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- PDB-5xhw: Crystal structure of HddC from Yersinia pseudotuberculosis -

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Basic information

Entry
Database: PDB / ID: 5xhw
TitleCrystal structure of HddC from Yersinia pseudotuberculosis
ComponentsPutative 6-deoxy-D-mannoheptose pathway protein
KeywordsTRANSFERASE / Nucleotransferase / HddC
Function / homology: / Nucleotidyl transferase domain / Nucleotidyl transferase / biosynthetic process / nucleotidyltransferase activity / Nucleotide-diphospho-sugar transferases / GTP binding / cytoplasm / Putative 6-deoxy-D-mannoheptose pathway protein
Function and homology information
Biological speciesYersinia pseudotuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsPark, J. / Kim, H. / Kim, S. / Shin, D.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Ministry of Education2015R1D1A1A01058942 Korea, Republic Of
CitationJournal: Biochim. Biophys. Acta / Year: 2018
Title: Crystal structure of d-glycero-alpha-d-manno-heptose-1-phosphate guanylyltransferase from Yersinia pseudotuberculosis.
Authors: Kim, H. / Park, J. / Kim, S. / Shin, D.H.
History
DepositionApr 24, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative 6-deoxy-D-mannoheptose pathway protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1685
Polymers26,7841
Non-polymers3844
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-16 kcal/mol
Surface area11190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.070, 81.070, 52.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Putative 6-deoxy-D-mannoheptose pathway protein / d-glycero-alpha-d-manno-heptose-1-phosphate guanylyltransferase


Mass: 26783.877 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis (bacteria) / Gene: hddC / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GJ90
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.35 Å3/Da / Density % sol: 63.3 % / Description: rod-shaped
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 0.1M HEPES pH 7.4, 1.8M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→14.96 Å / Num. obs: 52267 / % possible obs: 98.4 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 10.8
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.126 / Num. unique obs: 3516 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→14.779 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 23.11 / Stereochemistry target values: ML
Details: The structure factor file contains friedel pairs in F_PLUS/MINUS and I_PLUS/MINUS columns.
RfactorNum. reflection% reflection
Rfree0.2417 2239 5 %
Rwork0.2267 --
obs0.2275 44773 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→14.779 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 20 94 1899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011839
X-RAY DIFFRACTIONf_angle_d1.2982484
X-RAY DIFFRACTIONf_dihedral_angle_d12.974675
X-RAY DIFFRACTIONf_chiral_restr0.078272
X-RAY DIFFRACTIONf_plane_restr0.007313
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.04350.25771460.24342757X-RAY DIFFRACTION100
2.0435-2.09090.31591660.26442602X-RAY DIFFRACTION100
2.0909-2.1430.26981340.25212756X-RAY DIFFRACTION100
2.143-2.20080.23781080.24052773X-RAY DIFFRACTION100
2.2008-2.26530.31571140.25212644X-RAY DIFFRACTION100
2.2653-2.33810.28671260.25022778X-RAY DIFFRACTION100
2.3381-2.42140.22871560.24042668X-RAY DIFFRACTION100
2.4214-2.51790.28561480.24872712X-RAY DIFFRACTION100
2.5179-2.63180.27371660.24612659X-RAY DIFFRACTION100
2.6318-2.76970.29461360.24632712X-RAY DIFFRACTION100
2.7697-2.9420.21531720.23662679X-RAY DIFFRACTION100
2.942-3.16710.24431380.22742661X-RAY DIFFRACTION100
3.1671-3.4820.17851560.20832700X-RAY DIFFRACTION100
3.482-3.97730.22071380.19132660X-RAY DIFFRACTION100
3.9773-4.97890.2041160.19462577X-RAY DIFFRACTION94
4.9789-14.77960.28051190.2482196X-RAY DIFFRACTION81

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