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

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Basic information

Entry
Database: PDB / ID: 6mwf
TitleCrystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in complex with ligand HGN-0459
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 / 4-amino-N-(pyridin-2-yl)benzenesulfonamide / 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 / _citation.title
Revision 1.2Mar 11, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.3Oct 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_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)53,32010
Polymers52,4883
Non-polymers8327
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6830 Å2
ΔGint-55 kcal/mol
Surface area16740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.030, 67.930, 60.760
Angle α, β, γ (deg.)90.000, 96.580, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-378-

HOH

21B-310-

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 , 5 types, 455 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SFY / 4-amino-N-(pyridin-2-yl)benzenesulfonamide / Sulfapyridine / Sulfapyridine


Mass: 249.289 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H11N3O2S / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antibiotic*YM
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.29 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Hampton research Index HT screen, condition B7: 1344mM Potassium phosphate dibasic, 56mM sodium phosphate monobasic; BupsA.00122.a.A1.PW28261 BupsA.00122.a.A1.PW28612 at 14.37mg/ml + 9mM ...Details: Hampton research Index HT screen, condition B7: 1344mM Potassium phosphate dibasic, 56mM sodium phosphate monobasic; BupsA.00122.a.A1.PW28261 BupsA.00122.a.A1.PW28612 at 14.37mg/ml + 9mM compound bsi108635/HGN-0049; Cryo: 15% EG; Tray 300524b7, puck CVW3-4

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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: May 31, 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→33.661 Å / Num. obs: 46654 / % possible obs: 97.6 % / Redundancy: 3.037 % / Biso Wilson estimate: 23.499 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.098 / Rrim(I) all: 0.114 / Χ2: 0.717 / Net I/σ(I): 18.95
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.75-1.81.910.4481.9134040.7050.60696.5
1.8-1.841.9660.3942.3133210.7920.52897
1.84-1.92.0170.3522.8432640.8210.46997.3
1.9-1.962.0980.3033.5831420.8550.496.8
1.96-2.022.1590.234.9630010.9090.395.8
2.02-2.092.2410.1946.5629250.9360.25196.6
2.09-2.172.6080.1948.928490.9560.23997.1
2.17-2.263.0240.19610.927560.9690.23496.7
2.26-2.363.190.17912.5425730.9740.21296.6
2.36-2.473.3160.16714.6725370.9740.19797.7
2.47-2.613.5440.14418.0424250.9830.16896.7
2.61-2.773.90.14320.8422610.9880.16498
2.77-2.964.4710.12327.1222080.9950.138100
2.96-3.24.4480.09934.2120550.9960.111100
3.2-3.54.3660.0845.6618710.9980.0999.8
3.5-3.914.2970.0755.5517240.9980.07999.9
3.91-4.524.2140.04767.0615170.9990.05499.9
4.52-5.534.2240.04964.512780.9990.055100
5.53-7.834.2240.06358.4310040.9990.0799.3
7.83-33.6613.7350.03883.9953910.04495.1

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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→33.661 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 17.28
RfactorNum. reflection% reflectionSelection details
Rfree0.1842 2016 4.32 %0
Rwork0.1491 ---
obs0.1506 46647 97.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.33 Å2 / Biso mean: 21.3049 Å2 / Biso min: 3.98 Å2
Refinement stepCycle: final / Resolution: 1.75→33.661 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3472 0 45 459 3976
Biso mean--29.26 31.97 -
Num. residues----474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073661
X-RAY DIFFRACTIONf_angle_d0.9514993
X-RAY DIFFRACTIONf_dihedral_angle_d13.6722214
X-RAY DIFFRACTIONf_chiral_restr0.063578
X-RAY DIFFRACTIONf_plane_restr0.005667
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 (%)
1.75-1.79380.25521390.21053171331096
1.7938-1.84230.26021180.19153140325897
1.8423-1.89650.25741550.18463170332597
1.8965-1.95770.20631590.17253137329697
1.9577-2.02770.22941460.17043086323296
2.0277-2.10880.21711370.1583156329397
2.1088-2.20480.19011480.14533127327597
2.2048-2.3210.16471210.14513195331697
2.321-2.46640.20521280.14793178330697
2.4664-2.65680.17321590.14413144330397
2.6568-2.9240.17021530.14893234338799
2.924-3.34680.16741640.143832633427100
3.3468-4.21530.15741470.125932923439100
4.2153-33.66710.16161420.13953338348099
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)
17.58944.19821.38832.75410.74985.899-0.08190.64320.7237-0.4307-0.0381-0.3413-0.63780.50930.10950.2595-0.04330.01810.39570.1470.307626.1452-26.6189-32.7676
21.1353-0.83080.0952.02410.56721.88540.02710.38680.1571-0.41-0.0436-0.55430.04420.29160.01650.16420.01450.05740.28160.00610.202131.6376-43.66-29.8753
31.35380.34850.0031.60080.22751.6128-0.02650.3854-0.0446-0.16490.04050.02390.06260.0766-0.00350.11510.00520.00020.2153-0.00180.079818.3277-43.2243-31.1008
40.9334-0.78320.3553.3362.10763.2087-0.01220.00410.4185-0.0155-0.1138-0.0466-0.17720.05680.16250.1211-0.00740.00240.08370.03710.155419.3211-24.8393-18.9908
53.33880.6695-0.32293.6502-1.45922.2280.02340.1929-0.14850.0053-0.02980.44430.15380.1698-0.00060.07780.0164-0.00880.1367-0.01720.043120.9143-44.8122-23.1166
64.77762.88020.00254.7421-0.08080.8955-0.05420.03130.1532-0.0567-0.02010.09550.04650.0920.05590.10080.0285-0.00960.07250.00280.037925.0001-42.9619-8.3396
78.74992.4577-0.64227.7551.0742.720.0921-0.22880.4510.33680.1822-0.9225-0.12410.3521-0.20090.11590.0172-0.05170.2024-0.0070.270743.2748-37.4714-6.4756
83.82222.3012-1.62964.2349-0.4670.82450.2903-0.76290.07810.4486-0.292-0.1757-0.0330.3079-0.0520.17480.0193-0.04050.2214-0.0090.122428.1374-44.6067-0.1705
92.14570.3593-0.06242.2159-0.53621.2236-0.03650.0156-0.1065-0.0877-0.0116-0.21730.14080.18340.05320.11290.06090.00440.11-0.01090.117832.2001-49.7599-8.9374
101.66290.7495-0.22386.3892-0.37181.5539-0.01550.20770.0136-0.23830.0104-0.23760.05770.20150.00380.06340.0142-0.00630.15360.00230.088632.743-40.3748-15.8694
115.37213.38110.68737.61130.69522.785-0.10040.0727-0.1147-0.13680.06030.20510.2342-0.10260.03080.06040.04060.00380.0713-0.01110.086723.4336-48.342-10.3794
121.57780.2806-0.34321.6320.78912.15610.088-0.05360.2384-0.0133-0.04710.0395-0.19730.0563-0.00680.07680.0065-0.01560.06180.00520.119710.9045-31.3777-8.0054
130.99150.1417-0.11160.63880.34760.9404-0.00750.12580.1297-0.1244-0.02480.0872-0.1898-0.05550.01980.09140.0088-0.00630.07150.03090.09017.4-33.6241-13.0482
147.8541-2.00730.92973.5262-0.59063.78560.15070.27970.66110.0067-0.1028-0.0473-0.909-0.3234-0.02280.26710.04110.04870.1840.0460.14823.3603-33.7547-22.1267
154.316-2.46930.14711.4135-0.08360.00520.11310.62580.4479-0.9458-0.01220.83570.0001-0.8372-0.13230.31930.0323-0.10580.2530.06270.2675-3.11-26.5291-14.5508
161.64790.3468-0.12921.64620.23511.4270.039-0.0188-0.0070.04840.0266-0.04930.0332-0.0465-0.07190.06150.0054-0.00010.05730.01430.07086.9654-40.4846-7.2831
171.86281.9677-0.72753.7795-1.24361.4420.1468-0.1936-0.19310.1798-0.2129-0.220.04210.10070.05620.10490.0242-0.0030.0809-0.00430.096915.9609-41.2995-3.526
182.34461.92091.15312.09172.85467.75620.06530.1660.6237-0.0175-0.01160.0653-0.45490.35-0.09820.1548-0.0574-0.02850.12250.00990.186723.0918-22.84-7.0566
192.55240.58490.28756.22261.95283.54650.07720.2635-0.13380.05050.0512-0.02490.2767-0.0298-0.11180.07870.0082-0.00420.05490.00770.052111.6989-43.3868-14.3794
202.16990.9933-0.09663.911-1.3722.58080.00450.25250.178-0.1021-0.1079-0.2301-0.12850.22160.07960.07620.00240.05130.1776-0.00250.097524.2024-36.0198-27.249
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 28 through 40 )B28 - 40
2X-RAY DIFFRACTION2chain 'B' and (resid 41 through 74 )B41 - 74
3X-RAY DIFFRACTION3chain 'B' and (resid 75 through 131 )B75 - 131
4X-RAY DIFFRACTION4chain 'B' and (resid 132 through 146 )B132 - 146
5X-RAY DIFFRACTION5chain 'B' and (resid 147 through 159 )B147 - 159
6X-RAY DIFFRACTION6chain 'C' and (resid 0 through 16 )C0 - 16
7X-RAY DIFFRACTION7chain 'C' and (resid 17 through 33 )C17 - 33
8X-RAY DIFFRACTION8chain 'C' and (resid 34 through 74 )C34 - 74
9X-RAY DIFFRACTION9chain 'C' and (resid 75 through 122 )C75 - 122
10X-RAY DIFFRACTION10chain 'C' and (resid 123 through 146 )C123 - 146
11X-RAY DIFFRACTION11chain 'C' and (resid 147 through 159 )C147 - 159
12X-RAY DIFFRACTION12chain 'A' and (resid 1 through 33 )A1 - 33
13X-RAY DIFFRACTION13chain 'A' and (resid 34 through 53 )A34 - 53
14X-RAY DIFFRACTION14chain 'A' and (resid 54 through 67 )A54 - 67
15X-RAY DIFFRACTION15chain 'A' and (resid 68 through 74 )A68 - 74
16X-RAY DIFFRACTION16chain 'A' and (resid 75 through 122 )A75 - 122
17X-RAY DIFFRACTION17chain 'A' and (resid 123 through 139 )A123 - 139
18X-RAY DIFFRACTION18chain 'A' and (resid 140 through 146 )A140 - 146
19X-RAY DIFFRACTION19chain 'A' and (resid 147 through 159 )A147 - 159
20X-RAY DIFFRACTION20chain 'B' and (resid 1 through 27 )B1 - 27

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