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- PDB-5iwy: Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate... -

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Basic information

Entry
Database: PDB / ID: 5iwy
TitleCrystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Bacillus subtitis complexed with CMP and Mg2+
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, conserved site / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase superfamily / YgbB family / 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature.
Similarity search - Domain/homology
CYTIDINE-5'-MONOPHOSPHATE / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsLiu, Z.C. / Jin, Y. / Wang, G.G.
CitationJournal: Biosci. Rep. / Year: 2018
Title: Crystal structure of IspF from Bacillus subtilis and absence of protein complex assembly among IspD/IspE/IspF enzymes in the MEP pathway.
Authors: Liu, Z.C. / Jin, Y. / Liu, W.F. / Tao, Y. / Wang, G.G.
History
DepositionMar 23, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 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 / refine_hist / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.d_res_low / _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

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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)104,32516
Polymers102,8866
Non-polymers1,43910
Water4,612256
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)52,4869
Polymers51,4433
Non-polymers1,0436
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8230 Å2
ΔGint-59 kcal/mol
Surface area16720 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)51,8397
Polymers51,4433
Non-polymers3964
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6480 Å2
ΔGint-51 kcal/mol
Surface area17030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.057, 89.460, 87.986
Angle α, β, γ (deg.)90.00, 103.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 17147.693 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: ispF, yacN, BSU00910 / Production host: Escherichia coli (E. coli)
References: UniProt: Q06756, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N3O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.12 Å3/Da / Density % sol: 41.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 25mM Tris-HCl PH8.0, 0.1M NaCl, 0.1M Magnesium formate dihydrate, 12-15% w/v PEG 3350, 5mM CMP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.99→30 Å / Num. obs: 57544 / % possible obs: 98.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 14.3
Reflection shellResolution: 1.99→2.06 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 4.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T0A

1t0a


Resolution: 1.99→29.212 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.201 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2194 2819 4.9 %RANDOM
Rwork0.17358 ---
obs0.17589 54704 97.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.394 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å2-0 Å2-1.8 Å2
2---0.27 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.99→29.212 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7096 0 90 256 7442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0197304
X-RAY DIFFRACTIONr_bond_other_d0.0020.027194
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.9829862
X-RAY DIFFRACTIONr_angle_other_deg0.96316584
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2455924
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.31625.099302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.714151286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0071530
X-RAY DIFFRACTIONr_chiral_restr0.0970.21120
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028174
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021552
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_it2.6983.243720
X-RAY DIFFRACTIONr_mcbond_other2.6963.243719
X-RAY DIFFRACTIONr_mcangle_it3.9644.8424636
X-RAY DIFFRACTIONr_mcangle_other3.9634.8424637
X-RAY DIFFRACTIONr_scbond_it3.9083.9543584
X-RAY DIFFRACTIONr_scbond_other3.9073.9523580
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2015.6935221
X-RAY DIFFRACTIONr_long_range_B_refined8.06427.1958166
X-RAY DIFFRACTIONr_long_range_B_other8.03427.0598086
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.991→2.043 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 206 -
Rwork0.199 3922 -
obs--94.61 %

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