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

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Basic information

Entry
Database: PDB / ID: 3jvh
TitleCrystal structure of 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with FOL fragment 8395
Components2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
KeywordsLYASE / NIAID / SSGCID / Seattle Dtructural Genomics Center for Infectious Disease / fragment crystallography / Fragments of Life / zinc-binding fragment / Isoprene biosynthesis / Metal-binding / 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 / 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
Chem-HHV / 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: 1.69 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.
#2: Journal: Bioorg.Med.Chem.Lett. / Year: 2013
Title: Cytidine derivatives as IspF inhibitors of Burkolderia pseudomallei.
Authors: Zhang, Z. / Jakkaraju, S. / Blain, J. / Gogol, K. / Zhao, L. / Hartley, R.C. / Karlsson, C.A. / Staker, B.L. / Edwards, T.E. / Stewart, L.J. / Myler, P.J. / Clare, M. / Begley, D.W. / Horn, J.R. / Hagen, T.J.
History
DepositionSep 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Database references / Version format compliance
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Dec 11, 2013Group: Database references
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 / 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 / _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)59,40110
Polymers58,4613
Non-polymers9407
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7090 Å2
ΔGint-31.2 kcal/mol
Surface area16080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.120, 67.650, 60.000
Angle α, β, γ (deg.)90.000, 96.320, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-186-

HOH

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Components

#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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-HHV / 5-[(pyridin-3-ylmethyl)amino]-1H-pyrazole-4-carboxamide


Mass: 217.227 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H11N5O
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.02 Å3/Da / Density % sol: 39.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 20% PEG 3350, 0.2 M magnesium formate, 34.4 mg/mL protein, 0.4/0.4 uL drops, 20 mM fragment 8395, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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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: Sep 3, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 50817 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.268 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 26.57
Reflection shellResolution: 1.69→1.73 Å / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.7 / Num. measured obs: 6211 / Num. unique all: 3188 / Num. unique obs: 3188 / % possible all: 82.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3F0D

3f0d


Resolution: 1.69→19.5 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.177 / WRfactor Rwork: 0.155 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.883 / SU B: 3.791 / SU ML: 0.06 / SU R Cruickshank DPI: 0.099 / SU Rfree: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.195 2590 5.1 %RANDOM
Rwork0.167 ---
obs0.169 50816 97.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 47.46 Å2 / Biso mean: 14.092 Å2 / Biso min: 3.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20.01 Å2
2--0.06 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.69→19.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3406 0 57 321 3784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223565
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.9854841
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0115473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.08722.81153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.76515559
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6811537
X-RAY DIFFRACTIONr_chiral_restr0.0760.2557
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212739
X-RAY DIFFRACTIONr_mcbond_it0.5811.52294
X-RAY DIFFRACTIONr_mcangle_it1.02823638
X-RAY DIFFRACTIONr_scbond_it1.54431271
X-RAY DIFFRACTIONr_scangle_it2.5114.51194
LS refinement shellResolution: 1.69→1.734 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 157 -
Rwork0.286 2984 -
all-3141 -
obs--82.55 %
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)
11.33670.37740.35690.49670.39221.1811-0.01530.05050.2087-0.0119-0.01180.0672-0.0669-0.02790.02710.04150.00160.00450.0070.01220.05159.5049-31.9234-10.1214
210.0941-4.5914-3.9932.27176.13019.91520.47320.58231.4177-0.5466-0.3831-0.4723-1.077-0.4805-0.09010.2110.05180.03330.09190.08370.20970.9124-29.2848-20.5123
30.93790.29310.15121.14510.41461.17050.06560.11910.0162-0.03590.0094-0.00570.0461-0.2236-0.0750.0417-0.0113-0.00390.07240.02010.0192-0.14-40.8122-13.6767
41.34030.35310.10870.7707-0.19420.82280.0149-0.0814-0.00250.0644-0.0149-0.05710.0030.046100.04350.006-0.00360.0122-0.00130.03814.5277-37.3693-4.4522
51.62280.42280.58643.2031-0.21721.0335-0.10210.55550.09160.03970.0373-0.381-0.09410.2710.06480.0188-0.02920.03260.20230.05740.051223.5211-33.7241-28.0396
61.7362-0.9520.4883.0675-1.530.5092-0.12670.72060.0209-0.16120.0772-0.28860.16710.07890.04950.0629-0.01990.02550.3771-0.03390.054727.4278-38.7046-27.9817
73.2502-0.91180.81884.967-1.3291.7573-0.2020.9845-0.3144-0.11310.0338-0.5630.07160.16360.16820.083-0.0110.09820.3231-0.14730.066827.9555-47.8649-32.5566
81.25020.17130.45661.34410.29080.8152-0.03870.34250.1451-0.0390.00010.0481-0.03520.12710.03860.0211-0.00960.00590.10270.03580.013616.3169-35.6977-25.9638
92.33441.2424-0.04682.74790.17310.32770.078-0.140.08640.1054-0.1046-0.25340.05160.12730.02660.05290.0171-0.02140.06190.01550.066134.7358-39.264-6.2538
105.35820.1573-0.45180.5919-0.28541.00110.0111-0.3477-0.04540.17120.019-0.10670.02360.0705-0.03010.08850.038-0.03340.039-0.00010.065626.4741-45.6539-0.5021
111.43910.19250.20441.5087-0.21010.6444-0.0310.0532-0.1615-0.1027-0.0134-0.2120.17320.15430.04440.05790.05850.00570.0412-0.00010.072632.0388-48.9994-9.1557
121.00820.39990.12711.7956-0.17060.8149-0.0140.1932-0.0382-0.02310.0428-0.07940.06960.2119-0.02880.02830.0210.0010.0683-0.00960.065130.0398-42.7597-13.6621
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 57
2X-RAY DIFFRACTION2A58 - 70
3X-RAY DIFFRACTION3A71 - 94
4X-RAY DIFFRACTION4A95 - 158
5X-RAY DIFFRACTION5B1 - 30
6X-RAY DIFFRACTION6B31 - 58
7X-RAY DIFFRACTION7B59 - 93
8X-RAY DIFFRACTION8B94 - 158
9X-RAY DIFFRACTION9C1 - 40
10X-RAY DIFFRACTION10C41 - 75
11X-RAY DIFFRACTION11C76 - 120
12X-RAY DIFFRACTION12C121 - 159

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