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- PDB-4c8e: IspF (Burkholderia cenocepacia) 2CMP complex -

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Basic information

Entry
Database: PDB / ID: 4c8e
TitleIspF (Burkholderia cenocepacia) 2CMP complex
Components2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE
KeywordsLYASE
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'-MONOPHOSPHATE / DI(HYDROXYETHYL)ETHER / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Similarity search - Component
Biological speciesBURKHOLDERIA CENOCEPACIA (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsO'Rourke, P.E.F. / Kalinowska-Tluscik, J. / Fyfe, P.K. / Dawson, A. / Hunter, W.N.
CitationJournal: Bmc Struct.Biol. / Year: 2014
Title: Crystal Structures of Ispf from Plasmodium Falciparum and Burkholderia Cenocepacia: Comparisons Inform Antimicrobial Drug Target Assessment.
Authors: O Rourke, P.E. / Kalinowska-Tluscik, J. / Fyfe, P.K. / Dawson, A. / Hunter, W.N.
History
DepositionSep 30, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3May 29, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / struct_biol / Item: _exptl_crystal_grow.method
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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.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_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

Downloads & links

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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)60,26714
Polymers57,9303
Non-polymers2,33811
Water7,566420
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11730 Å2
ΔGint-173.1 kcal/mol
Surface area16080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.849, 89.316, 72.981
Angle α, β, γ (deg.)90.00, 104.18, 90.00
Int Tables number5
Space group name H-MC121

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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 / MECDP-SYNTHASE / MECPP-SYNTHASE / MECPS / 2C-METHYL-D-ERYTHRITOL-2 / 4-CYCLODIPHOSPHATE SYNTHASE


Mass: 19309.836 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA CENOCEPACIA (bacteria) / Strain: J2315 / Description: GENOMIC DNA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD
References: UniProt: B4EC22, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

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Non-polymers , 5 types, 431 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H14N3O8P
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsCYTIDINE-5'-MONOPHOSPHATE (C5P): TWO MOLECULES OF CMP PER ACTIVE SITE.
Sequence detailsALTHOUGH RESIDUE 3 IS LISTED AS PHENYLALANINE IN THE UNIPROT DATABASE, IT WAS FOUND TO BE VALINE ...ALTHOUGH RESIDUE 3 IS LISTED AS PHENYLALANINE IN THE UNIPROT DATABASE, IT WAS FOUND TO BE VALINE WHEN SEQUENCED.

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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: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PROTEIN WAS CRYSTALLISED BY HANGING-DROP VAPOUR DIFFUSION. BCISPF SAMPLE IN 100 MM NACL, 2MM MGCL2, 100 MM TRIS-HCL, PH 7.5; WAS CONCENTRATED TO 5 MG/ML, AND HAD CMP ADDED (20 MM ...Details: PROTEIN WAS CRYSTALLISED BY HANGING-DROP VAPOUR DIFFUSION. BCISPF SAMPLE IN 100 MM NACL, 2MM MGCL2, 100 MM TRIS-HCL, PH 7.5; WAS CONCENTRATED TO 5 MG/ML, AND HAD CMP ADDED (20 MM CONCENTRATION IN SAMPLE). CRYSTALS WERE OBTAINED BY MIXING 2 MICROLITRES OF SAMPLE WITH 2 MICROLITRES RESERVOIR AT 20 DEGREES C. RESERVOIR SOLUTION: 25% W/V PEG 3350, 2.2M (NH4)2SO4, 0.1 M SODIUM FORMATE, PH 5.0, 1% V/V DIOXANE. CRYO: 20% GLYCEROL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV PLUS PLUS / Detector: IMAGE PLATE / Date: Apr 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→19.32 Å / Num. obs: 47918 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3F0G

3f0g


Resolution: 1.9→70.76 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.902 / SU B: 3.529 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25064 2425 5.1 %RANDOM
Rwork0.20363 ---
obs0.20601 45493 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.204 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å2-0.67 Å2
2--0.53 Å20 Å2
3----1.24 Å2
Refinement stepCycle: LAST / Resolution: 1.9→70.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3564 0 141 420 4125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023880
X-RAY DIFFRACTIONr_bond_other_d0.0020.022599
X-RAY DIFFRACTIONr_angle_refined_deg1.5262.0225289
X-RAY DIFFRACTIONr_angle_other_deg0.93.0036291
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3525518
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.10923.585159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53815644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1381533
X-RAY DIFFRACTIONr_chiral_restr0.0860.2621
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024345
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02748
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 173 -
Rwork0.248 3310 -
obs--100 %

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