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

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Basic information

Entry
Database: PDB / ID: 6mwk
TitleCrystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in complex with ligand HGN-0883
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
Chem-K4Y / MALONIC ACID / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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 / 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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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
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)53,96615
Polymers52,4883
Non-polymers1,47812
Water7,945441
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7670 Å2
ΔGint-14 kcal/mol
Surface area16570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.330, 68.040, 60.670
Angle α, β, γ (deg.)90.000, 96.460, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-405-

HOH

21A-414-

HOH

31B-339-

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, 453 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-K4Y / 4-amino-N-(6-methoxypyrimidin-4-yl)benzene-1-sulfonamide


Mass: 280.303 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H12N4O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.3 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Hampton research Index screen, condition C9: 5% Jeffamine ED-2003, 1100mM sodium malonate dibasic, 100mM HEPES free acid / NaOH pH 7.5: BupsA.00122.a.A1.PW28612 at 14mg/ml + 9mM compound ...Details: Hampton research Index screen, condition C9: 5% Jeffamine ED-2003, 1100mM sodium malonate dibasic, 100mM HEPES free acid / NaOH pH 7.5: BupsA.00122.a.A1.PW28612 at 14mg/ml + 9mM compound bsi108673/HGN-0883: Cryo: 20% EG: Tray 300532c9, puck ZRJ4-4

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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: Jun 7, 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: 1.8→40.935 Å / Num. obs: 43844 / % possible obs: 99.4 % / Redundancy: 3.076 % / Biso Wilson estimate: 21.744 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.102 / Rrim(I) all: 0.118 / Χ2: 0.693 / Net I/σ(I): 17.88
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.851.9730.5092.0931790.830.63397.7
1.85-1.92.0310.4372.5131300.8620.54298.9
1.9-1.952.0790.3832.9730590.8830.47599.7
1.95-2.012.1310.294.0829710.9240.3699.9
2.01-2.082.1980.2355.2428900.9470.29299.7
2.08-2.152.3950.2046.9327800.9540.25199.4
2.15-2.232.8330.1928.7827100.970.23199.7
2.23-2.322.9990.17810.1925950.9780.21299.6
2.32-2.433.1510.16612.0224970.9820.19599.6
2.43-2.553.3010.15914.0423670.9840.18699.6
2.55-2.683.5550.13916.5922740.990.1699.6
2.68-2.854.1030.13519.6421570.9920.153100
2.85-3.044.4720.11325.3720250.9960.127100
3.04-3.294.4460.09930.9518890.9970.11199.8
3.29-3.64.3680.07443.5217520.9970.08399.8
3.6-4.024.340.0751.7515690.9990.07899.8
4.02-4.654.1750.05165.1913940.9990.05799.9
4.65-5.694.220.05959.1911890.9990.06699.5
5.69-8.054.1990.06755.439110.9980.07699.6
8.05-40.9353.7230.03681.515060.9990.04294.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(dev_3297)refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3qhd

3qhd


Resolution: 1.8→40.935 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 15.34
RfactorNum. reflection% reflectionSelection details
Rfree0.1785 1951 4.45 %0
Rwork0.1419 ---
obs0.1434 43836 99.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 78.55 Å2 / Biso mean: 19.7309 Å2 / Biso min: 4.33 Å2
Refinement stepCycle: final / Resolution: 1.8→40.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3534 0 84 448 4066
Biso mean--27.63 30.1 -
Num. residues----480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073746
X-RAY DIFFRACTIONf_angle_d0.9425099
X-RAY DIFFRACTIONf_dihedral_angle_d16.7122250
X-RAY DIFFRACTIONf_chiral_restr0.064581
X-RAY DIFFRACTIONf_plane_restr0.005679
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.8450.20141430.17722916305998
1.845-1.89490.22281570.17872955311299
1.8949-1.95070.22661450.176829583103100
1.9507-2.01360.18961410.151429853126100
2.0136-2.08560.19571310.143429933124100
2.0856-2.16910.18581370.14452999313699
2.1691-2.26780.18271310.146129913122100
2.2678-2.38730.18621300.143829563086100
2.3873-2.53690.17861560.139330053161100
2.5369-2.73270.16011310.145230073138100
2.7327-3.00770.20641390.141829953134100
3.0077-3.44270.15151250.13630443169100
3.4427-4.33670.15651250.119330553180100
4.3367-40.94570.16361600.13623026318699
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)
14.4645-2.51650.22747.07493.20746.7449-0.1853-2.04741.2881.40350.1288-0.5054-0.6110.6328-0.00230.4729-0.0374-0.09680.6286-0.19610.425831.4526-46.33199.2701
20.93010.099-0.01291.801-0.37641.0382-0.03320.0442-0.0898-0.10210.0031-0.16490.10710.13970.03660.08610.0337-0.00320.0951-0.00680.096932.3352-46.4876-11.2458
33.47790.7540.87761.72311.12742.4863-0.15270.013-0.1765-0.0790.09910.10750.2525-0.15470.04790.0650.0350.00720.0607-0.00070.112422.5385-49.2759-10.1015
41.39420.7-0.09352.83610.73151.32110.0548-0.05570.1983-0.0832-0.00290.0556-0.18250.0554-0.03110.07320.0165-0.02140.05580.01170.109910.8659-32.4995-8.3637
50.5227-0.19260.27050.3029-0.34350.38780.00940.11580.1406-0.0863-0.03180.025-0.1686-0.10110.01970.09810.00750.00350.08210.03320.09477.4521-33.5272-12.9625
64.46092.37131.43635.9623-0.17052.7389-0.00310.2650.65520.24710.02820.1355-0.6874-0.16590.08040.2550.03250.02740.1750.05550.16193.3884-33.0383-22.0263
71.50730.42520.09121.60650.56981.75080.00960.0170.0584-0.04880.04630.0048-0.0667-0.0862-0.06550.07260.00120.00370.06590.01710.06785.9331-38.7088-8.0631
83.52793.5221-0.10524.5376-0.721.05750.1207-0.0701-0.00620.2295-0.1189-0.0871-0.02580.1167-0.00190.08430.01360.00970.0798-0.02010.073517.7252-36.4892-4.4559
92.40820.66380.52976.50662.34173.61510.07390.2551-0.21610.06060.1555-0.15440.2479-0.0585-0.19940.0669-0.00330.00360.06990.01450.020411.721-43.3443-14.3785
101.63410.32640.23233.2719-0.52351.9563-0.01270.24550.1252-0.0241-0.038-0.2447-0.11710.1261-0.01340.06060.00840.02790.15160.0040.096224.6579-37.6116-25.7755
112.61940.872-0.08434.2299-1.64182.7847-0.00850.41970.4569-0.1895-0.0438-0.2923-0.22390.1390.02370.1232-0.00340.02450.23640.02590.145424.8601-33.72-30.6461
122.06651.0465-0.77213.5351-0.92342.2397-0.02690.37660.0424-0.14160.0303-0.5573-0.03480.01510.00980.15670.02050.03440.1661-0.04350.210734.4137-47.3457-25.4671
130.79260.2124-0.55661.24570.33560.5902-0.10020.72610.3809-0.67830.0004-1.1101-0.02620.8080.08930.3977-0.03370.18850.61390.05660.442636.7659-41.0723-37.0452
141.26230.43380.17251.2357-0.14711.1955-0.05720.375-0.0529-0.14870.07020.0370.06570.04320.00220.1089-0.00350.01370.2055-0.00130.076218.2067-42.7122-31.0159
150.506-0.43120.48062.15081.04331.9683-0.03310.06980.37440.021-0.10060.0649-0.1270.00740.07380.1287-0.00860.01140.11130.03670.159519.5174-24.4808-18.8728
162.4550.29760.05013.1756-0.83742.10280.03160.2748-0.2837-0.09190.03220.09090.14050.1402-0.00960.06660.0179-0.01160.1152-0.02610.076321.275-45.8337-23.2582
174.42142.22870.03093.62360.09880.6403-0.0068-0.07560.2020.0146-0.0311-0.1865-0.00830.14530.04310.11170.0162-0.00920.09590.00740.044133.2597-40.7138-7.4364
184.73692.3919-1.45583.098-1.220.57970.1321-0.39290.05480.2044-0.1398-0.1331-0.04820.11060.01350.1250.0347-0.02050.1077-0.01210.087127.0898-44.3394-2.1964
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 63 through 74 )C63 - 74
2X-RAY DIFFRACTION2chain 'C' and (resid 75 through 146 )C75 - 146
3X-RAY DIFFRACTION3chain 'C' and (resid 147 through 159 )C147 - 159
4X-RAY DIFFRACTION4chain 'A' and (resid 0 through 33 )A0 - 33
5X-RAY DIFFRACTION5chain 'A' and (resid 34 through 53 )A34 - 53
6X-RAY DIFFRACTION6chain 'A' and (resid 54 through 67 )A54 - 67
7X-RAY DIFFRACTION7chain 'A' and (resid 68 through 122 )A68 - 122
8X-RAY DIFFRACTION8chain 'A' and (resid 123 through 146 )A123 - 146
9X-RAY DIFFRACTION9chain 'A' and (resid 147 through 159 )A147 - 159
10X-RAY DIFFRACTION10chain 'B' and (resid 0 through 23 )B0 - 23
11X-RAY DIFFRACTION11chain 'B' and (resid 24 through 53 )B24 - 53
12X-RAY DIFFRACTION12chain 'B' and (resid 54 through 62 )B54 - 62
13X-RAY DIFFRACTION13chain 'B' and (resid 63 through 74 )B63 - 74
14X-RAY DIFFRACTION14chain 'B' and (resid 75 through 131 )B75 - 131
15X-RAY DIFFRACTION15chain 'B' and (resid 132 through 146 )B132 - 146
16X-RAY DIFFRACTION16chain 'B' and (resid 147 through 159 )B147 - 159
17X-RAY DIFFRACTION17chain 'C' and (resid 0 through 33 )C0 - 33
18X-RAY DIFFRACTION18chain 'C' and (resid 34 through 62 )C34 - 62

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