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- PDB-6mwi: Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate ... -

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Basic information

Entry
Database: PDB / ID: 6mwi
TitleCrystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in complex with ligand HGN-0456
Components2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
KeywordsLYASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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
ACETATE ION / 6-ethoxy-1,3-benzothiazole-2-sulfonamide / DI(HYDROXYETHYL)ETHER / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in complex with ligand HGN-0456.
Authors: Abendroth, J. / Dranow, D.M. / Pierce, P.G. / Horn, J.R. / Hagen, T.J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionOct 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author / Item: _citation.journal_abbrev
Revision 1.2Oct 11, 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
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_label_asym_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

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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)53,26411
Polymers52,4883
Non-polymers7768
Water8,593477
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-87 kcal/mol
Surface area17030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.000, 67.350, 60.790
Angle α, β, γ (deg.)90.000, 96.450, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-425-

HOH

21B-324-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 17495.881 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (strain 1710b) (bacteria)
Strain: 1710b / Gene: ispF, BURPS1710b_2511 / Plasmid: BupsA.00122.a.A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q3JRA0, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

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Non-polymers , 6 types, 485 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-EZL / 6-ethoxy-1,3-benzothiazole-2-sulfonamide / Ethoxzolamide


Mass: 258.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10N2O3S2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, inhibitor*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 2.27 Å3/Da / Density % sol: 45.85 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Hampton research Index HT screen, condition G8: 25% w/v PEG 3350, , 200mM ammonium acetate, 100mM HEPES free acid / NaOH pH 7.5: BupsA.00122.a.A1.PW28261 at 14.37mg/ml + 9mM compound ...Details: Hampton research Index HT screen, condition G8: 25% w/v PEG 3350, , 200mM ammonium acetate, 100mM HEPES free acid / NaOH pH 7.5: BupsA.00122.a.A1.PW28261 at 14.37mg/ml + 9mM compound bsi108633/HGN-0456: Cryo: 15% EG: Tray 300522g8, puck JZQ1-9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 30, 2018
RadiationMonochromator: RIGAKU VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→40.809 Å / Num. obs: 46628 / % possible obs: 98.3 % / Redundancy: 3.16 % / Biso Wilson estimate: 20.778 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.026 / Rrim(I) all: 0.03 / Χ2: 1.013 / Net I/σ(I): 27.93
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.75-1.81.9880.0946.3533290.9840.12195.4
1.8-1.842.0220.0817.4532960.9890.10596.7
1.84-1.92.0760.079.0732350.990.09197.7
1.9-1.962.1310.06510.5931820.9910.08499.2
1.96-2.022.2130.05213.6230860.9940.06698.9
2.02-2.092.2720.04616.1729590.9950.05998.4
2.09-2.172.7060.04221.1428870.9960.05298.5
2.17-2.263.070.0424.1127400.9970.04997.8
2.26-2.363.2370.03626.8826220.9970.04498.3
2.36-2.473.3950.03429.7625470.9980.0498.6
2.47-2.613.6110.03134.0224180.9980.03698.5
2.61-2.773.980.03137.1122830.9980.03699
2.77-2.964.670.02844.1121790.9990.03299.5
2.96-3.24.6850.02548.2220420.9990.02999.4
3.2-3.54.580.02254.7518350.9990.02499.5
3.5-3.914.5940.02159.2316900.9990.02398.9
3.91-4.524.5940.01962.8714940.9990.02198.9
4.52-5.534.6670.01961.93126410.02199.2
5.53-7.834.7080.021609870.9990.02399.3
7.83-40.8094.5730.01766.445530.9990.0297.7

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Processing

Software
NameVersionClassification
PHENIX(dev_3283)refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3qhd

3qhd


Resolution: 1.75→40.809 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.07
RfactorNum. reflection% reflectionSelection details
Rfree0.1702 2067 4.43 %0
Rwork0.1373 ---
obs0.1387 46624 98.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.13 Å2 / Biso mean: 17.8639 Å2 / Biso min: 2.8 Å2
Refinement stepCycle: final / Resolution: 1.75→40.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3514 0 38 485 4037
Biso mean--26.01 29.22 -
Num. residues----477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093688
X-RAY DIFFRACTIONf_angle_d1.025016
X-RAY DIFFRACTIONf_dihedral_angle_d15.2922242
X-RAY DIFFRACTIONf_chiral_restr0.07577
X-RAY DIFFRACTIONf_plane_restr0.006670
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.79070.21951290.16052859298895
1.7907-1.83550.20341500.15292883303396
1.8355-1.88510.24761370.15492926306398
1.8851-1.94060.1861250.15222998312399
1.9406-2.00320.17161340.13882972310699
2.0032-2.07480.1781220.13192972309498
2.0748-2.15790.18141460.13212986313298
2.1579-2.25610.15821460.13272953309998
2.2561-2.3750.16281530.13632918307198
2.375-2.52380.17461140.13812991310598
2.5238-2.71860.16941490.13832980312999
2.7186-2.99210.1791480.14292998314699
2.9921-3.42490.14991210.13223035315699
3.4249-4.31430.1571500.12293018316899
4.3143-40.81980.15321430.14093068321199
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)
14.49811.93-1.03843.5108-0.38931.20050.1268-0.40780.13670.2206-0.109-0.3573-0.14260.2317-0.00780.12260.0144-0.040.1139-0.00820.12735.9703-40.9331-4.9642
24.67450.8166-1.73722.9207-1.14151.2943-0.1-1.02340.25340.80550.0217-0.4565-0.15880.43910.04810.29130.033-0.1110.2901-0.05750.198326.5041-46.23585.671
31.740.6387-0.14412.1786-0.44891.3254-0.0284-0.0515-0.08540.04920.0262-0.13550.05990.040.00830.07240.0403-0.0020.0473-0.00730.081629.3853-49.3355-7.2916
47.99245.4424-5.44486.863-5.19666.6358-0.02060.38640.0658-0.37670.079-0.23390.20290.0918-0.03590.11540.05850.01890.1016-0.00260.158638.1494-50.6178-12.4853
51.12470.2567-0.16826.187-0.31571.4109-0.00450.1575-0.0104-0.1784-0.0041-0.29130.00690.12310.01780.03440.0066-0.00950.097-0.00390.068432.7659-40.0658-16.1967
63.59921.72690.54454.15180.59352.3991-0.2082-0.0037-0.1049-0.3280.14290.16890.2141-0.1190.04730.04490.0289-0.00360.0380.00080.062622.5311-49.397-10.1297
71.2080.03-0.40742.54971.13791.90130.0536-0.02820.1724-0.0508-0.05460.1127-0.17920.01390.01780.05780.0015-0.01610.03920.00530.102110.7265-32.1195-8.2184
81.18040.0908-0.13861.37020.3950.9767-0.01730.05750.2014-0.0802-0.00560.0788-0.1487-0.02010.03730.07390.0073-00.05930.02850.09068.0345-32.132-11.5935
95.6925-1.8510.00884.2727-0.28983.60940.10860.30110.5555-0.1374-0.0298-0.126-0.6696-0.2121-0.04370.18650.00380.02610.15960.04840.13773.5727-33.2071-21.9528
101.30710.3961-0.05341.39510.511.32020.0180.05520.0444-0.02640.03770.0134-0.0458-0.0763-0.04880.0657-0.00090.00380.04420.01540.05185.8333-38.8829-8.116
111.76321.5317-0.25462.5461-0.65081.13030.1063-0.1512-0.14550.1613-0.1228-0.20390.03340.0473-0.01040.07980.0193-0.00030.0391-0.00690.063515.2614-41.6656-3.8622
124.02841.52360.51171.24791.39263.20050.15730.06050.53320.1145-0.04330.1153-0.39040.27470.00860.1415-0.0429-0.00430.08510.01390.161623.1578-23.057-6.9404
131.6325-0.2631-0.23914.280.90382.39460.06660.2138-0.18140.01840.1099-0.17720.211-0.0411-0.16180.0472-0.00130.00860.05870.00460.038611.6954-43.4886-14.3827
141.55470.98710.01823.93-1.16161.9449-0.08710.32910.2397-0.16570.0429-0.1151-0.21160.15160.05550.0903-0.01310.03230.18140.03280.115424.5852-33.1328-28.9015
152.0101-1.10951.04263.6694-0.64492.143-0.02620.44630.1784-0.421-0.0809-0.58870.08250.23320.06550.10980.00750.06480.19860.0020.135631.8489-43.608-29.7527
161.33090.16750.19121.1430.0671.0621-0.01430.27660.0412-0.09650.020.0552-0.00470.041-0.00360.0754-0.00370.01090.15070.02210.059318.7806-39.7808-27.7099
173.88062.6301-0.40584.5698-0.02890.53510.04030.01640.07960.05-0.03680.04070.05160.0579-0.01970.09680.0117-0.01290.0578-0.00330.029124.7472-43.2563-8.278
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 17 through 53 )C17 - 53
2X-RAY DIFFRACTION2chain 'C' and (resid 54 through 74 )C54 - 74
3X-RAY DIFFRACTION3chain 'C' and (resid 75 through 107 )C75 - 107
4X-RAY DIFFRACTION4chain 'C' and (resid 108 through 122 )C108 - 122
5X-RAY DIFFRACTION5chain 'C' and (resid 123 through 146 )C123 - 146
6X-RAY DIFFRACTION6chain 'C' and (resid 147 through 159 )C147 - 159
7X-RAY DIFFRACTION7chain 'A' and (resid 1 through 30 )A1 - 30
8X-RAY DIFFRACTION8chain 'A' and (resid 31 through 53 )A31 - 53
9X-RAY DIFFRACTION9chain 'A' and (resid 54 through 67 )A54 - 67
10X-RAY DIFFRACTION10chain 'A' and (resid 68 through 121 )A68 - 121
11X-RAY DIFFRACTION11chain 'A' and (resid 122 through 139 )A122 - 139
12X-RAY DIFFRACTION12chain 'A' and (resid 140 through 146 )A140 - 146
13X-RAY DIFFRACTION13chain 'A' and (resid 147 through 159 )A147 - 159
14X-RAY DIFFRACTION14chain 'B' and (resid 0 through 40 )B0 - 40
15X-RAY DIFFRACTION15chain 'B' and (resid 41 through 74 )B41 - 74
16X-RAY DIFFRACTION16chain 'B' and (resid 75 through 159 )B75 - 159
17X-RAY DIFFRACTION17chain 'C' and (resid 0 through 16 )C0 - 16

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