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- PDB-1w57: Structure of the Bifunctional IspDF from Campylobacter jejuni con... -

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Basic information

Entry
Database: PDB / ID: 1w57
TitleStructure of the Bifunctional IspDF from Campylobacter jejuni containing Zn
ComponentsISPD/ISPF BIFUNCTIONAL ENZYME
KeywordsTRANSFERASE / BIFUNCTIONAL ENZYME / BIOSYNTHETIC PATHWAY / ISOPRENOIDS / BIFUNCTIONAL / NONMEVALONATE
Function / homology
Function and homology information


2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity / terpenoid biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / metal ion binding
Similarity search - Function
Bifunctional enzyme IspD/IspF / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 4-diphosphocytidyl-2C-methyl-D-erythritol synthase, conserved site / Cytidylyltransferase IspD/TarI / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 4-diphosphocytidyl-2C-methyl-D-erythritol synthase signature. / 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 ...Bifunctional enzyme IspD/IspF / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 4-diphosphocytidyl-2C-methyl-D-erythritol synthase, conserved site / Cytidylyltransferase IspD/TarI / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 4-diphosphocytidyl-2C-methyl-D-erythritol synthase signature. / 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. / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / 60s Ribosomal Protein L30; Chain: A; / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CYTIDINE-5'-MONOPHOSPHATE / GERANYL DIPHOSPHATE / Bifunctional enzyme IspD/IspF
Similarity search - Component
Biological speciesCAMPYLOBACTER JEJUNI (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsGabrielsen, M. / Bond, C.S. / Hunter, W.N.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Hexameric Assembly of the Bifunctional Methylerythritol 2,4-Cyclodiphosphate Synthase and Protein-Protein Associations in the Deoxy-Xylulose-Dependent Pathway of Isoprenoid Precursor Biosynthesis
Authors: Gabrielsen, M. / Bond, C.S. / Hallyburton, I. / Hecht, S. / Bacher, A. / Eisenreich, W. / Rohdich, F. / Hunter, W.N.
History
DepositionAug 6, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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
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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ISPD/ISPF BIFUNCTIONAL ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7705
Polymers41,7441
Non-polymers1,0264
Water1,02757
1
A: ISPD/ISPF BIFUNCTIONAL ENZYME
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)256,62130
Polymers250,4646
Non-polymers6,15624
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation12_554x,x-y,-z-1/21
crystal symmetry operation11_654-x+y+1,y,-z-1/21
crystal symmetry operation10_664-y+1,-x+1,-z-1/21
MethodPQS
Unit cell
Length a, b, c (Å)107.760, 107.760, 161.004
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-1374-

GPP

21A-2038-

HOH

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Components

#1: Protein ISPD/ISPF BIFUNCTIONAL ENZYME / 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE / 4-DIPHOSPHOCYTIDYL-2C-METHYL-D- ...2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE / 4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL SYNTHASE / MEP CYTIDYLYLTRANSFERASE / MCT / 2-C-METHYL-D-ERYTHRITOL 2 / 4-CYCLODIPHOSPHATE SYNTHASE / MECPS / MECDP-SYNTHASE / METHYLERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE / METHYLERYTHRITOL 2 / 4-CYCLODIPHOSPHATE SYNTHASE


Mass: 41744.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAMPYLOBACTER JEJUNI (Campylobacter) / Strain: JEJUNI NTCT 11168 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q9PM68, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N3O8P
#4: Chemical ChemComp-GPP / GERANYL DIPHOSPHATE


Mass: 314.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O7P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: 2-PHOSPHO-4-(CYTIDINE 5'-DIPHOSPHO)-2-C- METHYL-D-ERYTHRITOL = 2-C-METHYL-D- ...CATALYTIC ACTIVITY: 2-PHOSPHO-4-(CYTIDINE 5'-DIPHOSPHO)-2-C- METHYL-D-ERYTHRITOL = 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE + CMP.

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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: 3.2 Å3/Da / Density % sol: 62.2 %
Crystal growDetails: 35 % ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 160 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 21, 2002 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 367588 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 31.4 % / Biso Wilson estimate: 81.4 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 41.7
Reflection shellResolution: 3.1→3.21 Å / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 8.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W55

1w55


Resolution: 3.09→95.35 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.858 / SU B: 16.409 / SU ML: 0.299 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.511 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.295 509 4.83 %RANDOM
Rwork0.217 ---
obs0.221 367588 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 38.71 Å2
Baniso -1Baniso -2Baniso -3
1-4.789 Å22.394 Å20 Å2
2--4.789 Å20 Å2
3----7.183 Å2
Refinement stepCycle: LAST / Resolution: 3.09→95.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2908 0 62 57 3027
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0380.0223019
X-RAY DIFFRACTIONr_bond_other_d0.0020.022771
X-RAY DIFFRACTIONr_angle_refined_deg2.1281.9934073
X-RAY DIFFRACTIONr_angle_other_deg2.12436483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1420.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023257
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02576
X-RAY DIFFRACTIONr_nbd_refined0.2320.2610
X-RAY DIFFRACTIONr_nbd_other0.2680.23158
X-RAY DIFFRACTIONr_nbtor_refined0.2010.21402
X-RAY DIFFRACTIONr_nbtor_other0.1050.21979
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.266
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3680.2135
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3160.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1341.51828
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.00722946
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.46231191
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7874.51127
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: 3.09→3.17 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.252 38
Rwork0.204 732

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