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

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Basic information

Entry
Database: PDB / ID: 1ini
TitleCRYSTAL STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL (CDP-ME) SYNTHETASE (YGBP) INVOLVED IN MEVALONATE INDEPENDENT ISOPRENOID BIOSYNTHESIS, COMPLEXED WITH CDP-ME AND MG2+
Components4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL SYNTHETASE
KeywordsTRANSFERASE / YGBP / CYTIDYLYLTRANSFERASE / DEOXYXYLULOSE-5-PHOSPHATE PATHWAY (DXP) / ISOPRENOID BIOSYNTHESIS / CDPME / MG
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 / 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
4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.82 Å
AuthorsRichard, S.B. / Bowman, M.E. / Kwiatkowski, W. / Kang, I. / Chow, C. / Lillo, A. / 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
DepositionMay 14, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Aug 16, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_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 SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3183
Polymers25,7721
Non-polymers5462
Water1,856103
1
A: 4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL SYNTHETASE
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)52,6366
Polymers51,5452
Non-polymers1,0914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6320 Å2
ΔGint-26 kcal/mol
Surface area18520 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)129.990, 46.764, 38.387
Angle α, β, γ (deg.)90.00, 92.64, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CDM / 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL


Mass: 521.308 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H25N3O14P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.26 Å3/Da / Density % sol: 45.58 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, CALCIUM ACETATE, MAGNESIUM CHLORIDE, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.773 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 13, 2001
Details: flat mirror (vertical focusing); single crystal Si(311) bent monochromator (horizontal focusing)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.773 Å / Relative weight: 1
ReflectionResolution: 1.8→90 Å / Num. all: 20268 / Num. obs: 20268 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.026 / Rsym value: 0.026 / Net I/σ(I): 26.4
Reflection shellResolution: 1.81→1.83 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 641 / Rsym value: 0.308 / % possible all: 98.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1I52

1i52


Resolution: 1.82→44 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2293940.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.273 866 5.1 %RANDOM
Rwork0.222 ---
obs0.222 17144 82.9 %-
all-17144 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.77 Å2 / ksol: 0.3689 e/Å3
Displacement parametersBiso mean: 36.2 Å2
Baniso -1Baniso -2Baniso -3
1--7.95 Å20 Å2-1.83 Å2
2--5 Å20 Å2
3---2.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.82→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1716 0 34 103 1853
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it3.31.5
X-RAY DIFFRACTIONc_mcangle_it4.32
X-RAY DIFFRACTIONc_scbond_it4.642
X-RAY DIFFRACTIONc_scangle_it5.842.5
LS refinement shellResolution: 1.82→1.93 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.325 92 4.6 %
Rwork0.239 1894 -
obs-1894 57.9 %

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