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- PDB-5ddt: Crystal structure of IspD from Bacillus subtilis at 1.80 Angstrom... -

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Basic information

Entry
Database: PDB / ID: 5ddt
TitleCrystal structure of IspD from Bacillus subtilis at 1.80 Angstroms resolution, crystal form I
Components2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
KeywordsTRANSFERASE
Function / homology
Function and homology information


2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process
Similarity search - Function
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 4-diphosphocytidyl-2C-methyl-D-erythritol synthase, conserved site / Cytidylyltransferase IspD/TarI / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 4-diphosphocytidyl-2C-methyl-D-erythritol synthase signature. / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsJin, Y. / Liu, Z.C. / Wang, G.G.
CitationJournal: Sci Rep / Year: 2016
Title: A structural and functional study on the 2-C-methyl-d-erythritol-4-phosphate cytidyltransferase (IspD) from Bacillus subtilis.
Authors: Jin, Y. / Liu, Z. / Li, Y. / Liu, W. / Tao, Y. / Wang, G.
History
DepositionAug 25, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Database references
Revision 1.2Nov 8, 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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 4-phosphate cytidylyltransferase
B: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase


Theoretical massNumber of molelcules
Total (without water)51,7592
Polymers51,7592
Non-polymers00
Water8,251458
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-10 kcal/mol
Surface area21080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.339, 77.951, 91.473
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 4-diphosphocytidyl-2C-methyl-D-erythritol synthase / MEP cytidylyltransferase / MCT


Mass: 25879.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: ispD, yacM, BSU00900 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q06755, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M Trimethylamine N-oxide dehydrate, 0.1M Tris, pH 8.5, 20% (v/v)Polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.8→60 Å / Num. obs: 42387 / % possible obs: 99 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 21.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YC3

2yc3


Resolution: 1.8→59.33 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.971 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2155 2142 5.1 %RANDOM
Rwork0.17958 ---
obs0.18145 40202 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.023 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å20 Å2
2---0.37 Å2-0 Å2
3----0.49 Å2
Refinement stepCycle: 1 / Resolution: 1.8→59.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3634 0 0 458 4092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193688
X-RAY DIFFRACTIONr_bond_other_d0.0020.023624
X-RAY DIFFRACTIONr_angle_refined_deg1.6721.9624972
X-RAY DIFFRACTIONr_angle_other_deg0.95738350
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3775462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.30624.884172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92315692
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7021524
X-RAY DIFFRACTIONr_chiral_restr0.0970.2570
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024154
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02798
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_it2.3842.4571854
X-RAY DIFFRACTIONr_mcbond_other2.3792.4561853
X-RAY DIFFRACTIONr_mcangle_it3.5353.672314
X-RAY DIFFRACTIONr_mcangle_other3.5343.6722315
X-RAY DIFFRACTIONr_scbond_it3.3682.9511834
X-RAY DIFFRACTIONr_scbond_other3.3672.9511834
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3954.2152658
X-RAY DIFFRACTIONr_long_range_B_refined7.57521.3444492
X-RAY DIFFRACTIONr_long_range_B_other7.37920.4194219
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.797→1.843 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 163 -
Rwork0.239 2809 -
obs--95.75 %

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