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- PDB-3fpi: Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate... -

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Basic information

Entry
Database: PDB / ID: 3fpi
TitleCrystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase IspF complexed with Cytidine Triphosphate
Components2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
KeywordsLYASE / CSGID / alpha-beta sandwich / Isoprene biosynthesis / Metal-binding / Structural Genomics / Structural Genomics of National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / metal ion binding
Similarity search - Function
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, conserved site / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase superfamily / YgbB family / 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature. / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CYTIDINE-5'-TRIPHOSPHATE / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD/molecular replacement / Resolution: 2.8 Å
AuthorsKim, Y. / Maltseva, N. / Stam, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase IspF complexed with Cytidine Triphosphate
Authors: Kim, Y. / Maltseva, N. / Stam, J. / Anderson, W.F. / Joachimiak, A.
History
DepositionJan 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5657
Polymers17,6641
Non-polymers9026
Water1,36976
1
A: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
hetero molecules

A: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
hetero molecules

A: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,69521
Polymers52,9913
Non-polymers2,70518
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area10040 Å2
ΔGint-65 kcal/mol
Surface area17350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.639, 145.639, 145.639
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-165-

CL

21A-168-

MG

31A-244-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / / MECPS / MECDP-synthase


Mass: 17663.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal maltose binding protein fusion and 6-his tag with the TEV protease cut-site. The MBP fusion is removed in situ and the tag is removed during the purification
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: ispF, y0829, YPO3360, YPTB0771, YP_0327 / Plasmid: pMCSG19c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3
References: UniProt: Q8ZBP7, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

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Non-polymers , 6 types, 82 molecules

#2: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.0M Ammonium sulfate, 0.1M HEPES pH 7.0, 0.5 % w/v PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9786 Å
DetectorType: SBC-3 / Detector: CCD / Date: Nov 2, 2008 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.8→34.33 Å / Num. all: 12751 / Num. obs: 12751 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Biso Wilson estimate: 83.86 Å2 / Rmerge(I) obs: 0.095
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.968 / Mean I/σ(I) obs: 2.1 / Num. unique all: 620 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
RESOLVEmodel building
Cootmodel building
BALBESphasing
REFMAC5.5.0053refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD/molecular replacement
Starting model: 3F6M

3f6m


Resolution: 2.8→34.33 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 15.153 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.19
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.199 616 4.9 %RANDOM
Rwork0.17 ---
all0.172 12006 --
obs0.172 12006 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.782 Å2
Refinement stepCycle: LAST / Resolution: 2.8→34.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1213 0 52 76 1341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221284
X-RAY DIFFRACTIONr_angle_refined_deg1.7452.0171746
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4925164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.57224.23152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.04515206
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.763158
X-RAY DIFFRACTIONr_chiral_restr0.1010.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021948
X-RAY DIFFRACTIONr_mcbond_it0.9011.5803
X-RAY DIFFRACTIONr_mcangle_it1.79721277
X-RAY DIFFRACTIONr_scbond_it2.7023481
X-RAY DIFFRACTIONr_scangle_it4.714.5469
LS refinement shellResolution: 2.805→2.877 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 44 -
Rwork0.3 869 -
obs-913 98.49 %
Refinement TLS params.Method: refined / Origin x: 27.0826 Å / Origin y: 8.7153 Å / Origin z: 11.2289 Å
111213212223313233
T0.0315 Å20.0209 Å20.0396 Å2-0.0298 Å20.0236 Å2--0.0806 Å2
L1.5563 °20.1711 °2-0.429 °2-1.8095 °20.4238 °2--1.8703 °2
S-0.0144 Å °-0.0939 Å °-0.1863 Å °-0.1066 Å °-0.0184 Å °-0.1889 Å °0.0791 Å °0.1869 Å °0.0328 Å °

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