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- PDB-1h3m: Structure of 4-diphosphocytidyl-2C-methyl-D-erythritol synthetase -

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Basic information

Entry
Database: PDB / ID: 1h3m
TitleStructure of 4-diphosphocytidyl-2C-methyl-D-erythritol synthetase
Components2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE
KeywordsTRANSFERASE / ISOPRENOID / SYNTHETASE
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
PENTANE-1,5-DIAMINE / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKemp, L.E. / Bond, C.S. / Hunter, W.N.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structure of a Tetragonal Crystal Form of Escherichia Coli 2-C-Methyl-D-Erythritol 4-Phosphate Cytidylyltransferase
Authors: Kemp, L.E. / Bond, C.S. / Hunter, W.N.
#1: Journal: Nat.Struct.Biol. / Year: 2001
Title: Structure of Cdp-Me Synthetase in Mevalonate-Independent Isoprenoid Biosynthesis
Authors: Richard, S.B. / Bowman, M.E. / Kwiatkowski, W. / Chow, C. / Lillo, A.M. / Cane, D.E. / Noel, J.P.
History
DepositionSep 10, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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)51,6228
Polymers51,3422
Non-polymers2796
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)73.604, 73.604, 175.562
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.752795, -0.094528, -0.651433), (-0.071976, -0.971881, 0.224203), (-0.654309, 0.215666, 0.724823)
Vector: 96.894, 105.433, 23.337)

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Components

#1: Protein 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE


Mass: 25671.096 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: BL21(DE3) / Plasmid: PET 15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q46893, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-N2P / PENTANE-1,5-DIAMINE


Mass: 102.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H14N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION ALA 91 THR

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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: 2.23 Å3/Da / Density % sol: 50.1 %
Crystal growpH: 6
Details: 0.2M AMMONIUM SULPHATE, 0.1M SODIUM ACETATE, PH 5.6, 25% PEG 4000
Crystal grow
*PLUS
Temperature: 293 K / pH: 7.7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
19 mg/mlprotein1drop
2100 mM1dropNaCl
3100 mMTris-HCl1droppH7.7
40.1 Msodium acetate1reservoirpH5.6
525 %PEG40001reservoir
60.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 19619 / % possible obs: 99.5 % / Observed criterion σ(I): 1.5 / Redundancy: 4 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 37
Reflection shellResolution: 2.4→2.46 Å / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.1 / % possible all: 98.6
Reflection
*PLUS
Highest resolution: 2.4 Å / Redundancy: 4.1 % / Num. measured all: 81222 / Rmerge(I) obs: 0.031
Reflection shell
*PLUS
% possible obs: 94.7 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1INI

1ini


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.883 / SU B: 10.244 / SU ML: 0.242 / Cross valid method: THROUGHOUT / ESU R: 0.48 / ESU R Free: 0.348 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.333 1000 5.1 %RANDOM
Rwork0.237 ---
obs0.241 18554 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.08 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å20 Å2
2--1.21 Å20 Å2
3----2.42 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3307 0 12 86 3405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0213377
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6681.9534601
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1955429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1070.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022574
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2290.21599
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2170
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.280.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2670.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9441.52162
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.73723470
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3531215
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7844.51131
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.415 71
Rwork0.3 1294
Refinement
*PLUS
Highest resolution: 2.4 Å / Num. reflection obs: 18638 / Num. reflection Rfree: 981
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.67

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