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- PDB-4phr: Domain of unknown function 1792 (DUF1792) with manganese -

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Basic information

Entry
Database: PDB / ID: 4phr
TitleDomain of unknown function 1792 (DUF1792) with manganese
ComponentsPutative glycosyltransferase (GalT1)
KeywordsTRANSFERASE / Domain of unknown function 1792 (DUF1792) / Glycosyltransferase
Function / homology
Function and homology information


transferase activity / nucleotide binding
Similarity search - Function
Glycosyltransferase GT-D fold / Glycosyltransferase GT-D fold / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
ACETATE ION / : / URIDINE-5'-DIPHOSPHATE / Putative glycosyltransferase (GalT1)
Similarity search - Component
Biological speciesStreptococcus parasanguinis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsZhang, H. / Wu, H.
CitationJournal: Nat Commun / Year: 2014
Title: The highly conserved domain of unknown function 1792 has a distinct glycosyltransferase fold.
Authors: Zhang, H. / Zhu, F. / Yang, T. / Ding, L. / Zhou, M. / Li, J. / Haslam, S.M. / Dell, A. / Erlandsen, H. / Wu, H.
History
DepositionMay 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Oct 14, 2015Group: Data collection
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _pdbx_struct_oper_list.symmetry_operation / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative glycosyltransferase (GalT1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7235
Polymers32,1461
Non-polymers5774
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.474, 45.409, 78.782
Angle α, β, γ (deg.)90.00, 109.74, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-414-

HOH

21A-502-

HOH

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Components

#1: Protein Putative glycosyltransferase (GalT1)


Mass: 32145.566 Da / Num. of mol.: 1 / Fragment: UNP residues 1-272
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus parasanguinis (bacteria) / Strain: FW213 / Gene: galT1, Spaf_1933 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: I1ZPA1
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 1.87 Å3/Da / Density % sol: 34.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Tris buffer, PEG 1500, NaAcetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.34→50 Å / Num. obs: 52820 / % possible obs: 98.6 % / Redundancy: 5.5 % / Net I/σ(I): 52.6

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE: 1.7.1_743) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.34→37.64 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.188 2697 5.11 %
Rwork0.147 --
obs0.149 52818 98.6 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.5 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.581 Å20 Å2-0.6578 Å2
2---0.1003 Å20 Å2
3----0.4807 Å2
Refinement stepCycle: LAST / Resolution: 1.34→37.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2264 0 34 266 2564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052342
X-RAY DIFFRACTIONf_angle_d1.1533164
X-RAY DIFFRACTIONf_dihedral_angle_d14.222875
X-RAY DIFFRACTIONf_chiral_restr0.077341
X-RAY DIFFRACTIONf_plane_restr0.005401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3399-1.36420.25871290.19822301X-RAY DIFFRACTION86
1.3642-1.39050.24091540.16982572X-RAY DIFFRACTION99
1.3905-1.41880.24131670.15092666X-RAY DIFFRACTION99
1.4188-1.44970.21751520.14642593X-RAY DIFFRACTION99
1.4497-1.48340.22231310.13552659X-RAY DIFFRACTION99
1.4834-1.52050.18761300.13242658X-RAY DIFFRACTION99
1.5205-1.56160.2021350.12492687X-RAY DIFFRACTION99
1.5616-1.60760.18121560.11742576X-RAY DIFFRACTION99
1.6076-1.65950.18921360.12452638X-RAY DIFFRACTION99
1.6595-1.71880.21721300.13412651X-RAY DIFFRACTION99
1.7188-1.78760.20541410.13172627X-RAY DIFFRACTION99
1.7876-1.8690.18441400.13112637X-RAY DIFFRACTION99
1.869-1.96750.17651530.13452653X-RAY DIFFRACTION99
1.9675-2.09070.18881370.13872659X-RAY DIFFRACTION100
2.0907-2.25220.16571490.13642675X-RAY DIFFRACTION100
2.2522-2.47880.18621450.14182697X-RAY DIFFRACTION100
2.4788-2.83730.19781420.15682695X-RAY DIFFRACTION100
2.8373-3.57430.17061220.15462729X-RAY DIFFRACTION100
3.5743-37.65220.18471480.16292748X-RAY DIFFRACTION99

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