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

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Basic information

Entry
Database: PDB / ID: 6mwj
TitleCrystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in complex with ligand HGN-0863
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
5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Analysis of Burkholderia pseudomallei IspF in complex with sulfapyridine, sulfamonomethoxine, ethoxzolamide and acetazolamide
Authors: Grote, D. / Stewart, C.G. / Daraji, D.G. / Enayati, P. / Braverman, K.N. / Romanaggi, C. / Bolejack, M.J. / Yano, J.K. / Abendroth, J. / Dranow, D.M. / Pierce, P.G. / Lorimer, D.D. / ...Authors: Grote, D. / Stewart, C.G. / Daraji, D.G. / Enayati, P. / Braverman, K.N. / Romanaggi, C. / Bolejack, M.J. / Yano, J.K. / Abendroth, J. / Dranow, D.M. / Pierce, P.G. / Lorimer, D.D. / Horanyi, P.S. / Staker, B.L. / Edwards, T.E. / Myler, P.J. / Horn, J.R. / Hagen, T.J.
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 / _citation.title
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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.3Apr 9, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year

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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)53,14110
Polymers52,4883
Non-polymers6537
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7980 Å2
ΔGint-117 kcal/mol
Surface area16560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.050, 67.400, 60.210
Angle α, β, γ (deg.)90.000, 96.400, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-394-

HOH

21A-414-

HOH

31B-307-

HOH

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Components

#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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-AZM / 5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE


Mass: 222.245 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6N4O3S2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Optimization screen Bups122_quad_2, condition c4: 200mM Ammonium acetate, 100mM HEPES free acid/NaOH pH 7.5, 26% PEG 3350: BupsA.00122.a.A1.PW28612 at 14mg/ml + 9mM compound bsi108668/HGN- ...Details: Optimization screen Bups122_quad_2, condition c4: 200mM Ammonium acetate, 100mM HEPES free acid/NaOH pH 7.5, 26% PEG 3350: BupsA.00122.a.A1.PW28612 at 14mg/ml + 9mM compound bsi108668/HGN-0863: Cryo: 20% EG: Tray 302680c4, puck NZC8-7

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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: Aug 8, 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: 2.05→40.643 Å / Num. obs: 28468 / % possible obs: 97 % / Redundancy: 3.662 % / Biso Wilson estimate: 30.714 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Rrim(I) all: 0.04 / Χ2: 1.003 / Net I/σ(I): 25.23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.05-2.12.9260.1318.317890.9770.1683.2
2.1-2.163.340.11310.5620100.9880.13595.6
2.16-2.223.7450.10612.3919480.9910.12396.7
2.22-2.293.760.09313.419380.9940.10997.1
2.29-2.373.7520.0815.3918760.9950.09397.7
2.37-2.453.750.07216.7818360.9960.08497.9
2.45-2.543.7740.05819.8417540.9970.06797.6
2.54-2.653.7650.05221.5816980.9980.06198
2.65-2.763.7790.04823.7916390.9970.05698.5
2.76-2.93.7650.04225.4415730.9980.0598.9
2.9-3.063.7630.03729.0815320.9980.04399
3.06-3.243.7680.03232.2113970.9990.03899.1
3.24-3.473.7550.02837.8413430.9990.03298.9
3.47-3.743.7350.02642.1912650.9990.0399.2
3.74-4.13.7280.02544.5411290.9990.02998.9
4.1-4.583.6690.02247.9410560.9990.02699.8
4.58-5.293.6940.02446.689320.9990.02899.6
5.29-6.483.6970.02445.757820.9990.02899.9
6.48-9.173.6460.01948.436210.9990.02399.2
9.17-40.6433.4290.01851.253500.9990.02198

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Processing

Software
NameVersionClassification
PHENIX(dev_3297)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: 2.05→40.643 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.99
RfactorNum. reflection% reflectionSelection details
Rfree0.197 2043 7.18 %0
Rwork0.1492 ---
obs0.1526 28459 97.05 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 103.44 Å2 / Biso mean: 33.5325 Å2 / Biso min: 9.41 Å2
Refinement stepCycle: final / Resolution: 2.05→40.643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3500 0 28 277 3805
Biso mean--46.25 34.91 -
Num. residues----475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063611
X-RAY DIFFRACTIONf_angle_d0.7914900
X-RAY DIFFRACTIONf_dihedral_angle_d13.6342170
X-RAY DIFFRACTIONf_chiral_restr0.055562
X-RAY DIFFRACTIONf_plane_restr0.004655
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.09770.23241250.17441476X-RAY DIFFRACTION82
2.0977-2.15010.20221040.15751716X-RAY DIFFRACTION95
2.1501-2.20830.20161300.16381757X-RAY DIFFRACTION97
2.2083-2.27320.2431390.16171721X-RAY DIFFRACTION97
2.2732-2.34660.20571350.15751762X-RAY DIFFRACTION97
2.3466-2.43050.22091300.16851804X-RAY DIFFRACTION98
2.4305-2.52780.20471370.15851749X-RAY DIFFRACTION98
2.5278-2.64280.23631410.15681764X-RAY DIFFRACTION98
2.6428-2.78210.21341580.16011776X-RAY DIFFRACTION99
2.7821-2.95640.22181440.16411775X-RAY DIFFRACTION99
2.9564-3.18450.21061380.15431822X-RAY DIFFRACTION99
3.1845-3.50490.19231340.14651795X-RAY DIFFRACTION99
3.5049-4.01160.1861330.13591816X-RAY DIFFRACTION99
4.0116-5.05270.1541560.12011817X-RAY DIFFRACTION100
5.0527-40.65090.18221390.15151866X-RAY DIFFRACTION99
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)
13.86720.9802-1.23496.1732-2.87955.2077-0.0630.6207-0.3223-0.439-0.1678-0.73910.45690.51170.23650.24240.15510.03470.3878-0.04160.429438.7595-50.0255-12.8333
22.7223-0.1363-0.06812.2824-0.37583.1547-0.02810.7460.0894-0.13690.0294-0.40060.02860.3920.07780.12110.0271-0.01930.33770.01610.274532.6666-40.6136-15.613
38.32096.09653.93456.30433.21972.976-0.07070.41720.13190.03460.23870.33160.14080.0373-0.15940.08740.08360.03520.1408-0.04130.153223.6331-47.6191-10.4974
42.08770.1208-0.13322.74290.92452.72320.02320.31970.407-0.1163-0.0219-0.1119-0.26280.0582-0.01390.1334-0.0041-0.01980.11010.07040.20749.3684-32.4827-9.9403
52.49110.9877-1.27741.52171.72565.0531-0.11180.68350.6026-0.4767-0.13050.185-0.8245-0.3530.09370.3599-0.009-0.08540.33420.13350.22621.0924-31.0212-19.0647
62.36350.35810.07811.32250.0031.769-0.04730.15630.06560.06780.0265-0.1867-0.01720.02610.02660.13740.0016-0.01890.08420.03080.138310.9942-38.9567-6.1221
73.63540.92170.98347.5962.54215.87160.05760.4825-0.0874-0.0539-0.03010.22840.3514-0.1653-0.01650.1144-0.00410.02940.1521-0.00960.148611.7245-43.5331-14.2154
81.34510.3823-0.53381.4361-0.88362.8911-0.0050.82610.1968-0.17110.0759-0.1996-0.23440.30480.0460.2081-0.08460.03180.65950.13940.291223.8063-36.6263-27.3175
92.6294-0.07110.01147.0945-1.96162.1146-0.11241.2160.6292-0.3773-0.0309-0.5648-0.26990.36810.07880.2339-0.04580.04280.91110.17150.331225.6785-34.8826-29.7036
108.01664.2448-3.86173.4505-2.90852.5078-0.24110.46720.0958-0.5106-0.3228-0.85780.05980.74040.34280.28180.0030.07670.86320.03230.425135.5906-45.57-28.2793
111.6867-0.2360.37391.15330.14991.1438-0.07831.2270.371-0.24460.0623-0.2875-0.06140.4734-0.10280.2146-0.02870.080.80150.05620.133519.7103-39.4027-29.1955
124.42091.97220.65452.3391-0.63113.4320.03720.7712-0.3165-0.1712-0.0683-0.27620.23220.43870.02730.16270.03490.03580.5042-0.05260.156721.0959-45.9771-22.9602
134.59183.4866-0.68347.741-0.5291.66070.04250.09220.04180.0005-0.15830.08070.07310.12480.06680.15090.061-0.01270.1354-0.00540.136624.8175-43.0395-8.1903
147.47241.8773-0.84635.848-0.66481.59890.1771-0.15210.33580.5712-0.172-0.739-0.17910.38050.00590.24120.0369-0.09160.21980.03620.303335.9687-40.5278-4.8456
156.7739-1.1354-0.12243.5426-0.29933.9282-0.0955-0.38340.04950.40780.2152-0.2903-0.12220.3936-0.23830.26640.0442-0.03820.1516-0.03880.203620.5352-45.84971.4904
163.4159-0.85550.3891.3173-0.74440.4232-0.0739-1.61010.33771.03960.0882-0.7805-0.23990.94480.01130.4305-0.009-0.22530.6937-0.16490.554632.391-45.05526.6587
172.0511-0.2490.3563.6995-1.0082.2068-0.03910.1751-0.27220.0395-0.06-0.21490.20940.25550.13440.15910.0794-0.02420.1645-0.04510.241929.4996-49.0697-7.0584
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 108 through 121 )C108 - 121
2X-RAY DIFFRACTION2chain 'C' and (resid 122 through 146 )C122 - 146
3X-RAY DIFFRACTION3chain 'C' and (resid 147 through 159 )C147 - 159
4X-RAY DIFFRACTION4chain 'A' and (resid 0 through 53 )A0 - 53
5X-RAY DIFFRACTION5chain 'A' and (resid 54 through 74 )A54 - 74
6X-RAY DIFFRACTION6chain 'A' and (resid 75 through 146 )A75 - 146
7X-RAY DIFFRACTION7chain 'A' and (resid 147 through 159 )A147 - 159
8X-RAY DIFFRACTION8chain 'B' and (resid 0 through 27 )B0 - 27
9X-RAY DIFFRACTION9chain 'B' and (resid 28 through 53 )B28 - 53
10X-RAY DIFFRACTION10chain 'B' and (resid 54 through 67 )B54 - 67
11X-RAY DIFFRACTION11chain 'B' and (resid 68 through 146 )B68 - 146
12X-RAY DIFFRACTION12chain 'B' and (resid 147 through 159 )B147 - 159
13X-RAY DIFFRACTION13chain 'C' and (resid 0 through 16 )C0 - 16
14X-RAY DIFFRACTION14chain 'C' and (resid 17 through 53 )C17 - 53
15X-RAY DIFFRACTION15chain 'C' and (resid 54 through 62 )C54 - 62
16X-RAY DIFFRACTION16chain 'C' and (resid 63 through 74 )C63 - 74
17X-RAY DIFFRACTION17chain 'C' and (resid 75 through 107 )C75 - 107

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