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- PDB-3t80: Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate... -

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Basic information

Entry
Database: PDB / ID: 3t80
TitleCrystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Salmonella typhimurium bound to cytidine
Components2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
KeywordsLYASE / IspF / Isoprenoid biosynthesis / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / Alpha Beta
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
4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / PYROPHOSPHATE 2- / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID) / Staker, B.L. / Edwards, T.E.
CitationJournal: To be Published
Title: Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Salmonella typhimurium bound to cytidine
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Staker, B.L. / Edwards, T.E.
History
DepositionJul 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Structure summary
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Sep 13, 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_conn.ptnr2_label_seq_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

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


Theoretical massNumber of molelcules
Total (without water)106,43642
Polymers103,1696
Non-polymers3,26736
Water2,090116
1
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)53,34223
Polymers51,5843
Non-polymers1,75820
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10270 Å2
ΔGint-149 kcal/mol
Surface area15190 Å2
MethodPISA
2
D: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
E: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
F: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,09419
Polymers51,5843
Non-polymers1,50916
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9440 Å2
ΔGint-156 kcal/mol
Surface area15330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.013, 147.657, 56.919
Angle α, β, γ (deg.)90.00, 106.38, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 6 molecules ABCDEF

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


Mass: 17194.828 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: ispF, STM2929 / Plasmid: PMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MAGIC
References: UniProt: Q8ZMF7, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

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Non-polymers , 6 types, 152 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CTN / 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / CYTIDINE


Mass: 243.217 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H13N3O5
#5: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 3.91 Å3/Da / Density % sol: 68.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: SATYA.00122.A.AN1 15 mg/mL, 222391E7 (10% PEG8000, 100 mM imidazole, pH 8.0, 200 mM calcium acetate, 2 mM zinc acetate, 2 mM magnesium chloride), cryosolvent (25% ethylene glycol, 2 mM zinc ...Details: SATYA.00122.A.AN1 15 mg/mL, 222391E7 (10% PEG8000, 100 mM imidazole, pH 8.0, 200 mM calcium acetate, 2 mM zinc acetate, 2 mM magnesium chloride), cryosolvent (25% ethylene glycol, 2 mM zinc acetate, 2 mM magnsium chloride), VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 16, 2011
RadiationMonochromator: ACCEL DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 54267 / % possible obs: 98.9 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 19.876
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.501 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MxDCdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GHZ

3ghz


Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.924 / SU B: 15.494 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.294 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2751 5.1 %RANDOM
Rwork0.211 ---
obs0.212 54128 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.8 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 54.002 Å2
Baniso -1Baniso -2Baniso -3
1-2.35 Å20 Å23.57 Å2
2---1.25 Å20 Å2
3---0.91 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6693 0 190 116 6999
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196974
X-RAY DIFFRACTIONr_bond_other_d0.0030.024649
X-RAY DIFFRACTIONr_angle_refined_deg1.7441.9939422
X-RAY DIFFRACTIONr_angle_other_deg2.976311328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.475906
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67423.397262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.136151088
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9931546
X-RAY DIFFRACTIONr_chiral_restr0.0870.21084
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217780
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021392
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 202 -
Rwork0.277 3719 -
obs--99.49 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.98590.3585-0.28582.74040.19942.25960.0788-0.0841-0.12520.1501-0.0472-0.27450.1274-0.0225-0.03160.037-0.0076-0.05840.10310.02970.1172-23.910717.223111.7757
20.9951-0.81610.47611.76820.51252.37560.06240.0026-0.0201-0.00630.00090.10540.0066-0.3945-0.06330.04980.0463-0.02370.15160.02840.103-37.664933.84640.4017
32.3190.0962-0.32841.54690.92221.32320.1357-0.01110.1782-0.1563-0.0277-0.2455-0.1819-0.0085-0.1080.05120.01090.01080.0290.03340.141-14.347535.0211-0.3713
41.99590.46020.48052.26770.32271.36090.04060.1606-0.07720.0366-0.04980.0190.04580.01530.00930.1181-0.1125-0.0090.177-0.02610.0195-48.9274-18.082413.0105
52.5711-0.8103-0.61211.89130.39612.63090.0549-0.3456-0.32660.6803-0.11510.240.4035-0.16680.06020.4366-0.24880.03540.24740.0280.0866-50.8759-20.597237.0004
61.9808-0.0223-0.04613.0969-0.40131.24310.0604-0.13310.1360.455-0.1672-0.0665-0.01950.05570.10680.1765-0.1142-0.0250.1443-0.01920.0464-38.4128-2.574626.4109
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 156
2X-RAY DIFFRACTION2B0 - 156
3X-RAY DIFFRACTION3C0 - 156
4X-RAY DIFFRACTION4D0 - 156
5X-RAY DIFFRACTION5E0 - 156
6X-RAY DIFFRACTION6F0 - 156

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