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- PDB-5hs2: Crystal structure of IspD complexed with CTP and Mg2+ from Bacill... -

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Basic information

Entry
Database: PDB / ID: 5hs2
TitleCrystal structure of IspD complexed with CTP and Mg2+ from Bacillus subtilis at 1.90 Angstroms resolution
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
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
CYTIDINE-5'-TRIPHOSPHATE / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionJan 24, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 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_conn_angle / pdbx_struct_oper_list / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2664
Polymers51,7592
Non-polymers5072
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-23 kcal/mol
Surface area19430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.450, 49.430, 75.373
Angle α, β, γ (deg.)90.00, 101.41, 90.00
Int Tables number4
Space group name H-MP1211

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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 / Production host: Escherichia coli (E. coli)
References: UniProt: Q06755, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
#2: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.31 Å3/Da / Density % sol: 46.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M Magnesium chloride hexahydrate, 0.1M HEPES, 25% Polyethylene glycol 3350, 10mM CTP, 10mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.9→29.6 Å / Num. obs: 37021 / % possible obs: 98.8 % / Redundancy: 2.8 % / Net I/σ(I): 6.6
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 2.3 / % possible all: 99

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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: 1.9→29.6 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.126 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.159
RfactorNum. reflection% reflectionSelection details
Rfree0.25235 1798 4.9 %RANDOM
Rwork0.20439 ---
obs0.20662 35210 97.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.755 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å2-0 Å22.58 Å2
2---2.26 Å20 Å2
3---1.87 Å2
Refinement stepCycle: 1 / Resolution: 1.9→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3465 0 30 208 3703
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193546
X-RAY DIFFRACTIONr_bond_other_d0.0020.023460
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.9744791
X-RAY DIFFRACTIONr_angle_other_deg0.94337975
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6775438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.27325.03165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40315657
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8471522
X-RAY DIFFRACTIONr_chiral_restr0.0850.2554
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023949
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02758
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_it3.44.3271761
X-RAY DIFFRACTIONr_mcbond_other3.44.3261760
X-RAY DIFFRACTIONr_mcangle_it4.8686.4692196
X-RAY DIFFRACTIONr_mcangle_other4.8676.4712197
X-RAY DIFFRACTIONr_scbond_it3.6894.8071785
X-RAY DIFFRACTIONr_scbond_other3.694.8091784
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7526.9922595
X-RAY DIFFRACTIONr_long_range_B_refined8.334.3653955
X-RAY DIFFRACTIONr_long_range_B_other8.27934.2293874
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.896→1.945 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 118 -
Rwork0.302 2331 -
obs--87.84 %

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