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- PDB-2px7: Crystal structure of 2-C-methyl-D-erythritol 4-phosphate cytidyly... -

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Basic information

Entry
Database: PDB / ID: 2px7
TitleCrystal structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase from Thermus thermophilus HB8
Components2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
KeywordsTRANSFERASE / ttha0171 / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / ISPD_THET8 / ispD / Structural genomics / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI
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
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
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChen, L. / Tsukuda, M. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Chen, L.-Q. / Liu, Z.-J. / Lee, D. / Chang, S.-H. ...Chen, L. / Tsukuda, M. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Chen, L.-Q. / Liu, Z.-J. / Lee, D. / Chang, S.-H. / Nguyen, D. / Rose, J.P. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG) / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase from Thermus thermophilus HB8.
Authors: Chen, L. / Tsukuda, M. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Chen, L.-Q. / Liu, Z.-J. / Lee, D. / Chang, S.-H. / Nguyen, D. / Rose, J.P. / Wang, B.-C.
History
DepositionMay 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.5Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)50,4542
Polymers50,4542
Non-polymers00
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-25 kcal/mol
Surface area17380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.084, 104.084, 107.760
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 25226.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Species: Thermus thermophilus / Strain: HB8, DSM 579 / Gene: ispD, TTHA0171 / Plasmid: pET-19b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)
References: UniProt: Q5SLX2, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 3.34 Å3/Da / Density % sol: 63.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: USING 2 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (6.36 mg/ml) AND RESERVOIR SOLUTION CONTAINING 0.9M Li Sulfate, 0.09M HEPES pH 8.0, 0.01M Betaine, VAPOR DIFFUSION, ...Details: USING 2 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (6.36 mg/ml) AND RESERVOIR SOLUTION CONTAINING 0.9M Li Sulfate, 0.09M HEPES pH 8.0, 0.01M Betaine, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 28, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 33616 / % possible obs: 100 % / Redundancy: 11 % / Rsym value: 0.043 / Χ2: 0.942 / Net I/σ(I): 25.6
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 11 % / Num. unique all: 3339 / Rsym value: 0.286 / Χ2: 1.071 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YE7

1ye7
PDB Unreleased entry


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.921 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.206 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1699 5.1 %RANDOM
Rwork0.227 ---
obs0.228 33570 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.878 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20.53 Å20 Å2
2--1.05 Å20 Å2
3----1.58 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3006 0 0 160 3166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223067
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.9944184
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8955401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.01522.373118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68915464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6041530
X-RAY DIFFRACTIONr_chiral_restr0.10.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022330
X-RAY DIFFRACTIONr_nbd_refined0.2220.21344
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22056
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2157
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.211
X-RAY DIFFRACTIONr_mcbond_it0.7751.52021
X-RAY DIFFRACTIONr_mcangle_it1.42623220
X-RAY DIFFRACTIONr_scbond_it2.04831046
X-RAY DIFFRACTIONr_scangle_it3.4514.5964
LS refinement shellResolution: 2.2→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 117 -
Rwork0.245 2369 -
obs-2486 100 %

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