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- PDB-3re3: Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate... -

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Basic information

Entry
Database: PDB / ID: 3re3
TitleCrystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase from Francisella tularensis
Components2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
KeywordsLYASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta half sandwich / cytosol
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 / terpenoid biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / 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
PHOSPHATE ION / PYROPHOSPHATE 2- / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.645 Å
AuthorsKim, Y. / Makowska-Grzyska, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase from Francisella tularensis
Authors: Kim, Y. / Makowska-Grzyska, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionApr 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,61116
Polymers72,5984
Non-polymers1,01312
Water1,13563
1
A: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)55,43615
Polymers54,4483
Non-polymers98812
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area10030 Å2
ΔGint-200 kcal/mol
Surface area19900 Å2
MethodPISA
2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,13211
Polymers54,4483
Non-polymers6848
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8130 Å2
ΔGint-103 kcal/mol
Surface area19960 Å2
MethodPISA
3
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
hetero molecules

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
hetero molecules

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,83248
Polymers217,79312
Non-polymers3,03936
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area49060 Å2
ΔGint-515 kcal/mol
Surface area64200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.116, 96.116, 155.308
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 18149.443 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Strain: SCHU S4 / Gene: FTT_1128, ispF / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic
References: UniProt: Q5NFU1, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

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Non-polymers , 6 types, 75 molecules

#2: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.85 Å3/Da / Density % sol: 56.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.1 M Na2HPO4/KH2PO4 pH 6.2, 35% (v/v) MPD, 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: 0.97942 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 14, 2010 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. all: 23681 / Num. obs: 23681 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 68.48 Å2 / Rsym value: 0.112 / Net I/σ(I): 7.7
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 1165 / Rsym value: 0.734 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.645→41.619 Å / SU ML: 0.36 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1211 5.15 %random
Rwork0.173 ---
all0.176 23529 --
obs0.176 23529 99.09 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.037 Å2 / ksol: 0.277 e/Å3
Displacement parametersBiso mean: 72.9 Å2
Baniso -1Baniso -2Baniso -3
1-27.5441 Å2-0 Å20 Å2
2--27.5441 Å20 Å2
3----5.5734 Å2
Refinement stepCycle: LAST / Resolution: 2.645→41.619 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4531 0 54 63 4648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084768
X-RAY DIFFRACTIONf_angle_d1.1446411
X-RAY DIFFRACTIONf_dihedral_angle_d16.2081756
X-RAY DIFFRACTIONf_chiral_restr0.079740
X-RAY DIFFRACTIONf_plane_restr0.004796
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.6451-2.7510.37031260.28732402252896
2.751-2.87620.29041420.22342437257999
2.8762-3.02780.26461600.19932453261399
3.0278-3.21740.29431280.19642492262099
3.2174-3.46570.23131210.196925042625100
3.4657-3.81430.22041230.16224962619100
3.8143-4.36570.19441460.136325102656100
4.3657-5.49830.19121350.136625012636100
5.4983-41.62460.22911300.18912523265399
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)
10.3183-0.1246-0.32250.3532-0.04991.0891-0.21020.07480.0454-0.0852-0.10350.30630.5808-0.08110.14690.21130.06570.1170.8556-0.08680.199832.558834.936261.8525
20.6153-0.1223-0.34490.2056-0.16350.49320.0974-0.39450.24580.364-0.11770.06160.0662-0.0286-0.04370.8090.3274-0.0281.022-0.240.233727.277836.312668.2971
31.1371-0.05740.19861.44220.35120.17820.03830.0638-0.0933-0.1225-0.13150.0520.0274-0.32040.0580.28830.0462-0.00660.36120.05160.159734.908529.980449.2842
40.22740.1390.07560.3722-0.21720.3264-0.2197-0.17690.1313-0.0520.0980.01140.085-0.1035-0.01070.83060.00090.13370.09580.34210.189135.552420.7868105.4411
50.23120.0269-0.08211.0561-0.40160.6607-0.24660.0258-0.08080.047-0.0934-0.06370.1597-0.10790.11830.6777-0.26480.03160.71960.35010.292936.306724.662108.641
60.56730.4576-0.16020.7554-0.24121.1562-0.21-0.07020.14910.10820.25140.1657-0.04150.09920.00070.41340.00530.06180.34440.11310.380431.73865.4904106.5342
70.4680.0817-0.50180.5231-0.19680.53340.39110.3390.0970.2354-0.12370.1057-0.1019-0.4456-0.08770.515-0.1-0.05340.80110.19380.212126.26614.569275.1299
81.42420.0553-0.4692.54150.94780.5233-0.10030.3694-0.0479-0.0392-0.02060.16560.07490.0693-0.0290.9342-0.4387-0.10280.79740.45550.802226.188215.708673.5454
90.8088-0.5948-0.39350.55480.26631.69230.22540.34310.4144-0.13930.17140.1437-0.4548-0.82890.28840.3981-0.2276-0.34780.41450.13790.260621.23523.471886.8219
100.5745-0.04790.57340.7725-0.06780.5419-0.09890.6369-0.3363-0.00130.3873-0.0481-0.08330.292-0.20980.4789-0.14-0.0160.482-0.01140.473743.9863-0.906491.4372
110.9415-0.08170.58030.1385-0.17780.6780.4084-0.166-0.20930.16310.2898-0.16920.48930.00910.36430.8999-0.2954-0.02020.6103-0.35670.358368.63915.694883.3754
120.9079-0.4333-0.04730.6355-0.1441.01850.10030.0437-0.1666-0.30330.08950.31190.350.0731-0.12880.7037-0.0395-0.08530.34030.05480.294540.9168-6.832590.0476
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq -1:28)
2X-RAY DIFFRACTION2chain 'A' and (resseq 29:41)
3X-RAY DIFFRACTION3chain 'A' and (resseq 42:159)
4X-RAY DIFFRACTION4chain 'B' and (resseq 1:28)
5X-RAY DIFFRACTION5chain 'B' and (resseq 29:41)
6X-RAY DIFFRACTION6chain 'B' and (resseq 42:159)
7X-RAY DIFFRACTION7chain 'C' and (resseq 1:30)
8X-RAY DIFFRACTION8chain 'C' and (resseq 31:41)
9X-RAY DIFFRACTION9chain 'C' and (resseq 42:159)
10X-RAY DIFFRACTION10chain 'D' and (resseq 0:20)
11X-RAY DIFFRACTION11chain 'D' and (resseq 21:41)
12X-RAY DIFFRACTION12chain 'D' and (resseq 42:159)

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