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- PDB-3f1c: CRYSTAL STRUCTURE OF 2-C-methyl-D-erythritol 4-phosphate cytidyly... -

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Basic information

Entry
Database: PDB / ID: 3f1c
TitleCRYSTAL STRUCTURE OF 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase from Listeria monocytogenes
ComponentsPutative 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase 2
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / PSI-2 / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS / Isoprene biosynthesis / Nucleotidyltransferase
Function / homology
Function and homology information


D-ribitol-5-phosphate cytidylyltransferase / D-ribitol-5-phosphate cytidylyltransferase activity / poly(ribitol phosphate) teichoic acid biosynthetic process / isoprenoid biosynthetic process / cell wall organization
Similarity search - Function
Ribitol-5-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
Ribitol-5-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesListeria monocytogenes str. 4b F2365 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsPatskovsky, Y. / Ho, J. / Toro, R. / Gilmore, M. / Miller, S. / Groshong, C. / Sauder, J.M. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase from Listeria monocytogenes
Authors: Patskovsky, Y. / Ho, J. / Toro, R. / Gilmore, M. / Miller, S. / Groshong, C. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionOct 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 24, 2012Group: Structure summary
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase 2
B: Putative 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase 2


Theoretical massNumber of molelcules
Total (without water)55,8542
Polymers55,8542
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-22 kcal/mol
Surface area20780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.202, 45.938, 79.007
Angle α, β, γ (deg.)90.00, 108.89, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

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Components

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


Mass: 27926.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes str. 4b F2365 (bacteria)
Gene: ispD2, LMOf2365_1100 / Production host: Escherichia coli (E. coli)
References: UniProt: Q720Y7, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100MM POTASSIUM THIOCYANATE, PH 7.5, 30% PEG MME2000, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K, pH 7.50

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 22, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 24210 / % possible obs: 98.2 % / Observed criterion σ(I): -5 / Redundancy: 3.8 % / Biso Wilson estimate: 56.31 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 7.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 1.5 / % possible all: 100

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Processing

Software
NameVersionClassification
SHELXmodel building
REFMAC5.3.0034refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.641 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.397 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27672 764 3.2 %RANDOM
Rwork0.24075 ---
obs0.24195 22869 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.22 Å2
Baniso -1Baniso -2Baniso -3
1-1.53 Å20 Å20.24 Å2
2---1.33 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3658 0 0 67 3725
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223807
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2741.9625174
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8915481
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.24225.824182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.63815721
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1761516
X-RAY DIFFRACTIONr_chiral_restr0.0840.2609
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022828
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1440.31654
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2920.52595
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.5253
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.347
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3280.54
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.84122415
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.48633836
X-RAY DIFFRACTIONr_scbond_it6.11241546
X-RAY DIFFRACTIONr_scangle_it8.37161326
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1752 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.170.05
tight thermal2.351.5
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 47 -
Rwork0.287 1677 -
obs--99.31 %

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