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- PDB-1u3l: IspF with Mg and CDP -

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Basic information

Entry
Database: PDB / ID: 1u3l
TitleIspF with Mg and CDP
Components2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
KeywordsLYASE / MEP pathway / terpene biosynthesis
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 / ubiquinone biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / manganese ion binding / zinc ion binding / metal ion binding / identical protein 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'-DIPHOSPHATE / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsSteinbacher, S. / Kaiser, J. / Wungsintaweekul, J. / Hechst, S. / Eisenreich, W. / Gerhardt, S. / Bacher, A. / Rohdich, F.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase Involved in Mevalonate Independent Biosynthesis of Isoprenoids
Authors: Steinbacher, S. / Kaiser, J. / Wungsintaweekul, J. / Hechst, S. / Eisenreich, W. / Gerhardt, S. / Bacher, A. / Rohdich, F.
History
DepositionJul 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 19, 2016Group: Refinement description
Revision 1.4Aug 23, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4134
Polymers16,9211
Non-polymers4933
Water00
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)52,24012
Polymers50,7623
Non-polymers1,4799
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area9120 Å2
ΔGint-196 kcal/mol
Surface area15200 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)144.66, 144.66, 144.66
Angle α, β, γ (deg.)90, 90, 90
Int Tables number199
Space group name H-MI213
DetailsTrimer generated by crystallographic three-fold x,y,z y,z,x z,x,y

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Components

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


Mass: 16920.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ispF / Production host: Escherichia coli (E. coli)
References: UniProt: P62617, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CDP / CYTIDINE-5'-DIPHOSPHATE


Mass: 403.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N3O11P2

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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: 7.45 Å3/Da / Density % sol: 84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: ammonium formiate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.541 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. all: 17015 / Num. obs: 17015 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.064

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
X-PLORmodel building
X-PLORrefinement
CCP4(SCALA)data scaling
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1JY8

1jy8


Resolution: 2.5→8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.26 -random
Rwork0.24 --
all0.244 16531 -
obs0.244 16531 -
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1157 0 27 0 1184
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.88

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