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- PDB-6jq8: Crystal structure of HddC from Yersinia pseudotuberculosis comple... -

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Basic information

Entry
Database: PDB / ID: 6jq8
TitleCrystal structure of HddC from Yersinia pseudotuberculosis complexed with GMP-PN
ComponentsPutative 6-deoxy-D-mannoheptose pathway protein
KeywordsTRANSFERASE / HddC
Function / homologyNucleotidyl transferase domain / Nucleotidyl transferase / biosynthetic process / nucleotidyltransferase activity / Nucleotide-diphospho-sugar transferases / CITRIC ACID / AMINOPHOSPHONIC ACID-GUANYLATE ESTER / Putative 6-deoxy-D-mannoheptose pathway protein
Function and homology information
Biological speciesYersinia pseudotuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.546 Å
AuthorsShin, D.H. / Kim, M.S.
CitationJournal: Int J Mol Sci / Year: 2019
Title: GTP Preference of d-Glycero-alpha-d- manno -Heptose-1-Phosphate Guanylyltransferase from Yersinia pseudotuberculosis .
Authors: Kim, S. / Kim, M.S. / Jo, S. / Shin, D.H.
History
DepositionMar 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 28, 2020Group: Database references / Derived calculations / Category: citation / pdbx_struct_conn_angle / struct_conn
Item: _citation.title / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._citation.title / _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.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.value / _struct_conn.pdbx_dist_value / _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
Revision 1.3Mar 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)26,2075
Polymers25,3561
Non-polymers8514
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-7 kcal/mol
Surface area10930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.526, 80.526, 53.081
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


Mass: 25355.977 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: Q8GJ95
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GNH / AMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 442.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N6O10P2
#4: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 3.39 Å3/Da / Density % sol: 63.76 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.05M HEPES pH 7.5, 0.05M MgCl2, 1.2M Sodium Citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97928 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 1.546→44.32 Å / Num. obs: 49164 / % possible obs: 96.19 % / Redundancy: 12.4 % / Net I/σ(I): 43.89
Reflection shellHighest resolution: 1.546 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.546→44.319 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2288 1941 4.05 %
Rwork0.2067 --
obs0.2076 47960 96.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.546→44.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 55 156 1996
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061876
X-RAY DIFFRACTIONf_angle_d0.8992539
X-RAY DIFFRACTIONf_dihedral_angle_d8.3231103
X-RAY DIFFRACTIONf_chiral_restr0.061276
X-RAY DIFFRACTIONf_plane_restr0.005320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5458-1.58440.2641130.22422788X-RAY DIFFRACTION82
1.5844-1.62730.28591400.25583192X-RAY DIFFRACTION95
1.6273-1.67520.34091360.25583273X-RAY DIFFRACTION96
1.6752-1.72920.25261360.25263270X-RAY DIFFRACTION96
1.7292-1.79110.29341370.26243260X-RAY DIFFRACTION96
1.7911-1.86280.2631360.24163272X-RAY DIFFRACTION96
1.8628-1.94750.25491410.25293278X-RAY DIFFRACTION97
1.9475-2.05020.29551400.25253330X-RAY DIFFRACTION97
2.0502-2.17870.2371360.2363256X-RAY DIFFRACTION96
2.1787-2.34690.20891420.2073377X-RAY DIFFRACTION99
2.3469-2.5830.21821460.2083403X-RAY DIFFRACTION100
2.583-2.95670.23941450.21543397X-RAY DIFFRACTION99
2.9567-3.72490.19761470.18783441X-RAY DIFFRACTION100
3.7249-44.33680.19821460.15613482X-RAY DIFFRACTION99

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