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- PDB-1i52: CRYSTAL STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL (CDP... -

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Basic information

Entry
Database: PDB / ID: 1i52
TitleCRYSTAL STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL (CDP-ME) SYNTHASE (YGBP) INVOLVED IN MEVALONATE INDEPENDENT ISOPRENOID BIOSYNTHESIS
Components4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL SYNTHASE
KeywordsTRANSFERASE / CYTIDYLYLTRANSFERASE / DEOXYXYLULOSE-5-PHOSPHATE PATHWAY (DXP) / ISOPRENOID BIOSYNTHESYS / MEP
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 / magnesium ion binding / identical protein binding / cytosol
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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.5 Å
AuthorsRichard, S.B. / Bowman, M.E. / Kwiatkowski, W. / Kang, I. / Chow, C. / Lillo, M. / Cane, D.E. / Noel, J.P.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Structure of 4-diphosphocytidyl-2-C- methylerythritol synthetase involved in mevalonate- independent isoprenoid biosynthesis.
Authors: Richard, S.B. / Bowman, M.E. / Kwiatkowski, W. / Kang, I. / Chow, C. / Lillo, A.M. / Cane, D.E. / Noel, J.P.
History
DepositionFeb 23, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

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Assembly

Deposited unit
A: 4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3204
Polymers25,7721
Non-polymers5483
Water5,909328
1
A: 4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL SYNTHASE
hetero molecules

A: 4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6408
Polymers51,5452
Non-polymers1,0956
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)130.564, 47.074, 38.105
Angle α, β, γ (deg.)90.00, 93.78, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2246-

HOH

21A-2255-

HOH

DetailsThe second monomer of the biological assembly (dimer) is generated by the two fold axis: -X,Y,-Z

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Components

#1: Protein 4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL SYNTHASE


Mass: 25772.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ISPD / Plasmid: PHIS8 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q46893, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.27 Å3/Da / Density % sol: 45.71 %
Crystal growTemperature: 315.8 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, calcium acetate, magnesium chloride, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 42.8K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
135 mg/mlprotein1drop
210 %(w/v)PEG80001reservoir
30.2 Mcalcium acetate1reservoir
42 mMdithiothreitol1reservoir
50.1 MPIPES1reservoir
619 %(v/v)ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 2000 / Details: mirrors
RadiationMonochromator: Cyclindrically bent triangular Si(111) asymmetric cut, horizontal focus
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.5→90 Å / Num. all: 68287 / Num. obs: 68287 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.036 / Rsym value: 3.6 / Net I/σ(I): 22.5
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2.01 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 1.75 / Num. unique all: 2687 / Rsym value: 28.2 / % possible all: 73.3
Reflection
*PLUS
Num. obs: 34216 / Num. measured all: 68287

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Processing

Software
NameVersionClassification
SHARPphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.5→65.14 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1102364.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used maximum likelihood target using amplitudes
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1732 5 %RANDOM
Rwork0.227 ---
all0.227 34414 --
obs0.227 34414 92.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.21 Å2 / ksol: 0.3656 e/Å3
Displacement parametersBiso mean: 26.9 Å2
Baniso -1Baniso -2Baniso -3
1--7.19 Å20 Å2-0.15 Å2
2--7.92 Å20 Å2
3----0.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.5→65.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1718 0 31 328 2077
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d1
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.353 225 4.9 %
Rwork0.309 4324 -
obs--73.7 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 26.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1
LS refinement shell
*PLUS
Rfactor Rfree: 0.353 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.309

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