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- PDB-3r0i: IspC in complex with an N-methyl-substituted hydroxamic acid -

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Basic information

Entry
Database: PDB / ID: 3r0i
TitleIspC in complex with an N-methyl-substituted hydroxamic acid
Components1-deoxy-D-xylulose 5-phosphate reductoisomerase
KeywordsOXIDOREDUCTASE/ANTIBIOTIC / antimalarial agents / inhibitors / IspC / non-mevalonate pathway / Rossmann Fold / Reductoisomerase of Desoxy-xylulose-5P to Methyl-erythritol-3P / NADPH / Mn / reverse hydroxamic acid ligand binding / cytosol / OXIDOREDUCTASE-ANTIBIOTIC complex
Function / homology
Function and homology information


Dxr protein complex / 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 / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / NADPH binding / manganese ion binding / identical protein 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-C0K / : / 1-deoxy-D-xylulose 5-phosphate reductoisomerase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBehrendt, C.T. / Kunfermann, A. / Illarionova, V. / Matheeussen, A. / Pein, M.K. / Graewert, T. / Bacher, A. / Eisenreich, W. / Illarionov, B. / Fischer, M. ...Behrendt, C.T. / Kunfermann, A. / Illarionova, V. / Matheeussen, A. / Pein, M.K. / Graewert, T. / Bacher, A. / Eisenreich, W. / Illarionov, B. / Fischer, M. / Maes, L. / Groll, M. / Kurz, T.
CitationJournal: J.Med.Chem. / Year: 2011
Title: Reverse Fosmidomycin Derivatives against the Antimalarial Drug Target IspC (Dxr).
Authors: Behrendt, C.T. / Kunfermann, A. / Illarionova, V. / Matheeussen, A. / Pein, M.K. / Grawert, T. / Kaiser, J. / Bacher, A. / Eisenreich, W. / Illarionov, B. / Fischer, M. / Maes, L. / Groll, M. / Kurz, T.
History
DepositionMar 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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_ref_seq_dif.details / _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)90,4036
Polymers89,6752
Non-polymers7284
Water13,926773
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-32 kcal/mol
Surface area31250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.254, 54.584, 107.798
Angle α, β, γ (deg.)90.00, 93.17, 90.00
Int Tables number4
Space group name H-MP1211

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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: 44837.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: dxr, ispC, yaeM, b0173, JW0168 / Production host: Escherichia coli (E. coli)
References: UniProt: P45568, 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-C0K / {(1S)-1-(3,4-difluorophenyl)-4-[hydroxy(methyl)amino]-4-oxobutyl}phosphonic acid


Mass: 309.203 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H14F2NO5P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 773 / 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: 2.99 Å3/Da / Density % sol: 58.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 8% PEG 4K, 80 mM NaAc, 110mM HEPES, 100 mM Glycine, 100 mM Guanidinium-HCl, 10mM EDTA, 12mM DTT, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Aug 12, 2010 / Details: Mirrows
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 62373 / Num. obs: 62350 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2.5 / Rmerge(I) obs: 0.072
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
CNSrefinement
PROTEUM PLUSPLUSdata collection
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ONN

1onn


Resolution: 2.1→10 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.923 / SU B: 8.43 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(I): 2.5 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21659 3113 5 %RANDOM
Rwork0.16324 ---
all0.17 58544 --
obs0.16593 58544 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: 20.932 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20.08 Å2
2--0.26 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5963 0 42 773 6778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0226089
X-RAY DIFFRACTIONr_angle_refined_deg2.051.9788250
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3615782
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.62324.745255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.965151068
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.071541
X-RAY DIFFRACTIONr_chiral_restr0.1670.2968
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214521
X-RAY DIFFRACTIONr_mcbond_it1.1511.53918
X-RAY DIFFRACTIONr_mcangle_it2.01226290
X-RAY DIFFRACTIONr_scbond_it3.67932171
X-RAY DIFFRACTIONr_scangle_it5.9374.51960
LS refinement shellResolution: 2.1→2.152 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 213 -
Rwork0.219 4121 -
obs--99.49 %
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)
10.56520.0773-0.11960.2437-0.08780.69330.0218-0.0608-0.02080.036-0.0737-0.01540.0123-0.04920.05190.0657-0.0289-0.01110.0419-0.00950.0492-1.7643-7.313433.2361
20.57540.0872-0.13570.2412-0.01910.6440.04250.03470.03480.0066-0.0716-0.0239-0.0490.06160.02910.03910.0015-0.01040.04320.03710.08225.36178.27523.3369
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 398
2X-RAY DIFFRACTION2B1 - 398

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