2870C / DOXP/MEP PATHWAY / ISPC
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-FM6 / : / 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
AuthorsBjorkelid, C. / Jansson, A.M. / Bergfors, T. / Unge, T. / Mowbray, S.L. / Jones, T.A.
Citation
Journal: J.Med.Chem. / Year: 2013
Title: Dxr Inhibition by Potent Mono- and Disubstituted Fosmidomycin Analogues.
Authors: Jansson, A.M. / Wieckowska, A. / Bjorkelid, C. / Yahiaoui, S. / Sooriyaarachchi, S. / Lindh, M. / Bergfors, T. / Dharavath, S. / Desroses, M. / Suresh, S. / Andaloussi, M. / Nikhil, R. / ...Authors: Jansson, A.M. / Wieckowska, A. / Bjorkelid, C. / Yahiaoui, S. / Sooriyaarachchi, S. / Lindh, M. / Bergfors, T. / Dharavath, S. / Desroses, M. / Suresh, S. / Andaloussi, M. / Nikhil, R. / Sreevalli, S. / Srinivasa, B.R. / Larhed, M. / Jones, T.A. / Karlen, A. / Mowbray, S.L.
#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.
#3: 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. / Suresh, S. / Iyer, H. / Srinivasa, B.R. / Bergfors, T. / Unge, T. / Mowbray, S.L. / Larhed, M. ...Authors: Andaloussi, M. / Henriksson, L.M. / Wieckowska, A. / Lindh, M. / Bjorkelid, C. / Larsson, A.M. / Suresh, S. / Iyer, H. / Srinivasa, B.R. / Bergfors, T. / Unge, T. / Mowbray, S.L. / Larhed, M. / Jones, T.A. / Karlen, A.
#4: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structural Studies on Mycobacterium Tuberculosis Dxr in Complex with the Antibiotic Fr-900098.
Authors: Bjorkelid, C. / Bergfors, T. / Unge, T. / Mowbray, S.L. / Jones, T.A.
History
DepositionDec 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 2.0Jan 23, 2019Group: Atomic model / Data collection / Other
Category: atom_site / pdbx_database_proc / pdbx_database_status
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.pdbx_auth_atom_name / _pdbx_database_status.recvd_author_approval
Revision 2.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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

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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)85,6098
Polymers83,2002
Non-polymers2,4096
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-34.4 kcal/mol
Surface area28000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.740, 111.740, 136.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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: 41599.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR
References: UniProt: P64012, UniProt: P9WNS1*PLUS, 1-deoxy-D-xylulose-5-phosphate reductoisomerase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-FM6 / [(1S)-1-(3,4-dichlorophenyl)-3-[oxidanyl(phenylcarbonyl)amino]propyl]phosphonic acid / [3-[benzoyl(hydroxy)amino]-1-(3,4-dichlorophenyl)propyl]phosphonic acid


Mass: 404.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H16Cl2NO5P
#4: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.56 Å3/Da / Density % sol: 51.95 % / Description: NONE

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9552
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9552 Å / Relative weight: 1
ReflectionResolution: 2.3→58.23 Å / Num. obs: 39082 / % possible obs: 100 % / Observed criterion σ(I): 5 / Redundancy: 13.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.9
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0060refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→86.45 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 6.555 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.299 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.25407 1958 5 %RANDOM
Rwork0.20148 ---
obs0.20414 37056 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.047 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.3→86.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5442 0 148 123 5713
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225706
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.9837796
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3475739
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.16423.717226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.81415824
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1291544
X-RAY DIFFRACTIONr_chiral_restr0.0820.2916
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214304
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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% reflection
Rfree0.329 139 -
Rwork0.243 2706 -
obs--100 %

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