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- PDB-4a03: Crystal Structure of Mycobacterium tuberculosis DXR in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4a03
TitleCrystal Structure of Mycobacterium tuberculosis DXR in complex with the antibiotic FR900098 and cofactor NADPH
Components1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE
KeywordsOXIDOREDUCTASE / FR900098 / MEP PATHWAY
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
3-[ethanoyl(hydroxy)amino]propylphosphonic acid / : / 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: 1.65 Å
AuthorsBjorkelid, C. / Bergfors, T. / Jones, T.A.
CitationJournal: 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
DepositionSep 7, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Other
Revision 1.2Mar 28, 2012Group: Other
Revision 1.3Jun 6, 2012Group: Other
Revision 1.4Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.5May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.6Nov 27, 2019Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_database_status.status_code_sf
Revision 1.7Dec 20, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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)85,4899
Polymers83,4022
Non-polymers2,0877
Water9,530529
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-36.6 kcal/mol
Surface area27920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.510, 110.510, 137.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.15, -0.0909, -0.9845), (-0.0967, -0.9923, 0.0769), (-0.984, 0.0836, -0.1576)
Vector: 49.7936, 52.3708, 52.9899)

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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 2-389
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PEXP5CT/TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): AI
References: UniProt: P64012, UniProt: P9WNS1*PLUS, 1-deoxy-D-xylulose-5-phosphate reductoisomerase

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Non-polymers , 5 types, 536 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-F98 / 3-[ethanoyl(hydroxy)amino]propylphosphonic acid


Mass: 197.126 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12NO5P
#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 529 / 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: 2.44 Å3/Da / Density % sol: 49.66 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: SITTING-DROP VAPOR-DIFFUSION METHOD AT 293 K. 10% (W/V) PEG 20000, 20% (V/V) MONOMETHYL ETHER PEG 550, 0.1 M MES/IMIDAZOLE, PH 6.5, AND 0.03 M EACH OF DIETHYLENEGLYCOL, TRIETHYLENEGLYCOL, ...Details: SITTING-DROP VAPOR-DIFFUSION METHOD AT 293 K. 10% (W/V) PEG 20000, 20% (V/V) MONOMETHYL ETHER PEG 550, 0.1 M MES/IMIDAZOLE, PH 6.5, AND 0.03 M EACH OF DIETHYLENEGLYCOL, TRIETHYLENEGLYCOL, TETRAETHYLENEGLYCOL AND PENTAETHYLENEGLYCOL.

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9768
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9768 Å / Relative weight: 1
ReflectionResolution: 1.65→42.21 Å / Num. obs: 101922 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.4
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0060refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JCZ

2jcz
PDB Unreleased entry


Resolution: 1.65→42.21 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.659 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21607 5087 5 %RANDOM
Rwork0.18931 ---
obs0.19067 96739 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.132 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.65→42.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5546 0 128 529 6203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0215852
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.161.9778023
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8195768
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.31323.534232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.11315848
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4381546
X-RAY DIFFRACTIONr_chiral_restr0.0750.2941
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214442
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: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 332 -
Rwork0.237 7109 -
obs--100 %

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