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- PDB-5l03: Crystal structure of 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE... -

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Basic information

Entry
Database: PDB / ID: 5l03
TitleCrystal structure of 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE Synthase from BURKHOLDERIA PSEUDOMALLEI bound to L-tryptophan hydroxamate
Components2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
KeywordsLYASE / MEP Pathway / IspF / Inhibitor / Complex
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
N-hydroxy-L-tryptophanamide / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.469 Å
AuthorsBlain, J.M. / Ghose, D. / Gorman, J.L. / Goshu, G.M. / Ranieri, G. / Zhao, L. / Bode, B. / Meganathan, R. / Walter, R.L. / Hagen, T.J. / Horn, J.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R15AI113653-01 United States
National Science Foundation (NSF, United States)MCB-0953323 United States
CitationJournal: To Be Published
Title: Synthesis and Characterization of the Burkholderia pseudomallei IspF Inhibitor L-tryptophan hydroxamate
Authors: Blain, J.M. / Ghose, D. / Gorman, J.L. / Goshu, G.M. / Ranieri, G. / Zhao, L. / Bode, B. / Meganathan, R. / Walter, R.L. / Hagen, T.J. / Horn, J.R.
History
DepositionJul 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 6, 2024Group: 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 / struct_conn / struct_ncs_dom_lim
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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)50,9817
Polymers50,5663
Non-polymers4154
Water7,837435
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-101 kcal/mol
Surface area15520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.515, 68.126, 60.659
Angle α, β, γ (deg.)90.000, 96.930, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-387-

HOH

21A-442-

HOH

31A-467-

HOH

41B-317-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 1 and (name N or name...
21(chain B and (resseq 1 or (resid 2 and (name...
31(chain C and (resseq 1 or (resid 2 and (name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETMETMET(chain A and ((resid 1 and (name N or name...AA11
12METMETARGARG(chain A and ((resid 1 and (name N or name...AA1 - 1581 - 158
13METMETARGARG(chain A and ((resid 1 and (name N or name...AA1 - 1581 - 158
14METMETARGARG(chain A and ((resid 1 and (name N or name...AA1 - 1581 - 158
15METMETARGARG(chain A and ((resid 1 and (name N or name...AA1 - 1581 - 158
21METMETMETMET(chain B and (resseq 1 or (resid 2 and (name...BB11
22ASPASPASPASP(chain B and (resseq 1 or (resid 2 and (name...BB22
23METMETARGARG(chain B and (resseq 1 or (resid 2 and (name...BB1 - 1581 - 158
24METMETARGARG(chain B and (resseq 1 or (resid 2 and (name...BB1 - 1581 - 158
25METMETARGARG(chain B and (resseq 1 or (resid 2 and (name...BB1 - 1581 - 158
26METMETARGARG(chain B and (resseq 1 or (resid 2 and (name...BB1 - 1581 - 158
27METMETARGARG(chain B and (resseq 1 or (resid 2 and (name...BB1 - 1581 - 158
28METMETARGARG(chain B and (resseq 1 or (resid 2 and (name...BB1 - 1581 - 158
31METMETMETMET(chain C and (resseq 1 or (resid 2 and (name...CC11
32ASPASPASPASP(chain C and (resseq 1 or (resid 2 and (name...CC22
33METMETARGARG(chain C and (resseq 1 or (resid 2 and (name...CC1 - 1581 - 158
34METMETARGARG(chain C and (resseq 1 or (resid 2 and (name...CC1 - 1581 - 158
35METMETARGARG(chain C and (resseq 1 or (resid 2 and (name...CC1 - 1581 - 158
36METMETARGARG(chain C and (resseq 1 or (resid 2 and (name...CC1 - 1581 - 158
37METMETARGARG(chain C and (resseq 1 or (resid 2 and (name...CC1 - 1581 - 158
38METMETARGARG(chain C and (resseq 1 or (resid 2 and (name...CC1 - 1581 - 158

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Components

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


Mass: 16855.234 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: ispF, DP46_3085, ERS012314_03919, SY87_14040 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A069B2G5, 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-6ZB / N-hydroxy-L-tryptophanamide / N-hydroxy-L-tryptophanamide


Mass: 219.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13N3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 47.95 %
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: 1.469→30.7209 Å / Num. obs: 79230 / % possible obs: 99 % / Redundancy: 3.7 % / Net I/σ(I): 19.9

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Processing

Software
NameVersionClassification
PHENIX1.10_2142refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.469→30.714 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.05
RfactorNum. reflection% reflection
Rfree0.1995 3889 4.92 %
Rwork0.1788 --
obs0.1798 79098 98.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.65 Å2 / Biso mean: 28.6638 Å2 / Biso min: 9.67 Å2
Refinement stepCycle: final / Resolution: 1.469→30.714 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3286 0 19 435 3740
Biso mean--24.76 39.89 -
Num. residues----450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113363
X-RAY DIFFRACTIONf_angle_d0.9194549
X-RAY DIFFRACTIONf_chiral_restr0.087534
X-RAY DIFFRACTIONf_plane_restr0.005606
X-RAY DIFFRACTIONf_dihedral_angle_d18.5321182
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1797X-RAY DIFFRACTION4.71TORSIONAL
12B1797X-RAY DIFFRACTION4.71TORSIONAL
13C1797X-RAY DIFFRACTION4.71TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4688-1.48670.27541150.25782324243986
1.4867-1.50550.25081280.25382477260592
1.5055-1.52530.26181240.24392556268094
1.5253-1.54620.28161450.23022592273796
1.5462-1.56830.2211310.23652670280198
1.5683-1.59170.25561280.225127332861100
1.5917-1.61660.22831390.214127152854100
1.6166-1.64310.2371360.206326982834100
1.6431-1.67140.18741290.202927172846100
1.6714-1.70180.24511340.205227112845100
1.7018-1.73450.21931500.193427432893100
1.7345-1.76990.23161250.190726942819100
1.7699-1.80840.18371630.183426902853100
1.8084-1.85050.20261350.190627082843100
1.8505-1.89670.21961320.21132730286299
1.8967-1.9480.25281450.229127122857100
1.948-2.00530.2311590.188326732832100
2.0053-2.070.19971510.173527382889100
2.07-2.1440.17931360.173526852821100
2.144-2.22980.18751640.183327092873100
2.2298-2.33130.22961490.19282730287999
2.3313-2.45410.18711440.19092682282699
2.4541-2.60780.18111290.166527512880100
2.6078-2.8090.20421570.175227062863100
2.809-3.09150.2091610.169527282889100
3.0915-3.53830.17631120.159527712883100
3.5383-4.45570.16281460.145627302876100
4.4557-30.72090.181220.160528362958100
Refinement TLS params.Method: refined / Origin x: 16.4211 Å / Origin y: -39.5666 Å / Origin z: 15.3822 Å
111213212223313233
T0.0846 Å2-0.0196 Å20.0136 Å2-0.3065 Å20.0306 Å2--0.1115 Å2
L1.5435 °20.0262 °20.6117 °2-0.7936 °20.2166 °2--1.8692 °2
S-0.0768 Å °0.3966 Å °0.0624 Å °-0.0501 Å °0.0595 Å °-0.1165 Å °-0.0189 Å °0.5935 Å °0.0071 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 158
2X-RAY DIFFRACTION1allA163
3X-RAY DIFFRACTION1allB1 - 158
4X-RAY DIFFRACTION1allB163
5X-RAY DIFFRACTION1allC1 - 158
6X-RAY DIFFRACTION1allC163
7X-RAY DIFFRACTION1allS1 - 507
8X-RAY DIFFRACTION1allQ1

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