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- PDB-1knk: Crystal Structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate... -

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Basic information

Entry
Database: PDB / ID: 1knk
TitleCrystal Structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate Synthase (ispF) from E. coli involved in Mevalonate-Independent Isoprenoid Biosynthesis
Components2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
KeywordsMETAL BINDING PROTEIN / isoprenoids / deoxyxylulose/methyl-erythritol-phosphate pathway / cyclodiphosphate / MEP / YgbB / ispF / MECDP / 2-C-methyl-D-erythritol-2 / 4-cyclodiphosphate synthase
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
: / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Rigid body / Resolution: 2.8 Å
AuthorsRichard, S.B. / Ferrer, J.L. / Bowman, M.E. / Lillo, A.M. / Tetzlaff, C.N. / Cane, D.E. / Noel, J.P.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: Structure and mechanism of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase. An enzyme in the mevalonate-independent isoprenoid biosynthetic pathway.
Authors: Richard, S.B. / Ferrer, J.L. / Bowman, M.E. / Lillo, A.M. / Tetzlaff, C.N. / Cane, D.E. / Noel, J.P.
#1: Journal: Nat.Struct.Biol. / Year: 2001
Title: Structure of 4-diphosphocytidyl-2-C-methylerythritol Synthetase Involved in Mevalonate-Independent Isoprenoid Biosynthesis
Authors: Richard, S.B. / Bowman, M.E. / Kwiatkowski, W. / Kang, I. / Chow, C. / Lillo, A.M. / Cane, D.E. / Noel, J.P.
History
DepositionDec 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 16, 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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.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_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: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9752
Polymers16,9211
Non-polymers551
Water19811
1
A: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)50,9266
Polymers50,7623
Non-polymers1653
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area5720 Å2
ΔGint-34 kcal/mol
Surface area18090 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)145.630, 145.630, 145.630
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-202-

HOH

21A-206-

HOH

DetailsThe biological assembly is a homotrimer generated from the monomer in the asymmetric unit by the operations: z,x,y and y,z,x

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Components

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


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 / Plasmid: PHIS8 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62617
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: (NH4)2SO4, PEG 400, NaI, PIPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
113.5 mg/mlprotein1drop
20.8 Mammonium sulfate1reservoir
31 %(w/v)PEG4001reservoir
40.2 Msodium iodide1reservoir
52 mMDL-dithiothreitol1reservoir
60.1 MPIPES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 10, 2001
RadiationMonochromator: Si(111) OR Si(311) CRYSTALS, LN2 COOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 24117 / Num. obs: 24117 / % possible obs: 93.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 3.54 % / Biso Wilson estimate: 111.6 Å2 / Rsym value: 0.091 / Net I/σ(I): 15.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 5 / Num. unique all: 404 / Rsym value: 0.415 / % possible all: 96.9
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 99 Å / Num. obs: 11929 / Redundancy: 3.55 % / Num. measured all: 41619 / Rmerge(I) obs: 0.091
Reflection shell
*PLUS
% possible obs: 96.9 % / Rmerge(I) obs: 0.415

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: Rigid body
Starting model: PDB ENTRY 1KNJ

1knj


Resolution: 2.8→24.74 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 623227.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1088 4.8 %RANDOM
Rwork0.232 ---
all-22633 --
obs-22633 94.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.3984 Å2 / ksol: 0.369238 e/Å3
Displacement parametersBiso mean: 72.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2---0.16 Å20 Å2
3----0.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 2.8→24.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1166 0 1 11 1178
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d0.84
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.367 187 5.6 %
Rwork0.366 3179 -
obs-3179 84.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.253 / Rfactor Rwork: 0.243
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84
LS refinement shell
*PLUS
Rfactor Rfree: 0.367 / Rfactor Rwork: 0.366

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