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- PDB-3f0g: Co-crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphospha... -

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Basic information

Entry
Database: PDB / ID: 3f0g
TitleCo-crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase with CMP
Components2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
KeywordsLYASE / NIAID / SSGCID / Burkholderia pseudomallei / 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
CYTIDINE-5'-MONOPHOSPHATE / 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: 2.08 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
DepositionOct 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Dec 11, 2013Group: Database references
Revision 1.4Oct 25, 2017Group: Refinement description / Category: software
Revision 1.5Sep 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_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
D: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
E: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
F: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,93117
Polymers116,9236
Non-polymers2,00811
Water9,872548
1
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)59,3048
Polymers58,4613
Non-polymers8435
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8180 Å2
ΔGint-140 kcal/mol
Surface area16020 Å2
MethodPISA
2
D: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
E: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
F: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6279
Polymers58,4613
Non-polymers1,1666
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8800 Å2
ΔGint-142 kcal/mol
Surface area15700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.662, 69.760, 116.671
Angle α, β, γ (deg.)90.000, 130.040, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-303-

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.: 6
Source method: isolated from a genetically manipulated source
Details: Expressed with an N-terminal hexahis tag and 3C protease cleavage sequence, although crystallized without removing the affinity tag
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: ispF, mecS, BPSL2098 / Plasmid: AVA0421 / 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.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C9H14N3O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 548 / 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: 2.1 Å3/Da / Density % sol: 41.44 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: Crystal ID 200617a7, 34.4 mg/mL protein, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.08→89.44 Å / Num. obs: 49247 / % possible obs: 84.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.049 / Χ2: 1.167 / Net I/σ(I): 27.111
Reflection shellResolution: 2.08→2.15 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 6.7 / Num. unique all: 5180 / Χ2: 1.005 / % possible all: 89.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.5.0053refinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3F0D

3f0d


Resolution: 2.08→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.24 / WRfactor Rwork: 0.199 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.935 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.326 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.258 2457 5 %RANDOM
Rwork0.213 ---
obs0.216 48825 83.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.42 Å2 / Biso mean: 21.886 Å2 / Biso min: 8.59 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å20 Å2-0.74 Å2
2--0.83 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.08→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6834 0 111 548 7493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0227071
X-RAY DIFFRACTIONr_angle_refined_deg0.9771.999590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6015912
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.08322.89308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.427151129
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5211574
X-RAY DIFFRACTIONr_chiral_restr0.0610.21110
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215343
X-RAY DIFFRACTIONr_mcbond_it0.3991.54529
X-RAY DIFFRACTIONr_mcangle_it0.73627168
X-RAY DIFFRACTIONr_scbond_it0.89432542
X-RAY DIFFRACTIONr_scangle_it1.4934.52419
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.08-2.1360.3261760.2653517425486.812
2.136-2.1940.2612000.2123900418897.899
2.194-2.2580.493610.3661306407633.538
2.258-2.3270.3521380.2662407395064.43
2.327-2.4040.2392210.1913546380099.132
2.404-2.4880.2831830.1973487371498.815
2.488-2.5820.2261610.2023382357499.133
2.582-2.6870.2731600.2433203344897.535
2.687-2.8070.3181780.2213046329697.816
2.807-2.9430.2341570.2072966314099.459
2.943-3.1020.2531460.1992852302699.075
3.102-3.290.2271480.2072695285999.44
3.29-3.5170.273850.2391848266972.424
3.517-3.7990.298150.241380250215.787
3.799-4.160.236410.191804231736.47
4.16-4.650.2071140.1631974209199.857
4.65-5.3670.2381010.1871741184799.729
5.367-6.5670.237750.241494157599.619
6.567-9.2630.259620.2061166123399.594
9.263-89.4430.245350.24165471696.229

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