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- PDB-5x9q: Crystal structure of HldC from Burkholderia pseudomallei -

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Basic information

Entry
Database: PDB / ID: 5x9q
TitleCrystal structure of HldC from Burkholderia pseudomallei
ComponentsPutative cytidylyltransferase
KeywordsTRANSFERASE / d-glycero-beta-d-manno-heptose-1-phosphate adenylyltransferase / HldC / HldE2 / heptose biosynthesis pathway
Function / homology
Function and homology information


D-glycero-beta-D-manno-heptose 1-phosphate adenylyltransferase / phosphotransferase activity, alcohol group as acceptor / nucleotidyltransferase activity / carbohydrate metabolic process / ATP binding / cytoplasm
Similarity search - Function
RfaE bifunctional protein, domain II / : / Cytidylyltransferase-like / Cytidyltransferase-like domain / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
D-glycero-beta-D-manno-heptose 1-phosphate adenylyltransferase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPark, J. / Kim, H. / Kim, S. / Lee, D. / Shin, D.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation of Korea2015R1D1A1A01058942 Korea, Republic Of
CitationJournal: Proteins / Year: 2018
Title: Crystal structure of D-glycero-Beta-D-manno-heptose-1-phosphate adenylyltransferase from Burkholderia pseudomallei.
Authors: Park, J. / Kim, H. / Kim, S. / Lee, D. / Kim, M.S. / Shin, D.H.
History
DepositionMar 8, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative cytidylyltransferase
B: Putative cytidylyltransferase
C: Putative cytidylyltransferase
D: Putative cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0926
Polymers74,7024
Non-polymers3902
Water90150
1
A: Putative cytidylyltransferase
B: Putative cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5463
Polymers37,3512
Non-polymers1951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-3 kcal/mol
Surface area14240 Å2
MethodPISA
2
C: Putative cytidylyltransferase
D: Putative cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5463
Polymers37,3512
Non-polymers1951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-5 kcal/mol
Surface area14310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.890, 119.370, 76.703
Angle α, β, γ (deg.)90.00, 110.81, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein
Putative cytidylyltransferase / d-glycero-beta-d-manno-heptose-1-phosphate adenylyltransferase


Mass: 18675.459 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (strain K96243) (bacteria)
Strain: K96243 / Gene: BPSL0395 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q63XZ4
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES pH 6.5, 15% (w/w) PEG 3350, 0.56mM CYMAL-6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97927 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 2.4→34.9 Å / Num. obs: 46606 / % possible obs: 94.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 12.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.16 / Num. unique obs: 1938 / % possible all: 76.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLM7.2.1data reduction
Aimless0.5.28data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→34.592 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 27.07 / Stereochemistry target values: ML
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS AND I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2366 2321 5.2 %
Rwork0.216 --
obs0.2172 44619 91.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→34.592 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4780 0 24 50 4854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094888
X-RAY DIFFRACTIONf_angle_d1.4196628
X-RAY DIFFRACTIONf_dihedral_angle_d13.2671786
X-RAY DIFFRACTIONf_chiral_restr0.076770
X-RAY DIFFRACTIONf_plane_restr0.009856
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.4490.2201820.24561772X-RAY DIFFRACTION65
2.449-2.50230.315850.22741925X-RAY DIFFRACTION72
2.5023-2.56050.3151990.22982263X-RAY DIFFRACTION81
2.5605-2.62450.25871170.23612396X-RAY DIFFRACTION87
2.6245-2.69540.28431560.24762524X-RAY DIFFRACTION94
2.6954-2.77470.29681630.25312669X-RAY DIFFRACTION99
2.7747-2.86420.30061000.25812717X-RAY DIFFRACTION100
2.8642-2.96650.27811880.23542661X-RAY DIFFRACTION100
2.9665-3.08520.28761350.23862740X-RAY DIFFRACTION100
3.0852-3.22550.26341150.24192705X-RAY DIFFRACTION100
3.2255-3.39550.26121380.23442665X-RAY DIFFRACTION99
3.3955-3.6080.21051560.21442717X-RAY DIFFRACTION99
3.608-3.88620.23471710.19562641X-RAY DIFFRACTION99
3.8862-4.27670.17571680.17922646X-RAY DIFFRACTION98
4.2767-4.8940.19931680.17452604X-RAY DIFFRACTION97
4.894-6.16030.20761850.20732584X-RAY DIFFRACTION96
6.1603-34.5960.2432950.21382069X-RAY DIFFRACTION76

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