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- PDB-5l12: Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate ... -

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Basic information

Entry
Database: PDB / ID: 5l12
TitleCrystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase from BURKHOLDERIA PSEUDOMALLEI double mutant
Components2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
KeywordsLYASE / MEP pathway / IspF / Site-Directed Mutagenesis / Doulble Mutant
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
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.716 Å
AuthorsBlain, J.M. / Raneiri, G. / Walter, R.L. / Hagen, T.J. / Horn, J.R.
CitationJournal: To Be Published
Title: Enzyme Engineering for the Development of a High-Throughput Temperature Screen of Burkholderia pseudomallei IspF Inhibitors
Authors: Blain, J.M. / Raneiri, G. / Walter, R.L. / Hagen, T.J. / Horn, J.R.
History
DepositionJul 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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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)50,7686
Polymers50,5723
Non-polymers1963
Water7,026390
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-134 kcal/mol
Surface area15830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.859, 68.140, 60.408
Angle α, β, γ (deg.)90.000, 96.570, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-426-

HOH

21B-323-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA1 - 163
211chain BB1 - 163
311chain CC1 - 163

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Components

#1: Protein 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / MECPS


Mass: 16857.205 Da / Num. of mol.: 3 / Mutation: Q7E, Q151E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (strain 1106a) (bacteria)
Strain: 1106a / Gene: ispF, BURPS1106A_2400 / Production host: Escherichia coli (E. coli)
References: UniProt: A3NWD9, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2.36 Å3/Da / Density % sol: 47.93 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: Tris, NaCl, PEG 4000, ZnCl2

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.716→34.07 Å / Num. obs: 50230 / % possible obs: 100 % / Redundancy: 3.7 % / Net I/σ(I): 18.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementResolution: 1.716→34.07 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.95
RfactorNum. reflection% reflection
Rfree0.2036 2000 3.98 %
Rwork0.1648 --
obs0.1663 50218 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 128.3 Å2 / Biso mean: 43.4252 Å2 / Biso min: 16.54 Å2
Refinement stepCycle: final / Resolution: 1.716→34.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3289 0 3 390 3682
Biso mean--31.25 53.1 -
Num. residues----459
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153349
X-RAY DIFFRACTIONf_angle_d1.2494536
X-RAY DIFFRACTIONf_chiral_restr0.055538
X-RAY DIFFRACTIONf_plane_restr0.007606
X-RAY DIFFRACTIONf_dihedral_angle_d11.0461154
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2411X-RAY DIFFRACTION2.123TORSIONAL
12B2411X-RAY DIFFRACTION2.123TORSIONAL
13C2411X-RAY DIFFRACTION2.123TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.716-1.75850.28041340.24533230X-RAY DIFFRACTION93
1.7585-1.8060.25761420.22923425X-RAY DIFFRACTION100
1.806-1.85920.24811430.21723443X-RAY DIFFRACTION100
1.8592-1.91920.29031430.22463430X-RAY DIFFRACTION100
1.9192-1.98780.24741430.19543470X-RAY DIFFRACTION100
1.9878-2.06730.21441430.17493450X-RAY DIFFRACTION100
2.0673-2.16140.18841440.1653453X-RAY DIFFRACTION100
2.1614-2.27540.21511420.16653442X-RAY DIFFRACTION100
2.2754-2.41790.20871440.15543460X-RAY DIFFRACTION100
2.4179-2.60450.17271440.15623475X-RAY DIFFRACTION100
2.6045-2.86650.21441430.17093439X-RAY DIFFRACTION100
2.8665-3.2810.2041430.16673463X-RAY DIFFRACTION100
3.281-4.13250.18591450.14953485X-RAY DIFFRACTION100
4.1325-34.070.19251470.15093553X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 16.992 Å / Origin y: -39.7404 Å / Origin z: 14.9989 Å
111213212223313233
T0.1899 Å20.004 Å2-0.0023 Å2-0.4088 Å20.0406 Å2--0.163 Å2
L2.5529 °20.0898 °20.5621 °2-0.9628 °20.0207 °2--1.6229 °2
S-0.0622 Å °0.6268 Å °0.0941 Å °-0.0416 Å °0.0282 Å °-0.165 Å °0.0515 Å °0.5175 Å °0.0239 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 163
2X-RAY DIFFRACTION1allB1 - 163
3X-RAY DIFFRACTION1allC1 - 163
4X-RAY DIFFRACTION1allS1 - 458

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