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- PDB-3ike: Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate ... -

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Basic information

Entry
Database: PDB / ID: 3ike
TitleCrystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with cytosine
Components2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
KeywordsLYASE / NIAID / SSGCID / Seattle Structural Genomics Center for Infectious Disease / fragment / Isoprene biosynthesis / Metal-binding
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
6-AMINOPYRIMIDIN-2(1H)-ONE / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Citation
Journal: J Struct Funct Genomics / Year: 2011
Title: Leveraging structure determination with fragment screening for infectious disease drug targets: MECP synthase from Burkholderia pseudomallei.
Authors: Begley, D.W. / Hartley, R.C. / Davies, D.R. / Edwards, T.E. / Leonard, J.T. / Abendroth, J. / Burris, C.A. / Bhandari, J. / Myler, P.J. / Staker, B.L. / Stewart, L.J.
#1: Journal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionAug 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Sep 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _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
B: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
C: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,07711
Polymers52,4883
Non-polymers5898
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7700 Å2
ΔGint-135 kcal/mol
Surface area16180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.659, 68.064, 60.156
Angle α, β, γ (deg.)90.000, 96.290, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-194-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 17495.881 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: ispF, mecS, BPSL2098 / Production host: Escherichia coli (E. coli)
References: UniProt: Q63T71, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

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Non-polymers , 5 types, 249 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CYT / 6-AMINOPYRIMIDIN-2(1H)-ONE / CYTOSINE


Mass: 111.102 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H5N3O
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.28 Å3/Da / Density % sol: 46.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 20% PEG 3350, 0.2 M Mg Formate, 34.4 MG/ML protein, 0.4/0.4 uL drops, Crystal tracking ID 204112a1, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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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 SATURN 944+ / Detector: CCD / Date: Jul 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 21121 / % possible obs: 99.9 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.089 / Χ2: 1.01 / Net I/σ(I): 12.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2105 / Χ2: 1.027 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3F0E

3f0e


Resolution: 2.3→28.31 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.165 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.839 / SU B: 6.311 / SU ML: 0.155 / SU R Cruickshank DPI: 0.358 / SU Rfree: 0.235 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.358 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1084 5.1 %RANDOM
Rwork0.185 ---
obs0.187 21111 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 73.58 Å2 / Biso mean: 26.741 Å2 / Biso min: 5.49 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å20 Å20.14 Å2
2--1.62 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.3→28.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3398 0 29 241 3668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223472
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.9774704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.785453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.95322.8150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.07315538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7571536
X-RAY DIFFRACTIONr_chiral_restr0.0970.2544
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212656
X-RAY DIFFRACTIONr_mcbond_it0.8161.52264
X-RAY DIFFRACTIONr_mcangle_it1.47323575
X-RAY DIFFRACTIONr_scbond_it2.16131208
X-RAY DIFFRACTIONr_scangle_it3.4384.51129
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 80 -
Rwork0.269 1462 -
all-1542 -
obs--98.53 %

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