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- PDB-3mbm: Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate ... -

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Basic information

Entry
Database: PDB / ID: 3mbm
TitleCrystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with cytosine and FoL fragment 717, imidazo[2,1-b][1,3]thiazol-6-ylmethanol
Components2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
KeywordsLYASE / NIAID / Seattle Structural Genomics Center for Infectious Disease / SSGCID / IspF / cytosine / MEP pathway / fragment-based drug design / FBDD / Fragments of Life / Isoprene biosynthesis / Metal-binding
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 / 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. / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
imidazo[2,1-b][1,3]thiazol-6-ylmethanol / 6-AMINOPYRIMIDIN-2(1H)-ONE / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Citation
Journal: J Struct Funct Genomics / Year: 2011
Title: Leveraging structure determination with fragment screening for infectious disease drug targets: MECP synthase from Burkholderia pseudomallei.
Authors: Begley, D.W. / Hartley, R.C. / Davies, D.R. / Edwards, T.E. / Leonard, J.T. / Abendroth, J. / Burris, C.A. / Bhandari, J. / Myler, P.J. / Staker, B.L. / Stewart, L.J.
#1: Journal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionMar 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Database references / Version format compliance
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 6, 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 / struct_ref_seq_dif / struct_site
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_seq_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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)59,57613
Polymers58,4613
Non-polymers1,11410
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint-19 kcal/mol
Surface area16060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.543, 67.569, 60.030
Angle α, β, γ (deg.)90.000, 96.120, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-202-

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 / MECDP-synthase


Mass: 19487.109 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: ispF, mecS, BPSL2098 / Production host: Escherichia coli (E. coli)
References: UniProt: Q63T71, UniProt: Q3JRA0*PLUS, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

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Non-polymers , 5 types, 251 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CYT / 6-AMINOPYRIMIDIN-2(1H)-ONE / CYTOSINE


Mass: 111.102 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H5N3O
#4: Chemical ChemComp-717 / imidazo[2,1-b][1,3]thiazol-6-ylmethanol


Mass: 154.190 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H6N2OS
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.03 Å3/Da / Density % sol: 39.33 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG 4000, 100 mM Tris, 200 mM NaCl, 5 mM ZnCl2 with 34.4 mg/mL protein for 3 days. Crystal soaked in 25 mM cytosine and fragment 717 in same buffer for 3 weeks. VAPOR DIFFUSION, SITTING ...Details: 20% PEG 4000, 100 mM Tris, 200 mM NaCl, 5 mM ZnCl2 with 34.4 mg/mL protein for 3 days. Crystal soaked in 25 mM cytosine and fragment 717 in same buffer for 3 weeks. VAPOR DIFFUSION, SITTING DROP, temperature 289K, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 41626 / % possible obs: 88.4 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.081 / Χ2: 1.037 / Net I/σ(I): 20.1
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 2.52 / Num. unique all: 3545 / Χ2: 1.166 / % possible all: 81.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 34.26 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å26.03 Å
Translation2.5 Å26.03 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3ike

3ike


Resolution: 1.8→25.5 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.258 / WRfactor Rwork: 0.228 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.84 / SU B: 5.768 / SU ML: 0.088 / SU R Cruickshank DPI: 0.136 / SU Rfree: 0.124 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.217 2090 5 %RANDOM
Rwork0.188 ---
obs0.189 41626 95.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 50.35 Å2 / Biso mean: 6.423 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3417 0 65 241 3723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223553
X-RAY DIFFRACTIONr_bond_other_d0.0010.022358
X-RAY DIFFRACTIONr_angle_refined_deg1.7451.9924818
X-RAY DIFFRACTIONr_angle_other_deg1.07835714
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6355463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.35523.046151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2615547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9351535
X-RAY DIFFRACTIONr_chiral_restr0.0840.2551
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214038
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02723
X-RAY DIFFRACTIONr_mcbond_it0.5911.52300
X-RAY DIFFRACTIONr_mcbond_other0.1361.5954
X-RAY DIFFRACTIONr_mcangle_it1.02823634
X-RAY DIFFRACTIONr_scbond_it1.70331253
X-RAY DIFFRACTIONr_scangle_it2.6084.51181
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 156 -
Rwork0.225 2958 -
all-3114 -
obs--97.99 %
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)
12.32340.51840.29942.54571.01491.87660.01070.27140.2664-0.1362-0.03690.016-0.10450.05020.02620.2330.0086-0.02690.18410.05390.199711.632-34.084-12.326
22.51990.34210.53080.76780.18750.9625-0.04790.08990.43350.0399-0.05050.1184-0.1054-0.0640.09840.26270.00540.01080.16650.03520.25118.1-30.973-8.021
35.7554-0.15150.20013.973.32212.6350.21150.66130.8016-0.4388-0.37920.0928-0.3686-0.2770.16770.33790.0525-0.02090.38340.12730.31750.993-29.31-20.171
42.54950.3320.49390.9477-0.11741.13730.04010.24470.0873-0.02880.0122-0.0060.0814-0.1818-0.05230.255-0.0030.01410.20670.02680.16584.911-39.585-11.042
55.22671.7231.03133.09630.92063.26950.116-0.3980.07320.2116-0.1042-0.17220.0460.0771-0.01190.26670.00870.00960.18720.01440.19969.76-38.8371.403
62.25570.72090.28831.55310.18031.17430.01290.13650.06710.1228-0.0049-0.06970.00940.0742-0.0080.2620.0144-0.00540.14690.01310.207716.412-37.509-7.436
71.370.06620.62262.7387-0.6831.829-0.08220.65580.0917-0.03280.0692-0.1233-0.09610.31890.0130.1889-0.01220.03450.51110.04890.190724.224-36.194-26.928
830.4144-6.3055.322417.2467-5.01798.84460.07462.30582.3438-0.2516-0.5559-0.88540.11620.82240.48130.3196-0.1357-0.02530.67210.34010.323524.206-23.843-32.826
92.789-2.06930.73179.7404-2.54412.2024-0.42811.7952-0.2949-0.29490.6545-0.7650.21330.0136-0.22640.2157-0.16530.08131.7508-0.41710.252626.251-42.71-26.846
105.5005-0.11111.61391.64616.636324.4248-0.14710.20990.4389-0.264-0.0719-0.0703-1.09480.20420.2190.27860.03940.04270.52270.06860.311635.676-44.016-27.983
116.021-0.00263.36455.6030.42721.48640.20913.3123-1.7127-0.01050.1704-0.18550.31671.3839-0.37950.17390.00930.11412.0949-0.92710.491826.372-48.401-33.754
121.61880.30551.0121.69990.32671.4286-0.04980.64350.1491-0.05020.029-0.0054-0.02830.33490.02080.2301-0.00350.01420.43340.05330.167616.585-36.143-25.706
137.09014.57780.93215.84330.74940.5010.14930.0623-0.16620.1448-0.1198-0.27410.0610.1161-0.02940.28690.0198-0.01340.2032-0.00150.202227.031-41.592-7.215
142.9438-0.85960.64925.86111.60582.68570.0123-0.17240.11970.22340.0626-0.6427-0.12850.2669-0.07480.24150.0345-0.04060.24230.00320.367842.014-37.427-5.703
153.8615-0.72620.70220.4756-0.12490.88620.082-0.018-0.0530.1494-0.0164-0.08970.05030.0594-0.06560.31540.0498-0.03260.1395-0.00520.261525.742-45.544-4.173
1630.4599-3.06240.41877.6742-2.35381.093-0.1703-1.78630.9550.69610.2894-0.1478-0.1920.1386-0.11910.40130.0554-0.06760.3073-0.05140.231726.598-44.0414.422
172.0735-0.0940.29151.1493-0.51181.09220.03720.2349-0.3015-0.0046-0.0639-0.19060.12570.17260.02680.2740.0649-0.00760.2082-0.03680.266431.753-48.522-8.535
182.36240.09660.31891.1718-0.25920.92530.03140.4461-0.1209-0.0128-0.0571-0.14910.05650.22370.02560.24340.04360.01280.2575-0.01990.218731.113-43.808-13.664
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 20
2X-RAY DIFFRACTION2A21 - 57
3X-RAY DIFFRACTION3A58 - 70
4X-RAY DIFFRACTION4A71 - 105
5X-RAY DIFFRACTION5A106 - 121
6X-RAY DIFFRACTION6A122 - 158
7X-RAY DIFFRACTION7B1 - 26
8X-RAY DIFFRACTION8B27 - 38
9X-RAY DIFFRACTION9B39 - 56
10X-RAY DIFFRACTION10B57 - 66
11X-RAY DIFFRACTION11B73 - 93
12X-RAY DIFFRACTION12B94 - 158
13X-RAY DIFFRACTION13C1 - 18
14X-RAY DIFFRACTION14C19 - 38
15X-RAY DIFFRACTION15C39 - 58
16X-RAY DIFFRACTION16C59 - 74
17X-RAY DIFFRACTION17C75 - 113
18X-RAY DIFFRACTION18C114 - 158

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