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- PDB-6v3m: Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate ... -

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Basic information

Entry
Database: PDB / ID: 6v3m
TitleCrystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in compomplex with ligand HGN-0961 (BSI110840)
Components2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
KeywordsLYASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / Burkholderia pseudomallei / 2-C-methyl-D-erythritol 2 / 4-cyclodiphosphate synthase / HGN-0961
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
D-MALATE / Chem-QOG / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 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
DepositionNov 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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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)60,16418
Polymers58,4613
Non-polymers1,70315
Water8,377465
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8350 Å2
ΔGint-12 kcal/mol
Surface area16990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.310, 67.550, 60.570
Angle α, β, γ (deg.)90.000, 96.317, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-427-

HOH

21A-431-

HOH

31A-467-

HOH

41B-327-

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: 19487.109 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
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (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, 480 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-QOG / 5-{[(propan-2-yl)carbamoyl]amino}-1,3,4-thiadiazole-2-sulfonamide


Mass: 265.313 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H11N5O3S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H6O5
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.04 Å3/Da / Density % sol: 39.8 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: Bups122_opt3 screen: 100mM HEPES free acid / NaOH pH 7.4, 200mM ammonium acetate, 27% (w/V) PEG 3350: BupsA.00122.a.A1.PW28612 at 14.33mg/ml plus 1mM ZnCl2 and 10mM compound HGN- ...Details: Bups122_opt3 screen: 100mM HEPES free acid / NaOH pH 7.4, 200mM ammonium acetate, 27% (w/V) PEG 3350: BupsA.00122.a.A1.PW28612 at 14.33mg/ml plus 1mM ZnCl2 and 10mM compound HGN-0961/BSI110840: soaked over night with reservoir and 25mM compound: cryo: 20% EG + soak buffer: tray 310506a10: puck bno0-4. The ligand description was generated from a smiles string using phenix elbow. The ligand structure was minimized using GAMESS with the 3-21G basis. Restraints were extracted using phenix.elbow

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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: Nov 7, 2019
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 67221 / % possible obs: 98.5 % / Redundancy: 11.388 % / Biso Wilson estimate: 23.959 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.026 / Rrim(I) all: 0.027 / Χ2: 1.019 / Net I/σ(I): 49.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.55-1.594.5650.324.4747040.9410.3693.2
1.59-1.637.7210.2767.1646200.9770.29594.7
1.63-1.688.2130.2249.0445810.9860.23995.9
1.68-1.738.4880.19110.5445190.990.20397.5
1.73-1.798.8080.14813.6344070.9940.15798.4
1.79-1.859.1890.11817.5143080.9960.12499.4
1.85-1.929.5560.09222.2642010.9970.09799.8
1.92-29.9730.0729.4940010.9990.07499.9
2-2.0910.3990.05538.5638730.9990.057100
2.09-2.1910.7140.04547.3637060.9990.04799.9
2.19-2.3111.5790.0455.81352610.042100
2.31-2.4512.6910.03566.79333510.03699.9
2.45-2.6213.3950.0379.26314610.03199.9
2.62-2.8314.5960.02789.29293710.028100
2.83-3.116.2290.023104.88268110.02499.8
3.1-3.4719.2410.021129243710.021100
3.47-422.0160.018152.99217410.019100
4-4.921.8840.017164.59182010.01799.9
4.9-6.9321.6630.017161.53143910.018100
6.93-5020.5520.0161678060.9990.01699.6

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3qhd

3qhd


Resolution: 1.55→44.39 Å / SU ML: 0.1343 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.4689
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1693 1897 2.82 %0
Rwork0.1447 65311 --
obs0.1454 67208 98.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.76 Å2
Refinement stepCycle: LAST / Resolution: 1.55→44.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3519 0 92 465 4076
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01043747
X-RAY DIFFRACTIONf_angle_d1.16925105
X-RAY DIFFRACTIONf_chiral_restr0.0764583
X-RAY DIFFRACTIONf_plane_restr0.0066684
X-RAY DIFFRACTIONf_dihedral_angle_d20.19481356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.22361350.19644394X-RAY DIFFRACTION93.06
1.59-1.630.21861230.16594452X-RAY DIFFRACTION94.66
1.63-1.680.16881370.15344530X-RAY DIFFRACTION95.87
1.68-1.730.17651350.15724593X-RAY DIFFRACTION97.4
1.73-1.80.191220.15174638X-RAY DIFFRACTION98.49
1.8-1.870.17571470.1514682X-RAY DIFFRACTION99.44
1.87-1.950.19281370.15324726X-RAY DIFFRACTION99.92
1.95-2.060.16421360.14894739X-RAY DIFFRACTION100
2.06-2.180.1791440.1434722X-RAY DIFFRACTION99.96
2.18-2.350.16241280.14574709X-RAY DIFFRACTION99.98
2.35-2.590.16351450.14494738X-RAY DIFFRACTION99.88
2.59-2.960.1591450.14774744X-RAY DIFFRACTION99.98
2.96-3.730.16731200.13654801X-RAY DIFFRACTION100
3.74-44.390.15821430.13344843X-RAY DIFFRACTION99.88
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)
11.60355407613-0.0260696639046-0.1171572754950.9406178716730.4170033938521.888160377390.04107509331110.1891156076470.0983221110336-0.428005750947-0.070564586196-0.0637102407607-0.221246477573-0.015477930473-0.01804104060330.08410438834910.00629076581968-0.009279612691060.09687087834330.0255098562520.084955671734712.7275270157-37.7974532968-14.8959939068
21.03780026672-0.0430820445987-0.5441181685573.198360010071.285519286140.873809905320.142329617168-0.2887004269480.7777820195120.217638436003-0.1762847878740.426770905035-0.1938556917220.02530140760240.03902505786610.158122648427-0.008658095807080.02385443638010.0931229357813-0.04350889620380.2768884685617.6722258619-26.5090592466-0.0892480579613
31.786169328060.07406466823820.03299267222111.95816944210.9728268111491.57058459401-0.05460612962190.157124546480.305355537902-0.1161394503940.0168791932360.0897629828752-0.1996536255310.00368733468740.05076847043060.1079389368880.003005424875470.004636131744790.08968942280290.05089433715820.1173945246197.89920669307-31.7576783338-11.625550213
45.15420078596-0.5845204918460.3157736103347.92654706095-0.6076189225085.495470678880.0101587675660.4557573656350.621608662161-0.00635978405436-0.01048194106030.0625605549088-0.757658962731-0.3209147868140.02850303328390.2131319988280.01318524570430.00927901458620.2725026438990.07989118274180.1536663047523.19503087741-33.0846975498-21.7067013655
51.05297570547-2.262676217971.185114917694.92122224974-2.434144518523.6973127162-0.1234703352370.8533238316580.784294165129-0.827011206830.1808231868481.19584193673-0.479567915318-1.21155213924-0.1448081578350.3997728214740.0962709545794-0.09307897117740.3970291925380.182384968580.448756117517-2.98317448486-25.6122439485-12.962169147
61.825835652470.267767285285-0.05631429121981.221145457470.2249384954451.070232629480.05209836475930.1276086639090.0278295243225-0.02400172243110.00786228417215-0.04242404015660.0271409701283-0.103251817786-0.05100752107150.0880018286817-0.002399163282370.00496309631260.06501628821910.01970071863230.04426946080976.80867349097-40.4663869268-10.5129449138
72.176724321710.5529094071040.1769278653542.566243671090.8620234193272.075942719810.044113439154-0.127670520436-0.1143741253790.1942264201450.0455120350335-0.1851795198490.06274352856730.172193394234-0.09243408997970.129978580850.01413450903850.003243441211860.1001634894820.007538240179540.0964644980077.56920184045-40.7414742953-0.206371428539
84.747783808351.56766727618-0.7343537513026.493566200570.05687782229293.130290034160.0385138938446-0.140471371473-0.4472746867770.1440734118630.1135519875190.1373442183970.397914150723-0.134565763114-0.09794646871840.177499254826-0.01293135906010.01159124121450.07460205049150.0180407499630.1089635554125.79521080153-50.958315024-4.31121108797
94.579688908264.37936041576-0.5939990695795.85941965486-0.6684788286931.079704562710.125677707752-0.1954167955590.004535550614180.18541677817-0.188108533847-0.220544472216-0.07713749044340.1671863814560.01939591160610.115289908261-0.00117217394129-0.01942618707490.0785376184754-0.002136947894160.12684480215522.0028204564-35.5885175543-3.08960477776
102.906655086921.753734303280.192631864043.52948302717-0.2993371782362.67250914845-0.009441471841370.01753620487670.627596056018-0.0305724522022-0.01206678681510.386107707278-0.3803548515680.2295910281460.005298486030320.164371150731-0.0353394066904-0.01639335522590.1118549192450.0203771566810.26570660352223.038940368-22.6207811063-6.98836977416
112.12192713714-0.185500717418-0.1858490239164.712558344360.6873920138452.558867768960.04966032857210.287496267993-0.0916071739649-0.165420832620.0379779368981-0.1077511723430.154263217423-0.0837626547214-0.1052020873530.08373361137980.007201587265450.0006357963287970.08806752452380.007313369245590.045180874580511.6840961356-43.4710954959-14.3419882911
121.421239530570.5588863589250.2639060602363.14060598442-0.4124217583741.78429562063-0.1685485146730.7391753049710.0919248249211-0.02105221014580.248135172274-0.493605398525-0.2192571021770.1688580113920.1410985071140.0900761830431-0.04905847227580.07858076081820.3745124119040.1055389756360.10446417688323.8355071691-36.5319683521-27.3587903385
133.20980919264-0.3144955761530.4146351786314.05539033629-0.2591432381261.32301329938-0.06908805341960.8623805451670.575249543969-0.24811787294-0.0770604567355-0.394468680635-0.2000303965750.3363184857510.1177382279430.167792235075-0.02026868944080.01887026437220.4857350819950.1065400307720.19857344400525.7567650381-34.7858093571-29.6503827013
142.995784201020.686796078366-1.929452028583.23170750498-0.9739299644764.00107418717-0.01271779172260.6949640419640.201320492025-0.330937649478-0.0313477544541-0.684147051982-0.2328618866480.5665329557470.04593542296190.2334153263160.006566246626620.06820875042910.482104521819-0.004336994458790.28212002986735.5868515708-45.5211630123-28.4681434513
151.915766468330.033535920140.4661232213971.47682391284-0.01373323851771.31755463004-0.02258508326040.6839869203990.108113840691-0.231535663070.0312539443695-0.0154994943635-0.01505293891820.23418596143-0.03623804701410.137606340654-0.001235327440750.03861355781410.3864865494270.0426355900420.078065513294119.7080787407-39.5252000308-29.4243580132
163.679909174880.992530576813-0.1598559752884.42086434033-2.071749107272.595138090310.06078053827340.425693237827-0.197585906503-0.0393732971717-0.02291403188420.211044567170.1840781176640.258856069859-0.01098345218080.09468908243820.0257491086322-0.002560005857860.226487312553-0.02597849940470.056974577386721.168205601-45.9462945986-23.1836267293
172.577079307370.88002644487-0.4116820934994.11815552564-0.01257907908660.8056641546480.066352302157-0.1010660607310.1955924004080.152234705066-0.073761956989-0.43874572046-0.02584179930940.196270619508-0.01258075108830.133641361310.0128351574751-0.02571197954780.1118474849070.007411307332320.094508231725533.5551521219-40.6927355229-7.48239961888
185.164696206282.77488363544-2.025681077054.06817234694-1.513152200371.015424619650.256674087961-0.3892353374780.1735479913340.363755745943-0.208719904642-0.193090171886-0.1069769406130.223862012936-0.08382988021290.1576960029410.0310889813577-0.02302924770310.12758149738-0.01769088753290.13866844369229.7459724215-43.4446427023-3.62433193559
198.424545573574.136570426941.648933228466.159549399480.7041510694145.13347352389-0.0767032224436-0.4736652304220.4970553745960.4232812389520.003168610944840.00656122037385-0.292623886630.293915221670.01921465704380.226321274660.0334401764758-0.02411147301740.145393364348-0.01409758531580.15977843855620.2947803651-45.53440596341.65603226544
201.7169741531.213920920360.1762366190712.27389846725-0.2980897997523.195949585920.16850389028-1.819535354390.2852267617871.39671002604-0.21128871442-0.291057543538-0.3150725630440.545519388868-0.04086005455190.550785117591-0.0134639422142-0.1113744665830.570369255369-0.07628481187880.44964407594331.7391926437-46.12730683488.83113896186
211.306320336680.1220186478860.01140139815812.00653744592-0.4771224769571.09810846496-0.0174234306450.156619806349-0.111919167352-0.0953624240904-0.00868887383876-0.2271214946370.07961830163120.1556345437560.03925288232660.1137613991340.03181373285440.001131752892270.123667974604-0.01137181764260.1353426249632.2837451886-46.9003235185-11.1760329816
226.819218427794.69977363731.196099566146.647002100941.071696491812.40720015545-0.1029979838630.137726846505-0.253584517508-0.05040159583840.157030017844-0.08182600522160.149263206298-0.0424028489061-0.05329388084040.06951054446090.04546001940260.006474401958630.061938702205-0.01604281996380.085279793685723.3193165274-48.4234358403-10.4844359046
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 16 )
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 30 )
3X-RAY DIFFRACTION3chain 'A' and (resid 31 through 53 )
4X-RAY DIFFRACTION4chain 'A' and (resid 54 through 67 )
5X-RAY DIFFRACTION5chain 'A' and (resid 68 through 74 )
6X-RAY DIFFRACTION6chain 'A' and (resid 75 through 107 )
7X-RAY DIFFRACTION7chain 'A' and (resid 108 through 122 )
8X-RAY DIFFRACTION8chain 'A' and (resid 123 through 128 )
9X-RAY DIFFRACTION9chain 'A' and (resid 129 through 139 )
10X-RAY DIFFRACTION10chain 'A' and (resid 140 through 146 )
11X-RAY DIFFRACTION11chain 'A' and (resid 147 through 159 )
12X-RAY DIFFRACTION12chain 'B' and (resid 0 through 27 )
13X-RAY DIFFRACTION13chain 'B' and (resid 28 through 53 )
14X-RAY DIFFRACTION14chain 'B' and (resid 54 through 67 )
15X-RAY DIFFRACTION15chain 'B' and (resid 68 through 146 )
16X-RAY DIFFRACTION16chain 'B' and (resid 147 through 159 )
17X-RAY DIFFRACTION17chain 'C' and (resid 0 through 33 )
18X-RAY DIFFRACTION18chain 'C' and (resid 34 through 53 )
19X-RAY DIFFRACTION19chain 'C' and (resid 54 through 62 )
20X-RAY DIFFRACTION20chain 'C' and (resid 63 through 74 )
21X-RAY DIFFRACTION21chain 'C' and (resid 75 through 146 )
22X-RAY DIFFRACTION22chain 'C' and (resid 147 through 159 )

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