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- PDB-3pyd: crystal structure of 4-diphosphocytidyl-2-C-methyl-D-erythritol k... -

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Basic information

Entry
Database: PDB / ID: 3pyd
Titlecrystal structure of 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (IspE) from Mycobacterium tuberculosis
Components4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
KeywordsTRANSFERASE / kinase / 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
Function / homology
Function and homology information


4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase / 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / ATP binding
Similarity search - Function
4-diphosphocytidyl-2C-methyl-D-erythritol kinase / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup ...4-diphosphocytidyl-2C-methyl-D-erythritol kinase / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
4-diphosphocytidyl-2-C-methyl-D-erythritol kinase / 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.101 Å
AuthorsShan, S. / Chen, X.H. / Liu, T. / Zhao, H.C. / Rao, Z.H. / Lou, Z.Y.
CitationJournal: To be Published
Title: The Structural Basis for anti-TB Drug Discovery targeting of 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (IspE) from Mycobacterium tuberculosis
Authors: Shan, S. / Chen, X.H. / Liu, T. / Zhao, H.C. / Rao, Z.H. / Lou, Z.Y.
History
DepositionDec 13, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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-methyl-D-erythritol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5012
Polymers31,4091
Non-polymers921
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.584, 72.375, 107.393
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase / IspE / CMK / 4-(cytidine-5'-diphospho)-2-C-methyl-D-erythritol kinase


Mass: 31408.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: ispE, Rv1011, MT1040, MTCI237.28 / Production host: Escherichia coli (E. coli)
References: UniProt: P65178, UniProt: P9WKG7*PLUS, 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 3.25 Å3/Da / Density % sol: 62.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Bis-Tris propane (pH 7.0), 3.2M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 24625 / Num. obs: 24569 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UEK

1uek


Resolution: 2.101→37.57 Å / SU ML: 0.32 / σ(F): 0.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2443 1197 5.13 %random
Rwork0.1946 ---
all0.1988 24625 --
obs0.197 23346 94.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.848 Å2 / ksol: 0.395 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.119 Å20 Å2-0 Å2
2--0.0399 Å20 Å2
3----3.1589 Å2
Refinement stepCycle: LAST / Resolution: 2.101→37.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2145 0 6 190 2341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082188
X-RAY DIFFRACTIONf_angle_d1.1772987
X-RAY DIFFRACTIONf_dihedral_angle_d18.868779
X-RAY DIFFRACTIONf_chiral_restr0.082357
X-RAY DIFFRACTIONf_plane_restr0.006398
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1008-2.18490.2921230.231221087
2.1849-2.28440.30831270.2139230091
2.2844-2.40480.29351190.2107240994
2.4048-2.55540.27051490.2092239195
2.5554-2.75270.28081510.2094246196
2.7527-3.02960.25551250.1968249997
3.0296-3.46770.21631230.182258399
3.4677-4.36790.19111420.1563259599
4.3679-37.57560.21671380.1857270198

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