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- PDB-3ghz: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Salmon... -

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Basic information

Entry
Database: PDB / ID: 3ghz
Title2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Salmonella typhimurium
Components2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
KeywordsLYASE / structural genomics / IDP01038 / 2-C-methyl-D-erythritol 2 / 4-cyclodiphosphate synthase / Isoprene biosynthesis / Metal-binding / Center for Structural Genomics of Infectious Diseases / CSGID
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
PYROPHOSPHATE 2- / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsOsipiuk, J. / Gu, M. / Peterson, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: X-ray crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Salmonella typhimurium.
Authors: Osipiuk, J. / Gu, M. / Peterson, S. / Anderson, W.F. / Joachimiak, A.
History
DepositionMar 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 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.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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,04210
Polymers51,5843
Non-polymers4577
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-58 kcal/mol
Surface area16270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.974, 143.974, 143.974
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

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


Mass: 17194.828 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella 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
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.41 Å3/Da / Density % sol: 48.97 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Magnesium acetate,20% PEG-3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2008
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.03→46 Å / Num. all: 32255 / Num. obs: 32255 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Biso Wilson estimate: 50.5 Å2 / Rmerge(I) obs: 0.073 / Χ2: 1.611 / Net I/σ(I): 51.494
Reflection shellResolution: 2.03→2.07 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.801 / Mean I/σ(I) obs: 2.05 / Num. unique all: 1607 / Χ2: 1.094 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0054refinement
PDB_EXTRACT3.006data extraction
SBC-Collectdata collection
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GX1

1gx1


Resolution: 2.03→46 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 8.807 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.171 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1632 5.1 %RANDOM
Rwork0.166 ---
all0.168 32219 --
obs0.168 32219 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.6 Å2 / Biso mean: 32.007 Å2 / Biso min: 17.83 Å2
Refinement stepCycle: LAST / Resolution: 2.03→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3475 0 25 198 3698
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223700
X-RAY DIFFRACTIONr_bond_other_d0.0010.022523
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.985028
X-RAY DIFFRACTIONr_angle_other_deg0.93536174
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3865501
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.83523.419155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.8315634
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0761529
X-RAY DIFFRACTIONr_chiral_restr0.1010.2566
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214172
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02738
X-RAY DIFFRACTIONr_mcbond_it0.8551.52349
X-RAY DIFFRACTIONr_mcbond_other0.261.5987
X-RAY DIFFRACTIONr_mcangle_it1.42823762
X-RAY DIFFRACTIONr_scbond_it2.57331351
X-RAY DIFFRACTIONr_scangle_it3.8964.51247
LS refinement shellResolution: 2.028→2.081 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 128 -
Rwork0.22 2241 -
all-2369 -
obs-2369 99.79 %
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)
10.9986-0.37570.11942.0839-0.03961.7421-0.0025-0.0441-0.01990.10180.04410.0112-0.10690.0848-0.04160.05210.0292-0.01190.10190.06620.099952.142735.901211.0454
21.6214-0.7223-0.44252.20560.13173.09780.0537-0.0279-0.22320.03560.03610.12090.11910.1137-0.08980.0520.0228-0.03860.09030.07330.146951.330927.1368.1583
31.57380.1301-0.3231.57740.07712.6772-0.0677-0.253-0.79270.07650.00960.04080.68670.29910.05810.2510.0723-0.05290.17830.10440.469951.569611.52140.832
42.4496-0.1454-0.74422.0995-0.39212.66620.0273-0.1536-0.6922-0.0602-0.03440.29870.5041-0.02520.00710.1627-0.0005-0.10120.09290.05330.331644.588115.3125-4.1832
52.4965-0.12270.73782.9480.23131.62320.04280.197-0.0562-0.2843-0.0472-0.0129-0.13660.14960.00450.12020.0377-0.08090.0876-0.00180.112449.387136.762-14.0726
61.4652-0.0420.68732.05720.3042.09160.0810.0503-0.2045-0.1757-0.04510.3085-0.0298-0.127-0.03590.08880.0431-0.0880.08990.02120.172442.605633.7511-12.2666
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 117
2X-RAY DIFFRACTION2A118 - 156
3X-RAY DIFFRACTION3B0 - 78
4X-RAY DIFFRACTION4B79 - 156
5X-RAY DIFFRACTION5C0 - 29
6X-RAY DIFFRACTION6C30 - 156

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