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- PDB-3ke1: Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate ... -

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Basic information

Entry
Database: PDB / ID: 3ke1
TitleCrystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei in complex with a fragment-nucleoside fusion D000161829
Components2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
KeywordsLYASE / NIAID / SSGCID / Seattle Structural Genomics Center for Infectious Disease / fragment crystallography / FBDD / fragment-based drug-design / nucleoside analog / D000161829 / Isoprene biosynthesis / Metal-binding
Function / homology
Function and homology information


2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity / terpenoid biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / metal ion binding
Similarity search - Function
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, conserved site / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase superfamily / YgbB family / 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature. / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-deoxy-5'-[(pyridin-4-ylcarbonyl)amino]cytidine / : / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2013
Title: Cytidine derivatives as IspF inhibitors of Burkolderia pseudomallei.
Authors: Zhang, Z. / Jakkaraju, S. / Blain, J. / Gogol, K. / Zhao, L. / Hartley, R.C. / Karlsson, C.A. / Staker, B.L. / Edwards, T.E. / Stewart, L.J. / Myler, P.J. / Clare, M. / Begley, D.W. / Horn, J.R. / Hagen, T.J.
History
DepositionOct 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Dec 11, 2013Group: Database references
Revision 1.4Nov 1, 2017Group: Refinement description / Category: software
Revision 1.5Sep 6, 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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
B: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
C: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,73910
Polymers58,4613
Non-polymers1,2777
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7310 Å2
ΔGint-101 kcal/mol
Surface area14590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.083, 66.964, 59.166
Angle α, β, γ (deg.)90.000, 95.420, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-181-

HOH

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Components

#1: Protein 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / MECPS / MECDP-synthase


Mass: 19487.109 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: ispF, mecS, BPSL2098 / Production host: Escherichia coli (E. coli)
References: UniProt: Q63T71, UniProt: Q3JRA0*PLUS, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-829 / 5'-deoxy-5'-[(pyridin-4-ylcarbonyl)amino]cytidine


Mass: 347.326 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H17N5O5
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 1.97 Å3/Da / Density % sol: 37.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 20% PEG 3350, 0.2 M magnesium formate, 34.4 mg/mL protein, 5 mM D000161829 soaked for 10 days, crystal tracking ID 205278a10, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 3, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 28561 / % possible obs: 99.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.131 / Χ2: 1.034 / Net I/σ(I): 10.2
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2837 / Χ2: 0.947 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3foe

3foe


Resolution: 2.05→28.22 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.246 / WRfactor Rwork: 0.208 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.845 / SU B: 9.494 / SU ML: 0.115 / SU R Cruickshank DPI: 0.2 / SU Rfree: 0.167 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1435 5.1 %RANDOM
Rwork0.184 ---
obs0.186 28277 98.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 78.65 Å2 / Biso mean: 24.093 Å2 / Biso min: 9.15 Å2
Baniso -1Baniso -2Baniso -3
1--1.75 Å20 Å2-1.4 Å2
2--1.58 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.05→28.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3248 0 79 134 3461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223393
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.9964609
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4885440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.61722.797143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.48215506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8341535
X-RAY DIFFRACTIONr_chiral_restr0.0940.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212587
X-RAY DIFFRACTIONr_mcbond_it0.6681.52191
X-RAY DIFFRACTIONr_mcangle_it1.14223450
X-RAY DIFFRACTIONr_scbond_it1.90631202
X-RAY DIFFRACTIONr_scangle_it2.9344.51157
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 108 -
Rwork0.258 1935 -
all-2043 -
obs--97.29 %
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)
13.04440.18810.75721.09980.0992.3126-0.0225-0.40090.23890.08750.06730.0652-0.0403-0.2231-0.04480.05770.02150.00820.0704-0.01630.0489.6486-35.5355-9.5119
23.6494-0.31811.13212.0958-0.00712.3047-0.02140.79010.1114-0.12910.0476-0.1799-0.04520.563-0.02620.0649-0.00870.03130.22910.00910.026621.7662-37.7622-27.6831
34.1340.25120.50161.9857-0.54682.0918-0.0365-0.188-0.09020.08550.0688-0.22490.11060.3653-0.03230.1230.0689-0.02960.1188-0.00790.097430.6024-43.6056-8.2466
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 159
2X-RAY DIFFRACTION2B1 - 158
3X-RAY DIFFRACTION3C1 - 159

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